Contacts of the strand formed by residues 1426 - 1432 (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 GLY1426 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995B  LYS*     3.8     4.3    -      -       -      -
   1405B  MET*     3.2    21.4    +      -       -      +
   1406B  THR      3.2    22.7    -      -       -      -
   1407B  GLY      3.6     3.3    +      -       -      -
   1424B  MET*     3.9     6.1    -      -       -      +
   1425B  THR*     1.3    81.9    -      -       -      +
   1427B  GLY*     1.3    66.7    +      -       -      +
   1496B  PRO*     3.6     4.1    -      -       -      +
   1498B  SER*     3.5    10.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY1427 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1405B  MET*     4.0     3.1    -      -       -      -
   1407B  GLY*     3.6    15.2    -      -       -      -
   1408B  GLY      3.3    15.3    -      -       -      -
   1424B  MET*     5.0     1.4    -      -       -      +
   1426B  GLY*     1.3    72.2    -      -       -      -
   1428B  LEU*     1.3    62.9    +      -       -      -
   1496B  PRO*     3.1    26.5    -      -       -      +
   1499B  GLU*     2.7    23.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1428 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1405B  MET*     3.4     6.2    -      -       -      +
   1408B  GLY      3.1     7.3    +      -       -      +
   1409B  VAL*     3.2    13.0    -      -       +      +
   1410B  ILE      3.1    21.1    +      -       -      -
   1424B  MET*     5.6     0.7    -      -       -      -
   1427B  GLY*     1.3    80.5    -      -       -      +
   1429B  ALA*     1.3    61.6    +      -       -      +
   1430B  TYR*     4.5    10.8    -      -       +      -
   1460B  GLN*     3.8     9.9    -      -       -      +
   1493B  GLN*     4.0    15.3    -      -       +      +
   1494B  ALA      3.5    16.8    -      -       -      +
   1495B  VAL*     4.0    19.3    -      -       +      -
   1499B  GLU*     3.9    22.9    -      -       +      +
   1502B  SER*     4.2     9.2    -      -       -      +
   1504B  GLU*     3.6    33.0    -      -       +      -
   1505B  ALA*     4.5     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1429 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1402B  CYS*     3.8    24.0    -      -       -      -
   1405B  MET*     4.7     1.8    -      -       +      -
   1410B  ILE*     3.1    11.0    -      -       +      +
   1424B  MET*     4.8     3.8    -      -       +      +
   1428B  LEU*     1.3    76.6    -      -       -      +
   1430B  TYR*     1.3    64.7    +      -       -      +
   1431B  PHE*     3.5    24.7    -      -       +      -
   1492B  TRP      3.9     0.3    -      -       -      +
   1493B  GLN*     3.5     4.2    -      -       -      +
   1494B  ALA*     2.8    43.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1430 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1409B  VAL*     3.9    17.5    -      -       +      -
   1410B  ILE      2.8    17.3    +      -       -      +
   1411B  VAL*     3.5     9.1    -      -       +      -
   1412B  VAL*     2.8    27.4    +      -       -      +
   1428B  LEU*     4.2     8.6    -      -       +      +
   1429B  ALA*     1.3    74.3    -      -       -      +
   1431B  PHE*     1.3    65.6    +      -       -      +
   1432B  LEU      4.2     0.2    -      -       -      -
   1452B  ILE*     3.7    28.5    -      -       +      -
   1457B  GLY*     3.5    27.9    +      -       -      -
   1460B  GLN*     2.7    32.8    +      -       +      -
   1461B  LEU*     3.8    29.6    -      -       +      -
   1491B  PHE*     4.4     4.5    -      -       +      -
   1492B  TRP      3.5     2.7    -      -       -      -
   1493B  GLN*     3.0    38.9    +      -       +      -
   1504B  GLU*     4.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1431 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1401B  CYS*     3.9    16.8    -      -       -      -
   1402B  CYS*     4.3     4.9    -      -       -      -
   1412B  VAL*     3.6    34.5    -      -       +      +
   1414B  GLY      5.5     0.9    -      -       -      +
   1416B  VAL*     3.9    20.4    -      -       +      -
   1420B  VAL*     3.5    30.5    -      -       +      -
   1424B  MET*     6.0     0.2    -      -       +      -
   1429B  ALA*     3.5    31.9    -      -       +      -
   1430B  TYR*     1.3    75.0    -      -       -      +
   1432B  LEU*     1.3    62.8    +      -       -      +
   1433B  ASP*     3.4     6.7    +      -       -      +
   1438B  LEU*     3.6    28.7    -      -       +      -
   1449B  LEU*     5.0     2.2    -      -       +      -
   1491B  PHE*     3.3     4.8    -      -       -      -
   1492B  TRP*     2.8    42.1    +      -       -      +
   1494B  ALA*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1432 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1412B  VAL      3.0    15.9    +      -       -      +
   1413B  LEU*     3.9    20.9    -      -       -      +
   1414B  GLY*     4.0    18.3    -      -       -      +
   1415B  PRO      4.8     0.2    -      -       -      -
   1431B  PHE*     1.3    71.0    -      -       -      +
   1433B  ASP*     1.3    72.1    +      -       -      +
   1434B  GLU*     3.9    35.5    +      -       +      +
   1476B  LYS*     4.0     4.9    -      -       -      -
   1480B  ILE*     4.0    24.0    -      -       +      -
   1487B  TYR*     4.1    14.1    -      -       +      +
   1490B  LYS*     4.0    19.3    -      -       +      +
   1491B  PHE*     3.5    32.1    -      -       +      -
----------------------------------------------------------
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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