Contacts of the strand formed by residues 1321 - 1329 (chain B) in PDB entry 1OFD


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 MET1321 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1281B  GLY      4.5     2.5    -      -       -      +
   1284B  LEU*     4.5    12.3    -      -       +      -
   1285B  SER*     2.8    42.0    -      -       -      +
   1288B  ILE*     3.9    21.8    -      -       +      -
   1301B  ILE*     3.4     7.2    -      -       +      +
   1317B  ASN*     3.0    41.8    +      -       -      +
   1318B  LEU*     2.4    46.0    +      -       +      +
   1319B  ASP      4.5     0.9    -      -       -      +
   1320B  GLY*     1.3    82.0    -      -       -      +
   1322B  THR*     1.3    63.1    +      -       -      +
   1323B  LEU*     4.7     7.9    -      -       +      -
   1340B  GLY*     3.4     2.3    -      -       -      -
   1341B  GLU      3.1    12.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR1322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1300B  ASN*     3.8    13.3    +      -       -      -
   1301B  ILE      2.8    12.0    +      -       -      +
   1302B  THR*     3.3    16.0    -      -       +      +
   1303B  LEU      2.8    27.7    +      -       -      +
   1320B  GLY      5.1     0.5    -      -       -      -
   1321B  MET*     1.3    75.1    +      -       -      +
   1323B  LEU*     1.3    61.0    +      -       -      +
   1324B  HIS*     3.7    27.8    -      -       +      +
   1341B  GLU*     3.5    31.3    +      -       +      +
   1343B  VAL*     5.5     1.8    -      -       +      -
   1471B  HIS*     6.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1280B  VAL      4.2     9.0    -      -       -      +
   1281B  GLY*     4.5     7.9    -      -       -      -
   1284B  LEU*     5.8     0.7    -      -       +      -
   1303B  LEU*     3.5    35.4    -      -       +      +
   1305B  PHE*     4.4     3.6    -      -       +      -
   1313B  PHE*     4.2    21.8    -      -       +      -
   1314B  GLY*     3.5    28.5    -      -       -      +
   1317B  ASN*     3.4    29.6    -      -       -      +
   1321B  MET*     4.7     6.7    -      -       +      -
   1322B  THR*     1.3    81.8    -      -       -      +
   1324B  HIS*     1.3    60.1    +      -       -      +
   1341B  GLU      2.8    13.3    +      -       -      +
   1342B  ILE*     3.4     9.1    -      -       +      +
   1343B  VAL*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1302B  THR*     4.2    10.8    -      -       +      +
   1303B  LEU      2.8     7.6    +      -       -      +
   1304B  ASN*     3.4    29.2    -      -       +      +
   1305B  PHE*     2.7    37.1    +      -       -      -
   1313B  PHE*     4.7     0.2    -      -       -      -
   1322B  THR*     3.7    30.0    -      -       +      +
   1323B  LEU*     1.3    74.3    -      -       -      +
   1325B  LEU*     1.3    56.2    +      -       -      +
   1326B  GLN      4.2     0.2    -      -       -      -
   1343B  VAL*     3.4    35.6    -      -       +      +
   1471B  HIS*     4.6    15.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1273B  LEU*     4.2    13.0    -      -       +      -
   1305B  PHE*     3.5    23.3    -      -       +      +
   1307B  GLY      3.7    21.1    -      -       -      +
   1309B  ALA*     3.7    16.4    -      -       +      -
   1313B  PHE*     3.8    18.4    -      -       +      -
   1323B  LEU      4.2     0.2    +      -       -      -
   1324B  HIS*     1.3    74.5    -      -       -      +
   1326B  GLN*     1.3    63.1    +      -       -      +
   1327B  GLY      4.6     0.7    -      -       -      +
   1328B  GLU      3.4    25.1    -      -       -      +
   1329B  ALA*     3.8    13.5    -      -       +      -
   1343B  VAL      2.8    13.1    +      -       -      +
   1344B  ILE*     3.3    18.8    -      -       +      +
   1345B  VAL*     2.9    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1272B  ARG*     5.7     0.6    -      -       -      +
   1305B  PHE      2.9    14.8    +      -       -      +
   1306B  GLN*     3.3    31.7    +      -       +      +
   1307B  GLY      2.9    27.3    +      -       -      +
   1324B  HIS      4.2     0.2    -      -       -      -
   1325B  LEU*     1.3    73.0    -      -       -      +
   1327B  GLY*     1.3    57.5    +      -       -      +
   1345B  VAL*     3.3    15.2    -      -       +      +
   1346B  PRO      3.8    14.4    -      -       -      +
   1347B  HIS*     3.2    26.6    +      -       -      +
   1348B  PRO*     3.4    27.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381B  LYS*     4.7     4.5    +      -       -      -
   1307B  GLY      3.4     3.6    -      -       -      -
   1325B  LEU*     3.9     1.7    -      -       -      -
   1326B  GLN*     1.3    75.2    -      -       -      +
   1328B  GLU*     1.3    66.1    +      -       -      +
   1344B  ILE*     5.1     0.9    -      -       -      -
   1345B  VAL      2.8    19.9    +      -       -      +
   1346B  PRO*     3.7     6.4    -      -       -      +
   1347B  HIS*     3.3    30.1    +      -       -      +
   1359B  ILE*     3.5    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  ARG*     4.2     5.4    +      -       -      +
    368B  ALA*     3.4    37.6    -      -       +      +
    375B  GLU*     4.4     2.4    -      -       -      +
    381B  LYS*     2.9    42.0    +      -       +      +
   1307B  GLY      3.3     4.6    +      -       -      -
   1308B  ALA*     3.3    20.4    -      -       +      +
   1309B  ALA      2.9    22.9    +      -       -      -
   1325B  LEU*     3.4    11.3    -      -       -      +
   1326B  GLN      4.4     0.2    -      -       -      -
   1327B  GLY*     1.3    74.8    -      -       -      +
   1329B  ALA*     1.3    62.2    +      -       -      +
   1330B  ASN*     5.8     0.2    -      -       -      +
   1344B  ILE*     4.8     1.1    -      -       -      -
   1347B  HIS*     5.8     1.0    +      -       -      -
   1358B  VAL      4.9     2.5    -      -       -      +
   1359B  ILE*     3.6    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  ARG*     2.5    33.5    +      -       -      -
   1309B  ALA*     3.7    12.8    -      -       +      -
   1310B  GLY      5.1     0.2    -      -       -      +
   1313B  PHE*     4.5     4.0    -      -       +      -
   1325B  LEU*     3.8    17.0    -      -       +      -
   1328B  GLU*     1.3    76.3    -      -       -      +
   1330B  ASN*     1.3    58.4    +      -       -      +
   1333B  VAL*     3.5    27.8    -      -       +      -
   1344B  ILE*     4.3     2.0    -      -       +      +
   1359B  ILE      2.9    11.2    +      -       -      +
   1360B  ILE*     3.7     8.1    -      -       +      -
----------------------------------------------------------
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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