Contacts of the strand formed by residues 1353 - 1362 (chain A) in PDB entry 4YKN


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 LYS1353 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1352A  ASP*     1.3    91.6    +      -       +      +
   1354A  ILE*     1.3    66.9    +      -       -      +
   1375A  ARG*     3.9    34.9    +      -       +      +
   1376A  VAL*     3.5    19.9    -      -       -      +
   1377A  PRO*     4.0    21.3    -      -       +      +
   1378A  CYS*     4.4     0.6    -      -       -      -
   1408A  SER*     3.3     5.2    -      -       -      -
   1409A  VAL*     2.9    34.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1344A  VAL*     4.1    15.0    -      -       +      -
   1346A  VAL*     4.8     3.4    -      -       +      -
   1353A  LYS*     1.3    81.0    -      -       -      +
   1355A  TYR*     1.3    66.9    +      -       -      +
   1374A  GLN      4.1     0.7    -      -       -      +
   1375A  ARG*     3.5     1.8    -      -       -      -
   1376A  VAL*     3.0    39.7    +      -       +      +
   1377A  PRO      4.3     3.1    -      -       -      +
   1378A  CYS*     3.6    34.3    -      -       +      +
   1381A  PRO*     3.9    27.6    -      -       +      -
   1383A  TRP*     4.2    13.7    -      -       +      -
   1406A  ILE*     4.6     8.5    -      -       +      -
   1407A  CYS      3.1    14.1    -      -       -      +
   1408A  SER*     4.1    11.7    -      -       -      +
   1422A  LEU*     4.2    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1354A  ILE*     1.3    78.8    -      -       -      +
   1356A  VAL*     1.3    71.7    +      -       -      +
   1357A  ARG*     3.8    14.1    +      -       +      -
   1372A  ASN*     3.6    39.2    +      -       +      -
   1373A  THR*     3.8    15.7    -      -       -      +
   1374A  GLN      4.0     8.1    -      -       -      +
   1375A  ARG*     4.3    14.6    -      -       +      -
   1383A  TRP*     3.9     7.9    -      -       -      +
   1406A  ILE*     3.4     4.1    -      -       -      +
   1407A  CYS*     2.8    57.9    +      -       +      +
   1409A  VAL*     3.6    29.8    -      -       +      -
   1419A  HIS*     3.0    25.6    +      +       -      -
   1455A  LEU*     4.0    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1338A  ILE*     3.8    23.8    -      -       +      -
   1355A  TYR*     1.3    72.9    -      -       -      +
   1357A  ARG*     1.3    62.3    +      -       -      +
   1358A  THR*     3.9    21.1    +      -       +      +
   1371A  VAL      4.2     0.3    -      -       -      +
   1372A  ASN*     3.6     2.3    -      -       -      -
   1373A  THR*     2.9    42.1    +      -       +      +
   1383A  TRP*     3.6    34.3    -      -       +      -
   1404A  LEU*     4.6     2.9    -      -       +      -
   1405A  SER      3.3    11.2    -      -       -      +
   1406A  ILE*     4.2     8.7    -      -       +      -
   1473A  LEU*     4.0    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349A  ASP*     3.0    34.0    +      -       -      +
    373A  ARG*     5.7     0.4    -      -       -      +
   1355A  TYR*     3.8    17.3    +      -       +      -
   1356A  VAL*     1.3    71.7    -      -       -      +
   1358A  THR*     1.3    61.8    +      -       -      +
   1369A  ASP*     5.5     2.2    +      -       -      -
   1370A  ASN*     2.9    36.6    +      -       -      +
   1372A  ASN*     3.0    47.4    +      -       -      +
   1404A  LEU*     3.1     4.7    -      -       -      +
   1405A  SER*     2.8    47.9    +      -       -      +
   1407A  CYS*     3.9     4.7    -      -       -      -
   1455A  LEU*     3.6    36.8    -      -       -      +
   1456A  LEU*     3.5    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR1358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1338A  ILE*     4.1     8.3    -      -       +      -
   1356A  VAL*     3.9    17.5    -      -       +      +
   1357A  ARG*     1.3    79.2    -      -       -      +
   1359A  GLY*     1.3    58.5    +      -       -      +
   1370A  ASN*     3.3    12.1    -      -       -      +
   1371A  VAL      2.8    38.9    +      -       -      +
   1387A  LEU*     3.5    22.6    -      -       +      +
   1389A  TYR*     2.7    31.6    +      -       -      +
   1402A  LEU*     4.4     4.5    -      -       +      -
   1403A  CYS      3.4     8.7    -      -       -      -
   1404A  LEU*     4.0    11.7    -      -       +      +
   1456A  LEU*     4.2     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1358A  THR*     1.3    79.2    -      -       -      +
   1360A  ILE*     1.3    65.4    +      -       -      -
   1361A  TYR*     3.7     8.5    -      -       -      -
   1369A  ASP      5.4     0.7    -      -       -      -
   1370A  ASN*     3.6    21.1    -      -       -      -
   1389A  TYR*     4.5     5.6    -      -       -      -
   1402A  LEU*     3.5     4.5    -      -       -      +
   1403A  CYS*     2.8    34.8    +      -       -      +
   1456A  LEU*     4.3     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1334A  LEU*     3.8    26.9    -      -       +      -
   1336A  ILE*     4.4     3.6    -      -       +      -
   1359A  GLY*     1.3    72.1    -      -       -      -
   1361A  TYR*     1.3    62.9    +      -       -      +
   1366A  PRO*     3.5     5.5    -      -       -      +
   1367A  LEU*     2.9    43.9    +      -       +      -
   1368A  CYS*     4.3    18.9    +      -       -      +
   1370A  ASN*     4.9     0.6    -      -       -      +
   1389A  TYR*     3.9    23.6    -      -       +      -
   1391A  ILE*     5.2     2.2    -      -       +      -
   1396A  LEU*     4.2    10.3    -      -       +      -
   1400A  ALA*     4.4     2.2    -      -       +      -
   1401A  ARG      3.6     3.6    -      -       -      +
   1402A  LEU*     3.6    26.0    -      -       +      -
   1429A  LEU*     3.9    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1359A  GLY      3.7    12.3    -      -       -      -
   1360A  ILE*     1.3    79.4    -      -       -      +
   1362A  HIS*     1.3    58.5    +      -       -      +
   1363A  GLY      3.9    10.6    +      -       -      +
   1364A  GLY      3.5    22.4    -      -       -      -
   1365A  GLU      3.4     3.1    -      -       -      -
   1366A  PRO*     3.5    35.1    -      -       +      +
   1367A  LEU*     4.3     3.4    -      -       -      -
   1370A  ASN*     3.4    34.1    +      -       -      -
   1399A  ALA      4.4     0.3    -      -       -      +
   1400A  ALA*     3.5     2.8    -      -       -      -
   1401A  ARG*     2.9    37.1    +      -       -      +
   1403A  CYS*     3.9    26.2    -      -       +      -
   1456A  LEU*     3.7    23.1    -      -       +      +
   1458A  PRO*     3.9    19.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS1362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1361A  TYR*     1.3    71.8    -      -       -      +
   1363A  GLY*     1.3    66.6    +      -       -      +
   1364A  GLY      3.5     0.2    +      -       -      -
   1365A  GLU*     2.8    36.6    +      -       -      +
   1367A  LEU*     3.6    28.6    -      -       +      +
   1397A  PRO*     3.8    28.6    -      -       +      +
   1399A  ALA*     4.0    29.2    +      -       +      +
   1400A  ALA*     4.8     0.9    -      -       -      +
----------------------------------------------------------
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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