Contacts of the strand formed by residues 312 - 320 (chain C) in PDB entry 1K4R


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 PHE 312 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307C  CYS*     3.4    38.8    -      -       +      -
    308C  ASP      3.7    13.0    -      -       -      -
    309C  LYS*     4.6     5.8    +      -       -      +
    310C  THR      3.6     5.0    -      -       -      +
    311C  LYS*     1.3    77.2    -      -       -      +
    313C  THR*     1.3    68.6    +      -       -      +
    330C  VAL*     3.7    18.6    -      -       +      -
    331C  THR      3.3     7.9    -      -       -      -
    332C  PHE*     3.5    22.2    -      +       +      -
    340C  ILE*     3.9    22.4    -      -       +      -
    341C  PRO*     3.8    15.5    -      -       +      -
    364C  ILE*     4.1     7.2    -      -       +      -
    385C  VAL*     3.6    30.1    -      -       +      +
    388C  LEU*     3.8    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 313 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311C  LYS      5.1     2.0    +      -       -      +
    312C  PHE*     1.3    80.4    -      -       -      +
    314C  TRP*     1.3    63.7    +      -       -      +
    330C  VAL*     3.3     7.4    -      -       -      +
    331C  THR*     2.9    45.7    +      -       -      +
    388C  LEU*     3.6    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 314 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313C  THR*     1.3    76.0    -      -       -      +
    315C  LYS*     1.3    60.9    +      -       -      +
    316C  ARG      4.0     9.2    -      -       -      -
    317C  ALA*     4.4    16.6    -      -       +      +
    318C  PRO*     4.0    22.0    -      -       +      -
    328C  MET*     3.8    22.9    -      -       +      -
    329C  GLU      3.9     1.1    -      -       -      -
    330C  VAL*     3.6    27.4    -      -       +      -
    331C  THR*     5.1     0.7    -      -       -      -
    383C  ILE*     4.0    14.8    -      -       +      -
    385C  VAL*     3.8    20.0    -      -       +      -
    388C  LEU*     3.4    29.6    -      -       +      +
    389C  SER*     3.2    23.2    +      -       -      -
    390C  HIS*     3.5    34.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 315 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313C  THR      3.7     2.4    +      -       -      -
    314C  TRP*     1.3    74.0    -      -       -      +
    316C  ARG*     1.3    66.3    +      -       +      +
    317C  ALA      4.2     0.7    -      -       -      -
    329C  GLU*     2.7    45.9    +      -       +      +
    330C  VAL      4.5     2.2    -      -       -      -
    331C  THR*     3.3    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 316 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  TRP*     3.6    70.5    +      -       +      +
    105B  CYS      5.4     0.2    +      -       -      -
    150C  TYR*     3.5    25.4    +      -       -      +
    314C  TRP*     4.0     2.8    -      -       -      -
    315C  LYS*     1.3    87.2    -      -       +      +
    317C  ALA*     1.3    67.3    +      -       -      +
    328C  MET*     3.5     3.1    -      -       -      +
    329C  GLU*     3.0    54.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 317 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  TRP*     4.4     0.9    -      -       -      -
    314C  TRP*     4.4    13.0    -      -       +      +
    315C  LYS      4.2     0.6    -      -       -      -
    316C  ARG*     1.3    77.1    -      -       -      +
    318C  PRO*     1.3    80.7    -      -       +      +
    319C  THR*     3.3    10.2    +      -       -      +
    327C  VAL      3.9     2.3    -      -       -      +
    390C  HIS*     3.9    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 318 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314C  TRP*     4.0    25.1    -      -       +      -
    316C  ARG      3.8     0.4    -      -       -      -
    317C  ALA*     1.3    91.0    -      -       +      +
    319C  THR*     1.3    58.9    +      -       -      +
    326C  VAL*     3.8    17.9    -      -       +      -
    327C  VAL      3.3     9.4    -      -       -      +
    328C  MET*     3.9     5.8    -      -       +      -
    383C  ILE*     3.9    22.7    -      -       +      -
    390C  HIS*     3.6    33.1    -      -       +      +
    392C  TRP*     3.5    23.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 319 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  TRP*     3.2    42.2    -      -       +      +
    106B  GLY      4.0     4.8    +      -       -      -
    107B  LEU*     3.6    27.8    -      -       -      +
    108B  PHE*     4.0     7.2    -      -       +      -
    317C  ALA      3.9     3.8    -      -       -      -
    318C  PRO*     1.3    76.5    -      -       -      +
    320C  ASP*     1.3    66.2    +      -       -      +
    321C  SER      3.4     0.2    +      -       -      -
    326C  VAL*     3.5     4.3    -      -       -      +
    327C  VAL*     2.9    40.7    +      -       +      +
    392C  TRP*     3.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 320 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  LEU*     6.4     1.1    -      -       +      -
    108B  PHE*     3.2    29.7    +      -       -      +
    319C  THR*     1.3    76.0    +      -       -      +
    321C  SER*     1.3    61.7    +      -       -      +
    322C  GLY*     3.3    17.0    +      -       -      -
    324C  ASP*     4.8     7.9    +      -       -      +
    325C  THR      4.0     8.2    -      -       -      +
    392C  TRP*     3.6    25.7    -      -       +      -
    394C  GLN*     4.9     9.5    +      -       -      -
    395C  LYS*     5.0     9.2    +      -       -      +
----------------------------------------------------------
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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