Contacts of the strand formed by residues 1321 - 1329 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1281A  GLY*     4.5     3.4    -      -       -      +
   1284A  LEU*     4.5    13.5    -      -       +      -
   1285A  SER*     2.6    40.2    -      -       -      +
   1288A  ILE*     3.9    22.4    -      -       +      -
   1301A  ILE*     3.4     6.3    -      -       +      +
   1317A  ASN*     3.0    35.0    +      -       -      +
   1318A  LEU*     2.4    47.9    +      -       +      +
   1319A  ASP      4.6     0.4    -      -       -      +
   1320A  GLY*     1.3    82.0    -      -       -      +
   1322A  THR*     1.3    62.8    +      -       -      +
   1323A  LEU*     5.0     6.3    -      -       +      -
   1340A  GLY*     3.3     3.5    -      -       -      -
   1341A  GLU      3.2    11.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR1322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1300A  ASN*     4.6     6.4    +      -       -      -
   1301A  ILE      2.8     9.6    +      -       -      +
   1302A  THR*     3.3    18.5    +      -       +      +
   1303A  LEU      2.8    28.2    +      -       -      +
   1320A  GLY      4.1     0.9    -      -       -      -
   1321A  MET*     1.3    73.2    +      -       -      +
   1323A  LEU*     1.3    66.2    +      -       -      +
   1324A  HIS*     3.8    29.8    -      -       +      +
   1341A  GLU*     3.4    33.5    +      -       +      +
   1343A  VAL*     5.2     2.2    -      -       +      -
   1471A  HIS*     5.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1280A  VAL      4.1     8.5    -      -       -      +
   1281A  GLY*     4.6     7.4    -      -       -      -
   1284A  LEU*     6.0     0.4    -      -       +      -
   1303A  LEU*     3.5    35.9    -      -       +      +
   1305A  PHE*     4.2     4.3    -      -       +      -
   1313A  PHE*     4.0    21.8    -      -       +      -
   1314A  GLY*     3.3    34.8    -      -       -      +
   1317A  ASN*     3.6    24.0    -      -       -      +
   1321A  MET*     5.0     5.6    -      -       +      -
   1322A  THR*     1.3    80.8    -      -       -      +
   1324A  HIS*     1.3    57.4    +      -       -      +
   1341A  GLU      2.9    12.0    +      -       -      +
   1342A  ILE*     3.4     7.6    -      -       +      +
   1343A  VAL*     2.8    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1302A  THR*     4.0    10.3    -      -       +      +
   1303A  LEU      2.8     9.8    +      -       -      +
   1304A  ASN*     3.4    27.8    -      -       +      +
   1305A  PHE*     2.7    36.5    +      -       -      +
   1313A  PHE*     4.8     0.2    -      -       -      -
   1322A  THR*     3.8    25.4    -      -       +      +
   1323A  LEU*     1.3    72.3    -      -       -      +
   1325A  LEU*     1.3    57.3    +      -       -      +
   1326A  GLN      4.3     0.2    -      -       -      -
   1343A  VAL*     3.4    34.7    +      -       +      +
   1471A  HIS*     4.5    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1273A  LEU*     4.3    10.8    -      -       +      -
   1305A  PHE*     3.5    23.1    -      -       +      +
   1307A  GLY      3.7    21.1    -      -       -      +
   1309A  ALA*     3.7    17.0    -      -       +      -
   1313A  PHE*     3.8    20.4    -      -       +      -
   1324A  HIS*     1.3    75.4    -      -       -      +
   1326A  GLN*     1.3    66.6    +      -       -      +
   1327A  GLY      3.9     0.6    +      -       -      +
   1328A  GLU      3.6    27.4    -      -       -      +
   1329A  ALA*     3.9     9.6    -      -       +      -
   1343A  VAL      2.8    13.8    +      -       -      +
   1344A  ILE*     3.3    16.6    -      -       +      -
   1345A  VAL*     2.9    30.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1305A  PHE      2.9    13.8    +      -       -      +
   1306A  GLN*     3.4    29.7    +      -       +      +
   1307A  GLY      2.9    26.3    +      -       -      -
   1324A  HIS      4.3     0.2    -      -       -      -
   1325A  LEU*     1.3    71.2    -      -       -      +
   1327A  GLY*     1.3    57.8    +      -       -      +
   1345A  VAL*     3.2    12.6    -      -       +      +
   1346A  PRO      3.6    16.4    -      -       -      +
   1347A  HIS*     3.0    25.9    +      -       -      +
   1348A  PRO*     2.9    36.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  LYS*     4.7     5.5    +      -       -      +
   1307A  GLY      3.3     7.6    -      -       -      -
   1325A  LEU*     3.9     1.7    -      -       -      -
   1326A  GLN*     1.3    74.9    -      -       -      +
   1328A  GLU*     1.3    67.1    +      -       -      +
   1344A  ILE*     5.1     0.4    -      -       -      -
   1345A  VAL      2.7    17.9    +      -       -      +
   1346A  PRO*     3.7     6.6    -      -       -      +
   1347A  HIS*     3.4    24.5    -      -       -      -
   1359A  ILE*     3.5    12.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  ARG*     4.4     4.3    +      -       -      +
    355A  CYS*     5.8     2.1    -      -       -      -
    368A  ALA*     3.5    34.0    -      -       +      +
    369A  GLY*     5.3     0.2    -      -       -      -
    381A  LYS*     3.0    43.1    +      -       +      +
   1307A  GLY      3.3     6.1    +      -       -      +
   1308A  ALA*     3.3    22.3    +      -       +      +
   1309A  ALA      2.9    23.4    +      -       -      -
   1325A  LEU*     3.6    10.5    -      -       -      +
   1326A  GLN      4.3     0.4    -      -       -      -
   1327A  GLY*     1.3    74.5    -      -       -      +
   1329A  ALA*     1.3    62.0    +      -       -      +
   1330A  ASN*     5.9     0.2    -      -       -      +
   1344A  ILE*     4.6     0.7    -      -       -      -
   1347A  HIS*     5.7     1.6    +      -       -      -
   1358A  VAL      4.9     1.0    -      -       -      +
   1359A  ILE*     3.6    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  ARG*     2.3    34.3    +      -       -      -
   1309A  ALA*     3.8    12.8    -      -       +      -
   1313A  PHE*     4.5     3.6    -      -       +      -
   1325A  LEU*     3.9    16.6    -      -       +      -
   1328A  GLU*     1.3    75.4    -      -       -      +
   1330A  ASN*     1.3    59.2    +      -       -      +
   1333A  VAL*     3.5    27.8    -      -       +      -
   1344A  ILE*     4.2     3.1    -      -       +      +
   1359A  ILE      2.8    11.1    +      -       -      +
   1360A  ILE*     3.6     8.4    -      -       +      -
----------------------------------------------------------
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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