Contacts of the strand formed by residues 1256 - 1263 (chain B) in PDB entry 5NPK


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 ARG1256 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1251B  GLU*     4.1     1.4    -      -       -      +
   1252B  ARG*     2.9    36.2    +      -       +      +
   1253B  GLY      3.3    18.5    +      -       -      +
   1254B  GLY*     3.1    12.8    -      -       -      +
   1255B  GLY*     1.3    79.9    -      -       -      +
   1257B  GLN*     1.3    67.9    +      -       -      +
   1290B  THR*     5.1     3.2    -      -       -      +
   1308B  VAL      3.8     5.8    +      -       -      +
   1309B  ARG*     3.0    19.4    -      -       -      +
   1310B  LYS*     2.1    63.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1257 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1249B  ILE*     3.8    11.1    -      -       +      +
   1250B  GLU      3.4     8.1    -      -       -      +
   1251B  GLU*     3.1    40.3    +      -       -      +
   1252B  ARG*     4.7     3.8    -      -       -      +
   1255B  GLY      4.8     3.6    -      -       -      +
   1256B  ARG*     1.3    76.7    -      -       -      +
   1258B  ARG*     1.3    62.3    +      -       -      +
   1307B  ASP*     4.2     0.5    -      -       -      +
   1308B  VAL*     3.0    35.8    +      -       +      +
   1309B  ARG      5.5     1.2    +      -       -      +
   1312B  ALA      3.9    10.9    -      -       -      +
   1313B  ASN*     4.3     2.3    +      -       -      -
   1314B  ALA*     3.2    40.2    +      -       +      +
   1315B  SER*     5.5     1.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1248B  VAL      3.8     0.2    -      -       -      +
   1249B  ILE*     3.6     2.9    -      -       -      -
   1250B  GLU*     2.8    59.4    +      -       +      +
   1252B  ARG*     3.4    47.5    -      -       -      +
   1257B  GLN*     1.3    76.7    -      -       -      +
   1259B  ILE*     1.3    63.4    +      -       -      +
   1260B  VAL*     4.0     9.1    +      -       +      +
   1293B  ARG*     4.2    14.8    -      -       -      +
   1303B  ARG*     3.7    21.1    -      -       -      +
   1305B  VAL*     3.5    19.9    -      -       -      +
   1306B  ILE      3.3    12.6    -      -       -      +
   1307B  ASP*     3.5    15.4    +      -       -      +
   1308B  VAL*     4.4     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1247B  ALA*     4.1    12.8    -      -       +      -
   1248B  VAL      3.4     8.7    -      -       -      +
   1249B  ILE*     4.3    15.3    -      -       +      -
   1258B  ARG*     1.3    75.0    -      -       -      +
   1260B  VAL*     1.3    64.7    +      -       -      +
   1261B  VAL*     4.1     9.4    -      -       +      -
   1304B  VAL      3.6     1.2    -      -       -      +
   1305B  VAL*     3.4     5.2    -      -       -      +
   1306B  ILE*     2.9    48.9    +      -       +      +
   1308B  VAL*     4.4    11.4    -      -       +      -
   1314B  ALA*     3.9    24.5    -      -       +      +
   1317B  ILE*     4.4    13.0    -      -       +      -
   1318B  LEU*     4.0    37.7    -      -       +      +
   1321B  LEU*     4.6     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1246B  ARG      3.9     0.5    -      -       -      +
   1247B  ALA*     3.3     1.9    -      -       -      -
   1248B  VAL*     2.9    42.4    +      -       +      +
   1250B  GLU*     3.7    34.1    -      -       +      +
   1258B  ARG*     4.0    15.3    -      -       +      +
   1259B  ILE*     1.3    78.9    -      -       -      +
   1261B  VAL*     1.3    61.9    +      -       -      +
   1262B  THR*     3.9    21.0    +      -       +      +
   1303B  ARG*     3.5    38.4    -      -       +      +
   1304B  VAL      3.5     3.8    -      -       -      +
   1305B  VAL*     4.7     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1245B  SER*     3.9    11.4    -      -       -      -
   1246B  ARG      3.4     7.0    -      -       -      +
   1247B  ALA*     3.8    17.3    -      -       +      -
   1259B  ILE*     4.1    11.2    -      -       +      -
   1260B  VAL*     1.3    75.3    -      -       -      +
   1262B  THR*     1.3    61.6    +      -       -      +
   1263B  GLU      3.5    20.4    -      -       -      +
   1264B  ILE*     4.0    16.2    -      -       +      -
   1273B  MET*     5.1     0.4    -      -       +      -
   1302B  VAL*     3.9     2.1    -      -       -      +
   1303B  ARG*     3.2     5.7    +      -       -      -
   1304B  VAL*     2.8    54.8    +      -       +      +
   1306B  ILE*     4.8     8.7    -      -       +      -
   1327B  LEU*     4.1    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1246B  ARG*     3.0    26.0    +      -       -      +
   1248B  VAL*     6.2     1.3    -      -       +      -
   1260B  VAL*     3.9    22.1    +      -       +      +
   1261B  VAL*     1.3    77.2    -      -       -      +
   1263B  GLU*     1.3    68.4    +      -       -      +
   1300B  THR      5.9     0.9    -      -       -      +
   1302B  VAL*     3.3    36.5    +      -       -      +
   1303B  ARG*     4.9     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU1263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1220B  THR      4.0     5.2    -      -       -      +
   1221B  ALA*     3.3    18.5    -      -       +      +
   1222B  GLY*     2.8    38.1    +      -       -      +
   1245B  SER*     3.1     9.1    -      -       -      -
   1246B  ARG*     2.9    65.4    +      -       +      +
   1261B  VAL*     3.5     3.9    -      -       -      +
   1262B  THR*     1.3    88.9    +      -       -      +
   1264B  ILE*     1.3    63.9    +      -       -      +
   1302B  VAL*     4.6     3.6    -      -       -      -
   1485B  ARG      4.8     1.2    -      -       -      +
----------------------------------------------------------
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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