Contacts of the strand formed by residues 251 - 258 (chain C) in PDB entry 3KQG


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 TYR 251 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  LEU*     4.2    12.3    -      -       -      +
    209C  PHE*     3.8    29.8    -      +       +      +
    210C  SER      4.2     6.2    +      -       -      -
    245C  THR      5.2     0.5    +      -       -      -
    246C  ALA*     3.4    40.5    +      -       +      -
    249C  LEU*     3.4    35.6    -      -       +      +
    250C  ILE*     1.3    75.1    -      -       -      +
    252C  TRP*     1.3    63.0    +      -       -      +
    253C  ILE*     3.8     1.6    -      -       -      +
    297C  ASN*     3.2     4.7    -      -       -      +
    298C  ILE*     2.7    39.6    +      -       +      +
    316C  LEU*     3.0    35.5    -      -       +      +
    317C  PHE      3.6     9.6    -      -       -      -
    318C  ILE*     3.5    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 252 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214C  LYS      3.2    20.2    +      -       -      -
    215C  THR      4.0     1.3    -      -       -      -
    216C  TRP*     3.4    33.2    -      +       +      +
    219C  ALA*     4.7     4.0    -      -       +      -
    230C  LEU*     4.6     5.6    -      -       +      +
    251C  TYR*     1.3    74.0    -      -       -      +
    253C  ILE*     1.3    62.7    +      -       -      +
    295C  CYS*     3.5    30.1    -      -       +      -
    296C  GLY      3.2    33.9    -      -       -      -
    297C  ASN*     3.7    10.4    -      -       +      +
    309C  ALA*     3.8    14.1    -      -       +      -
    310C  PRO      3.4    27.1    -      -       -      -
    311C  CYS*     4.2     6.5    -      -       -      -
    313C  LYS      3.1    24.9    +      -       -      -
    315C  PHE*     3.5    33.7    -      +       +      +
    316C  LEU      2.7     8.3    +      -       -      -
    317C  PHE*     3.8    13.4    -      -       +      +
    318C  ILE      3.2    22.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 253 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  TRP*     2.8    31.9    +      -       -      -
    230C  LEU*     3.7    11.0    -      -       -      +
    231C  THR*     3.6    24.5    -      -       +      +
    233C  VAL*     4.4     3.8    -      -       +      -
    251C  TYR      3.5     3.3    +      -       -      +
    252C  TRP*     1.3    79.5    -      -       -      +
    254C  GLY*     1.3    54.2    +      -       -      +
    255C  LEU*     2.8    24.9    +      -       +      +
    266C  TRP*     4.1     9.9    -      -       +      -
    296C  GLY      3.2    17.3    +      -       -      +
    297C  ASN*     4.4     2.5    -      -       -      -
    298C  ILE*     3.5    34.5    -      -       +      -
    306C  TRP*     3.7    35.2    -      -       +      +
    318C  ILE*     4.6     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 254 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  TRP*     4.0     5.4    -      -       -      -
    230C  LEU*     3.5    20.7    -      -       -      +
    231C  THR      2.8    21.5    +      -       -      -
    253C  ILE*     1.3    68.9    -      -       -      +
    255C  LEU*     1.3    58.7    +      -       -      +
    256C  THR*     3.5     1.0    +      -       -      +
    265C  SER      3.1     7.6    -      -       -      +
    266C  TRP*     3.3     9.3    -      -       -      -
    267C  VAL*     3.0    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 255 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  TRP*     3.3     9.2    +      -       -      -
    253C  ILE*     2.8    12.7    +      -       +      -
    254C  GLY*     1.3    73.0    -      -       -      +
    256C  THR*     1.3    64.0    +      -       -      +
    264C  TRP*     3.7    20.6    -      -       +      -
    265C  SER      3.6     8.5    -      -       -      +
    266C  TRP*     3.6    16.9    -      -       +      -
    272C  PHE*     3.6    31.2    -      -       +      -
    281C  TRP*     3.8    17.9    -      -       +      -
    295C  CYS*     3.3     1.0    -      -       -      -
    296C  GLY*     2.8    44.2    +      -       -      +
    306C  TRP*     3.5    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 256 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  TRP*     3.5    33.9    -      -       +      -
    254C  GLY      4.2     4.5    -      -       -      +
    255C  LEU*     1.3    75.6    -      -       -      +
    257C  LYS*     1.3    68.0    +      -       -      +
    258C  ALA*     5.5     1.3    -      -       +      -
    264C  TRP*     3.7    10.2    -      -       -      -
    265C  SER*     2.7    51.0    +      -       -      +
    267C  VAL*     4.6     7.6    -      -       +      +
    294C  HIS      3.3    13.5    +      -       -      -
    295C  CYS*     3.4     9.4    -      -       -      -
    311C  CYS*     4.6     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 257 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256C  THR*     1.3    81.2    +      -       -      +
    258C  ALA*     1.3    61.2    +      -       -      +
    262C  GLY*     3.5    32.5    -      -       -      +
    263C  ASP      3.3     6.1    -      -       -      +
    264C  TRP*     3.6    28.9    -      -       +      +
    286C  PRO*     6.1     0.4    -      -       -      -
    288C  ASN*     3.6    24.0    -      -       -      +
    293C  GLU      2.9    19.9    +      -       -      -
    294C  HIS*     2.9    53.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 258 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256C  THR*     3.6     1.8    +      -       +      -
    257C  LYS*     1.3    76.1    -      -       -      +
    259C  GLY*     1.3    69.0    +      -       -      +
    261C  GLU      4.4     0.2    +      -       -      -
    262C  GLY*     3.7     1.5    +      -       -      -
    263C  ASP*     2.9    30.6    +      -       -      +
    265C  SER*     3.6    22.2    -      -       -      +
----------------------------------------------------------
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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