Contacts of the strand formed by residues 312 - 320 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307B  CYS*     3.4    38.6    -      -       +      -
    308B  ASP      3.7    13.2    -      -       -      -
    309B  LYS      4.6     5.8    +      -       -      +
    310B  THR      3.6     4.6    -      -       -      +
    311B  LYS*     1.3    77.8    -      -       -      +
    313B  THR*     1.3    68.0    +      -       -      +
    330B  VAL*     3.7    18.8    -      -       +      -
    331B  THR      3.3     8.3    -      -       -      -
    332B  PHE*     3.5    22.9    -      +       +      -
    340B  ILE*     3.9    23.6    -      -       +      -
    341B  PRO*     3.8    15.5    -      -       +      -
    364B  ILE*     4.1     6.5    -      -       +      -
    385B  VAL*     3.6    31.0    -      -       +      +
    388B  LEU*     3.8    30.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311B  LYS      5.1     3.0    +      -       -      +
    312B  PHE*     1.3    80.1    -      -       -      +
    314B  TRP*     1.3    64.2    +      -       -      +
    330B  VAL*     3.3     7.3    -      -       -      +
    331B  THR*     2.9    46.4    +      -       -      +
    388B  LEU*     3.6    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313B  THR*     1.3    76.4    -      -       -      +
    315B  LYS*     1.3    60.8    +      -       -      +
    316B  ARG      4.0     9.0    -      -       -      -
    317B  ALA*     4.4    16.6    -      -       +      +
    318B  PRO*     4.0    21.5    -      -       +      -
    328B  MET*     3.8    22.9    -      -       +      -
    329B  GLU      3.9     1.1    -      -       -      -
    330B  VAL*     3.6    27.4    -      -       +      -
    331B  THR*     5.1     0.2    -      -       -      -
    383B  ILE*     4.0    13.9    -      -       +      -
    385B  VAL*     3.8    20.0    -      -       +      -
    388B  LEU*     3.4    30.6    -      -       +      +
    389B  SER*     3.2    23.9    +      -       -      -
    390B  HIS*     3.5    32.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313B  THR      3.7     3.0    +      -       -      -
    314B  TRP*     1.3    73.4    -      -       -      +
    316B  ARG*     1.3    66.3    +      -       +      +
    317B  ALA      4.2     0.4    -      -       -      -
    329B  GLU*     2.7    45.7    +      -       +      +
    330B  VAL      5.0     2.2    -      -       -      -
    331B  THR*     3.3    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  TYR*     3.5    25.4    +      -       -      +
    314B  TRP*     4.0     2.2    -      -       -      -
    315B  LYS*     1.3    86.8    -      -       +      +
    317B  ALA*     1.3    66.6    +      -       -      +
    328B  MET*     3.5     3.5    -      -       -      +
    329B  GLU*     3.0    53.6    +      -       -      +
    101C  TRP*     3.6    72.2    +      -       +      +
    105C  CYS      5.4     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314B  TRP*     4.4    12.8    -      -       +      +
    315B  LYS      4.2     0.8    -      -       -      -
    316B  ARG*     1.3    78.1    -      -       -      +
    318B  PRO*     1.3    80.8    -      -       +      +
    319B  THR*     3.3    10.0    +      -       -      +
    327B  VAL      3.9     2.4    -      -       -      +
    390B  HIS*     3.9    17.9    -      -       +      +
    101C  TRP*     4.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314B  TRP*     4.0    24.0    -      -       +      -
    316B  ARG      3.8     0.2    -      -       -      -
    317B  ALA*     1.3    90.0    -      -       +      +
    319B  THR*     1.3    60.6    +      -       -      +
    326B  VAL*     3.8    18.2    -      -       +      -
    327B  VAL      3.3     9.6    -      -       -      +
    328B  MET*     3.9     4.9    -      -       +      -
    383B  ILE*     3.9    23.1    -      -       +      -
    390B  HIS*     3.6    31.9    -      -       +      +
    392B  TRP*     3.5    21.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  ALA      3.9     3.6    -      -       -      -
    318B  PRO*     1.3    75.8    -      -       -      +
    320B  ASP*     1.3    66.9    +      -       -      +
    321B  SER      3.4     0.3    +      -       -      -
    326B  VAL*     3.5     3.9    -      -       -      +
    327B  VAL*     2.9    41.1    +      -       +      -
    392B  TRP*     3.9     8.1    -      -       -      -
    101C  TRP*     3.2    41.7    -      -       +      +
    106C  GLY      4.0     5.2    +      -       -      -
    107C  LEU*     3.6    28.1    -      -       -      +
    108C  PHE*     4.0     7.0    -      -       +      -
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Residues in contact with ASP 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319B  THR*     1.3    76.6    +      -       -      +
    321B  SER*     1.3    62.6    +      -       -      +
    322B  GLY*     3.3    18.1    +      -       -      +
    324B  ASP*     4.8     7.3    +      -       -      +
    325B  THR      4.0     7.6    -      -       -      +
    392B  TRP*     3.6    25.8    -      -       +      -
    394B  GLN*     4.9     9.3    +      -       -      -
    395B  LYS*     5.0     9.0    +      -       -      +
    107C  LEU*     6.4     1.1    -      -       +      -
    108C  PHE*     3.2    28.5    +      -       -      +
----------------------------------------------------------
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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