Contacts of the strand formed by residues 361 - 372 (chain A) in PDB entry 5KG2


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 ARG 361 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  LEU*     4.0    28.1    +      -       -      +
    316A  PRO*     2.8    33.3    +      -       -      +
    317A  LYS*     4.5     4.8    -      -       -      +
    319A  ILE*     4.5     5.7    -      -       -      +
    355A  ASP*     2.8    41.4    +      -       -      +
    356A  ARG*     3.3    26.5    +      -       -      +
    359A  ASN*     3.8    17.2    -      -       +      +
    360A  ASP*     1.3    78.5    -      -       -      +
    362A  VAL*     1.3    59.3    +      -       -      +
    390A  TYR*     4.2     1.4    +      -       -      -
    429A  PHE*     3.5    35.5    -      -       +      +
    430A  SER      3.2    16.4    -      -       -      +
    431A  ALA*     4.6     1.1    -      -       -      -
    432A  SER*     3.4    10.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  ARG*     3.5    24.5    -      -       -      +
    361A  ARG*     1.3    79.8    -      -       -      +
    363A  ALA*     1.3    67.7    +      -       -      +
    364A  THR*     3.7     7.6    -      -       +      +
    390A  TYR*     3.3     9.9    -      -       +      +
    429A  PHE*     3.3     4.4    -      -       -      -
    430A  SER*     2.9    47.9    +      -       -      +
    431A  ALA      4.8     0.7    -      -       -      +
    432A  SER*     3.5    24.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  LEU*     4.1     2.5    -      -       +      -
    362A  VAL*     1.3    76.7    -      -       -      +
    364A  THR*     1.3    60.7    +      -       -      +
    365A  GLN      3.9     0.2    -      -       -      -
    387A  LEU*     3.6    18.1    -      -       +      +
    390A  TYR*     2.7    27.0    +      -       -      +
    426A  ALA*     3.7    27.8    -      -       +      -
    427A  THR      3.7    13.9    -      -       -      +
    428A  LYS      4.1     0.7    -      -       -      -
    429A  PHE*     3.6    21.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  VAL*     3.7    13.7    -      -       +      +
    363A  ALA*     1.3    78.2    -      -       -      +
    365A  GLN*     1.3    60.0    +      -       -      +
    386A  ALA*     4.0     5.0    -      -       -      +
    387A  LEU*     3.1    27.8    +      -       -      +
    388A  THR*     5.8     0.2    -      -       -      +
    427A  THR      3.1     4.6    +      -       -      -
    428A  LYS*     2.9    33.5    +      -       -      +
    430A  SER*     3.8    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  ALA      3.9     0.2    -      -       -      -
    364A  THR*     1.3    81.6    -      -       -      +
    366A  LEU*     1.3    64.3    +      -       -      +
    367A  VAL*     4.3     6.0    -      -       +      +
    384A  CYS*     3.6    36.4    -      -       +      +
    385A  CYS      3.7    11.5    +      -       -      +
    387A  LEU*     3.8     5.4    -      -       -      +
    425A  CYS      3.7     0.2    -      -       -      +
    426A  ALA*     3.5     4.0    -      -       -      -
    427A  THR*     2.9    45.9    +      -       -      +
    428A  LYS*     2.9    41.6    +      -       +      +
      1P    A      4.7     7.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 366 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  LEU*     3.9    25.6    -      -       +      -
    365A  GLN*     1.3    72.9    -      -       -      +
    367A  VAL*     1.3    63.2    +      -       -      +
    368A  VAL*     4.0    16.3    +      -       +      -
    383A  ARG      4.0     0.3    -      -       -      +
    384A  CYS*     3.3     2.1    -      -       -      -
    385A  CYS*     2.9    62.1    +      -       -      +
    386A  ALA      4.5     2.0    -      -       -      +
    387A  LEU*     3.8    23.4    -      -       +      +
    395A  MET*     3.8    39.0    -      -       +      +
    398A  ASP*     4.7     2.9    -      -       +      +
    399A  ALA*     4.7     2.2    -      -       +      -
    424A  LEU*     4.5     8.3    -      -       +      -
    425A  CYS      3.5    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 367 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  GLN*     4.3    11.4    -      -       -      +
    366A  LEU*     1.3    77.5    -      -       -      +
    368A  VAL*     1.3    65.6    +      -       -      +
    369A  SER*     4.3     1.3    +      -       -      +
    382A  ARG*     3.5    48.7    -      -       +      +
    383A  ARG      3.6     5.4    -      -       -      +
    384A  CYS*     4.4     7.2    -      -       +      -
    423A  PHE*     3.7     2.1    -      -       +      +
    424A  LEU*     3.5     4.5    -      -       -      -
    425A  CYS*     2.8    44.8    +      -       +      +
    427A  THR*     4.1    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 368 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  LEU*     5.0     5.6    -      -       +      -
    366A  LEU*     4.1    14.8    -      -       +      +
    367A  VAL*     1.3    78.3    -      -       -      +
    369A  SER*     1.3    64.5    +      -       -      +
    370A  ILE*     4.9     2.2    -      -       +      -
    381A  LEU*     3.8     1.6    -      -       -      +
    382A  ARG*     3.4     2.1    -      -       -      -
    383A  ARG*     2.8    40.2    +      -       -      +
    385A  CYS*     4.9     2.7    -      -       -      -
    399A  ALA*     3.6    38.1    -      -       +      +
    402A  VAL*     3.9    13.7    -      -       +      -
    403A  ILE*     3.6    27.8    -      -       +      +
    423A  PHE      3.4     3.8    -      -       -      +
    424A  LEU*     3.8    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 369 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  VAL*     5.3     0.2    -      -       -      -
    368A  VAL*     1.3    76.7    -      -       -      +
    370A  ILE*     1.3    67.5    +      -       -      +
    379A  SER*     2.8    32.4    +      -       -      -
    381A  LEU      3.1     7.8    +      -       -      -
    382A  ARG*     4.3    14.6    +      -       -      +
    421A  MET*     3.8     5.0    -      -       -      +
    422A  LEU*     3.6     0.7    -      -       -      +
    423A  PHE*     2.9    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 370 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  VAL*     4.9     1.8    -      -       +      -
    369A  SER*     1.3    82.1    +      -       -      +
    371A  ARG*     1.3    64.4    +      -       -      +
    372A  VAL*     4.5     8.5    -      -       +      -
    379A  SER*     3.8     0.3    +      -       -      -
    380A  SER*     2.9    22.2    +      -       -      -
    381A  LEU*     3.0    32.1    +      -       +      +
    403A  ILE*     4.0    29.6    -      -       +      -
    406A  CYS*     3.9    33.7    -      -       +      -
    415A  TRP*     5.2     0.4    -      -       +      -
    419A  LEU*     4.0    22.4    -      -       +      -
    421A  MET*     3.2    15.7    -      -       -      +
    422A  LEU*     3.7    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 371 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324A  ASN*     5.8     5.3    +      -       -      +
    370A  ILE*     1.3    76.5    -      -       -      +
    372A  VAL*     1.3    68.9    +      -       -      +
    375A  ASP      2.7    24.7    +      -       -      +
    376A  LYS*     3.1    20.3    +      -       -      +
    377A  ARG      2.9    20.6    +      -       -      +
    378A  LEU*     3.4    20.1    -      -       -      +
    380A  SER*     3.3    11.7    -      -       -      +
    419A  LEU*     3.5     9.5    -      -       -      +
    420A  THR*     3.0    40.7    +      -       -      +
    421A  MET*     3.2    28.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 372 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370A  ILE*     4.5    10.5    -      -       +      -
    371A  ARG*     1.3    84.3    +      -       -      +
    373A  GLN*     1.3    69.2    +      -       -      +
    374A  GLY      3.2     0.2    +      -       -      -
    375A  ASP*     3.1    25.5    +      -       +      +
    380A  SER*     2.9    26.1    +      -       -      +
    381A  LEU*     6.2     0.4    -      -       +      -
    406A  CYS*     5.8     5.2    -      -       +      +
    417A  PRO*     4.4    21.1    -      -       +      +
    418A  PRO      4.0     4.5    -      -       -      +
    419A  LEU*     4.4    13.2    -      -       +      -
    420A  THR*     3.9     2.8    +      -       -      -
----------------------------------------------------------
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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