Contacts of the strand formed by residues 1426 - 1432 (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 GLY1426 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995A  LYS*     3.9     3.6    -      -       -      -
   1405A  MET*     3.4    20.8    +      -       -      +
   1406A  THR      3.4    21.6    -      -       -      -
   1407A  GLY      3.6     1.2    +      -       -      -
   1424A  MET*     3.7     7.4    -      -       -      +
   1425A  THR*     1.3    80.7    -      -       -      +
   1427A  GLY*     1.3    66.4    +      -       -      +
   1496A  PRO*     3.4     6.0    -      -       -      +
   1498A  SER*     3.4    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY1427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1405A  MET*     4.1     3.4    -      -       -      -
   1406A  THR      3.7     0.2    +      -       -      -
   1407A  GLY*     3.5    16.9    -      -       -      -
   1408A  GLY      3.3    14.4    -      -       -      -
   1424A  MET*     5.1     1.4    -      -       -      +
   1426A  GLY*     1.3    75.8    -      -       -      +
   1428A  LEU*     1.3    63.6    +      -       -      +
   1496A  PRO*     3.1    22.2    -      -       -      +
   1499A  GLU*     2.8    24.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1428 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1405A  MET*     3.4     6.1    -      -       -      +
   1408A  GLY      3.1     8.1    +      -       -      +
   1409A  VAL*     3.3     9.8    -      -       +      +
   1410A  ILE      3.0    22.2    +      -       -      -
   1424A  MET*     5.6     1.1    -      -       -      -
   1427A  GLY*     1.3    82.2    -      -       -      +
   1429A  ALA*     1.3    61.9    +      -       -      +
   1430A  TYR*     4.0    16.8    -      -       +      +
   1460A  GLN*     3.5    22.7    -      -       -      +
   1493A  GLN*     4.1     9.6    -      -       +      +
   1494A  ALA      3.8    13.7    -      -       -      +
   1495A  VAL*     4.3    16.2    -      -       +      -
   1499A  GLU*     3.8    25.1    -      -       +      +
   1502A  SER*     4.4     6.3    -      -       -      +
   1504A  GLU*     3.6    22.4    -      -       +      -
   1505A  ALA*     4.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1402A  CYS*     3.9    20.2    -      -       -      -
   1405A  MET*     4.9     0.2    -      -       +      -
   1410A  ILE*     3.1    11.4    -      -       +      +
   1424A  MET*     4.9     5.8    -      -       -      -
   1428A  LEU*     1.3    76.9    -      -       -      +
   1430A  TYR*     1.3    65.0    +      -       -      +
   1431A  PHE*     3.6    28.0    -      -       +      -
   1492A  TRP      4.0     0.2    -      -       -      +
   1493A  GLN*     3.5     5.4    -      -       -      +
   1494A  ALA*     2.9    38.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1409A  VAL*     3.8    14.4    -      -       +      -
   1410A  ILE      2.7    16.3    +      -       -      +
   1411A  VAL*     3.4    14.6    -      -       +      +
   1412A  VAL*     2.9    28.1    +      -       -      +
   1428A  LEU*     4.0    10.1    -      -       +      +
   1429A  ALA*     1.3    75.0    -      -       -      +
   1431A  PHE*     1.3    65.0    +      -       -      +
   1452A  ILE*     3.8    26.0    -      -       +      -
   1457A  GLY*     3.4    28.7    +      -       -      -
   1460A  GLN*     2.6    33.1    +      -       +      -
   1461A  LEU*     3.7    27.4    -      -       +      -
   1491A  PHE*     4.3     5.6    -      -       +      -
   1492A  TRP      3.5     5.4    -      -       -      +
   1493A  GLN*     3.2    38.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE1431 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1401A  CYS*     4.0     6.5    -      -       -      -
   1402A  CYS*     4.4     9.9    -      -       -      -
   1412A  VAL*     3.6    34.3    -      -       +      +
   1414A  GLY      5.6     0.7    -      -       -      +
   1416A  VAL*     3.9    26.5    -      -       +      -
   1420A  VAL*     3.6    29.8    -      -       +      -
   1424A  MET*     5.8     0.7    -      -       +      -
   1429A  ALA*     3.6    32.1    -      -       +      -
   1430A  TYR*     1.3    75.2    -      -       -      +
   1432A  LEU*     1.3    62.6    +      -       -      +
   1433A  ASP*     3.4    17.1    +      -       -      +
   1438A  LEU*     3.5    18.6    -      -       +      -
   1449A  LEU*     5.0     2.9    -      -       +      -
   1491A  PHE*     3.2     4.3    -      -       -      -
   1492A  TRP*     2.8    43.4    +      -       -      +
   1494A  ALA*     4.0    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1432 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1412A  VAL      3.0    15.1    +      -       -      +
   1413A  LEU*     3.8    20.6    -      -       -      +
   1414A  GLY*     3.9    18.3    -      -       -      +
   1415A  PRO      4.7     0.2    -      -       -      -
   1431A  PHE*     1.3    69.6    -      -       -      +
   1433A  ASP*     1.3    71.1    +      -       -      +
   1434A  GLU*     3.5    32.3    +      -       +      +
   1476A  LYS*     4.2     4.0    -      -       -      -
   1480A  ILE*     3.9    26.5    -      -       +      -
   1487A  TYR*     4.2    11.0    -      -       +      -
   1490A  LYS*     4.0    22.2    -      -       +      -
   1491A  PHE*     3.5    35.4    -      -       +      -
----------------------------------------------------------
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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