Contacts of the helix formed by residues 1357 - 1376 (chain U) in PDB entry 6FF7


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ASN1357 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1181U  ASN      5.6     4.5    -      -       -      -
   1355U  ILE*     3.4     5.3    +      -       -      +
   1356U  LYS*     1.3    83.0    +      -       +      +
   1358U  MET*     1.3    65.5    +      -       -      +
   1359U  PRO*     3.5     7.0    -      -       +      -
   1360U  GLN*     3.5    11.0    +      -       +      +
   1361U  MET*     3.2    20.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET1358 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1182U  VAL*     6.2     3.1    -      -       +      -
   1202U  GLY*     3.8    25.8    -      -       -      +
   1205U  GLU*     5.4     4.0    -      -       +      -
   1206U  TYR*     3.8    20.7    -      -       +      +
   1209U  ALA*     5.6     0.2    -      -       -      +
   1357U  ASN*     1.3    73.9    -      -       -      +
   1359U  PRO*     1.4    60.7    -      -       -      +
   1361U  MET*     2.9     9.8    +      -       -      +
   1362U  ALA*     2.8    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO1359 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1357U  ASN*     3.5     5.0    -      -       +      -
   1358U  MET*     1.4    77.0    -      -       -      +
   1360U  GLN*     1.3    56.9    +      -       -      +
   1362U  ALA*     3.8     6.6    -      -       +      +
   1363U  ASN*     2.9    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1360 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1355U  ILE*     5.3     5.6    -      -       -      -
   1356U  LYS*     4.8     7.6    -      -       +      +
   1357U  ASN*     3.5    21.3    +      -       +      +
   1358U  MET      3.2     0.6    -      -       -      -
   1359U  PRO*     1.3    78.9    -      -       -      +
   1361U  MET*     1.3    56.7    +      -       -      +
   1363U  ASN*     3.4     7.0    -      -       -      +
   1364U  PHE*     3.0    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET1361 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1206U  TYR*     5.7     4.3    -      -       +      +
   1209U  ALA*     4.7    12.3    -      -       +      -
   1355U  ILE*     4.8    13.2    -      -       +      +
   1357U  ASN      3.2    10.8    +      -       -      +
   1358U  MET*     2.9    12.3    +      -       -      +
   1360U  GLN*     1.3    77.8    -      -       -      +
   1362U  ALA*     1.3    59.4    +      -       -      +
   1364U  PHE*     3.1     8.1    +      -       -      +
   1365U  VAL*     2.8    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA1362 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1205U  GLU*     5.7     7.0    -      -       +      +
   1209U  ALA*     4.5    15.4    -      -       +      +
   1358U  MET      2.8    17.9    +      -       -      +
   1359U  PRO*     3.9     7.9    -      -       +      +
   1361U  MET*     1.3    72.6    -      -       -      +
   1363U  ASN*     1.3    62.5    +      -       -      +
   1365U  VAL*     4.2     3.1    -      -       -      +
   1366U  TYR*     3.2    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN1363 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1359U  PRO      2.9    18.3    +      -       -      +
   1360U  GLN*     3.4     9.6    -      -       -      +
   1362U  ALA*     1.3    74.3    -      -       -      +
   1364U  PHE*     1.3    65.1    +      -       -      +
   1366U  TYR*     3.1     7.7    +      -       -      +
   1367U  ASN*     3.0    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1364 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1360U  GLN      3.0    11.4    +      -       -      +
   1361U  MET*     3.1    11.0    +      -       -      +
   1363U  ASN*     1.3    78.4    -      -       -      +
   1365U  VAL*     1.3    57.8    +      -       -      +
   1367U  ASN*     3.4     5.8    +      -       -      +
   1368U  MET*     2.8    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1365 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1209U  ALA*     4.3    22.0    -      -       +      +
   1212U  MET*     5.0     7.2    -      -       +      -
   1213U  TYR*     5.0    12.1    -      -       +      +
   1361U  MET      2.8    20.3    +      -       -      +
   1362U  ALA*     4.3     6.1    -      -       -      +
   1364U  PHE*     1.3    70.2    -      -       -      +
   1366U  TYR*     1.3    61.5    +      -       -      +
   1368U  MET*     3.8     6.5    -      -       -      +
   1369U  TYR*     2.9    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1366 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1362U  ALA      3.2    13.3    +      -       -      +
   1363U  ASN*     3.1    11.3    +      -       -      +
   1365U  VAL*     1.3    78.5    -      -       -      +
   1367U  ASN*     1.3    57.4    +      -       -      +
   1369U  TYR*     3.3     5.3    +      -       -      +
   1370U  MET*     2.9    31.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN1367 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1363U  ASN      3.0    15.4    +      -       -      +
   1364U  PHE*     3.8     6.1    -      -       -      +
   1366U  TYR*     1.3    76.4    -      -       -      +
   1368U  MET*     1.3    62.4    +      -       -      +
   1370U  MET*     3.4     6.4    +      -       -      +
   1371U  HIS*     3.0    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET1368 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1216U  LEU*     5.6     9.8    -      -       +      +
   1364U  PHE      2.8    21.7    +      -       -      +
   1365U  VAL*     3.8     8.5    -      -       -      +
   1367U  ASN*     1.3    73.4    -      -       -      +
   1369U  TYR*     1.3    56.6    +      -       -      +
   1371U  HIS*     3.4     7.5    +      -       -      +
   1372U  LEU*     3.1    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1369 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1216U  LEU*     5.8     7.4    -      -       +      +
   1365U  VAL      2.9    19.7    +      -       -      +
   1366U  TYR*     3.7     4.9    -      -       -      +
   1368U  MET*     1.3    72.8    -      -       -      +
   1370U  MET*     1.3    60.3    +      -       -      +
   1371U  HIS      3.1     1.3    -      -       -      -
   1372U  LEU*     3.0     7.7    +      -       -      +
   1373U  ILE*     2.8    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET1370 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1366U  TYR      2.9    18.3    +      -       -      +
   1367U  ASN*     3.4     6.3    +      -       -      +
   1369U  TYR*     1.3    76.1    -      -       -      +
   1371U  HIS*     1.3    59.3    +      -       -      +
   1373U  ILE*     4.0     7.9    -      -       -      +
   1374U  GLN*     3.6    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1371 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1367U  ASN      3.0    16.9    +      -       -      +
   1368U  MET*     3.6     8.5    -      -       -      +
   1370U  MET*     1.3    79.5    -      -       -      +
   1372U  LEU*     1.3    57.3    +      -       -      +
   1373U  ILE      3.4     0.2    -      -       -      -
   1374U  GLN*     3.7     5.2    +      -       -      +
   1375U  THR*     3.3    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1372 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1216U  LEU*     5.8     8.1    -      -       +      +
   1250U  LEU*     6.0     6.3    -      -       +      -
   1368U  MET      3.1    15.1    +      -       -      +
   1369U  TYR*     3.0     9.3    +      -       -      +
   1371U  HIS*     1.3    77.4    -      -       -      +
   1373U  ILE*     1.3    60.2    +      -       -      +
   1374U  GLN      3.3     0.4    -      -       -      -
   1375U  THR*     3.8     4.3    -      -       -      +
   1376U  THR*     2.9    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1373 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1369U  TYR      2.8    14.4    +      -       -      +
   1370U  MET*     4.3     8.5    -      -       -      +
   1371U  HIS      3.4     0.2    -      -       -      -
   1372U  LEU*     1.3    78.4    -      -       -      +
   1374U  GLN*     1.3    59.3    +      -       -      +
   1376U  THR      3.0    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1374 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1370U  MET      3.6    16.7    +      -       -      +
   1371U  HIS*     4.0     5.6    -      -       -      +
   1372U  LEU      3.3     0.2    -      -       -      -
   1373U  ILE*     1.3    81.0    -      -       -      +
   1375U  THR*     1.3    58.9    +      -       -      +
   1376U  THR      3.6     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR1375 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1371U  HIS      3.3    17.4    +      -       -      -
   1372U  LEU*     4.6     2.9    -      -       -      -
   1374U  GLN*     1.3    80.4    -      -       -      +
   1376U  THR*     1.3    58.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR1376 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1372U  LEU*     2.9    19.3    +      -       -      +
   1373U  ILE*     3.0    21.1    -      -       -      +
   1374U  GLN      4.6     0.7    -      -       -      +
   1375U  THR*     1.3    79.2    -      -       -      +
   1377U  HIS*     1.3    66.4    +      -       -      +
   1378U  HIS      5.4     0.4    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il