Contacts of the strand formed by residues 507 - 516 (chain C) in PDB entry 3U1K


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 ALA 507 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488C  ALA*     5.3     0.4    -      -       -      -
    489C  CYS*     3.6    15.7    -      -       -      +
    506C  VAL*     1.3    77.4    -      -       -      +
    508C  GLY*     1.3    58.9    +      -       -      +
    548C  ALA*     3.3     5.5    -      -       -      -
    549C  GLY      3.0    29.6    +      -       -      +
    582C  LYS*     3.7    19.4    -      -       +      +
    585C  ILE*     3.9    17.0    -      -       +      -
    586C  LEU*     3.6    26.1    -      -       +      +
    589C  MET*     4.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 508 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388C  ARG*     4.5     4.0    +      -       -      -
    485C  MET*     3.6    29.3    +      -       -      +
    488C  ALA*     4.9     1.4    -      -       -      +
    489C  CYS*     3.5    13.7    -      -       -      -
    507C  ALA*     1.3    76.2    -      -       -      +
    509C  VAL*     1.3    64.0    +      -       -      +
    547C  ILE      3.4    10.5    -      -       -      -
    548C  ALA*     3.7     4.9    -      -       -      +
    582C  LYS*     5.6     1.1    -      -       -      -
    585C  ILE*     3.5    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 509 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367C  LEU*     4.3    13.2    -      -       +      -
    388C  ARG*     5.3     2.9    -      -       -      +
    482C  SER*     4.9     0.9    -      -       -      -
    485C  MET*     3.6    10.4    -      -       -      +
    508C  GLY*     1.3    76.3    -      -       -      +
    510C  ALA*     1.3    71.1    +      -       -      +
    511C  ILE*     4.5     4.5    -      -       +      -
    532C  ASP*     4.0    28.5    -      -       +      +
    545C  PHE      3.6     1.4    -      -       -      +
    546C  LYS*     3.6     0.7    -      -       -      -
    547C  ILE*     3.0    33.4    +      -       -      +
    578C  ALA*     3.9    40.4    -      -       +      +
    581C  ALA*     4.2     9.4    -      -       +      -
    582C  LYS*     4.6     4.3    -      -       +      +
    585C  ILE*     4.1     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 510 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    482C  SER*     4.0    23.0    +      -       -      +
    509C  VAL*     1.3    76.9    -      -       -      +
    511C  ILE*     1.3    62.8    +      -       -      +
    532C  ASP*     2.9    28.5    +      -       -      +
    533C  ILE*     3.5    13.3    +      -       +      +
    544C  ASP*     3.3    25.8    -      -       -      +
    545C  PHE      3.2     4.0    -      -       -      +
    546C  LYS*     3.9    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 511 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509C  VAL*     4.5     5.6    -      -       +      -
    510C  ALA*     1.3    77.4    -      -       -      +
    512C  GLY*     1.3    69.9    +      -       -      +
    529C  LEU*     3.9    21.3    -      -       +      -
    530C  LEU      3.1    20.6    -      -       -      +
    531C  THR*     3.9    13.9    -      -       +      -
    533C  ILE*     4.2     2.2    -      -       -      -
    543C  MET*     3.6     8.2    -      -       +      +
    544C  ASP      4.0     0.2    -      -       -      -
    545C  PHE*     2.8    47.0    +      -       +      +
    547C  ILE*     5.1     0.4    -      -       +      -
    574C  ALA*     3.3    15.0    -      -       +      +
    577C  GLN*     4.0     5.4    -      -       +      +
    578C  ALA*     3.0    51.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 512 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511C  ILE*     1.3    82.6    -      -       -      +
    513C  LEU*     1.3    63.7    +      -       -      +
    529C  LEU*     3.6     3.8    -      -       -      +
    530C  LEU*     2.8    33.3    +      -       -      -
    533C  ILE*     3.5    23.0    -      -       -      +
    537C  GLU      5.4     1.8    -      -       -      -
    543C  MET*     3.6    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 513 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    512C  GLY*     1.3    75.1    -      -       -      +
    514C  VAL*     1.3    68.6    +      -       -      +
    515C  THR*     3.7    17.5    -      -       +      -
    527C  TYR*     3.9    24.7    -      -       +      -
    528C  ARG      3.4    15.7    -      -       -      +
    529C  LEU*     4.0     7.2    -      -       +      -
    530C  LEU*     4.7     2.6    -      -       -      +
    537C  GLU      5.1     1.6    +      -       -      +
    541C  GLY*     3.6     3.1    -      -       -      -
    542C  ASP*     2.8    48.3    +      -       +      +
    543C  MET*     3.8    27.8    +      -       +      +
    566C  ILE*     4.0    22.7    -      -       +      -
    570C  ILE*     4.0    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 514 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348C  PHE*     5.4     5.4    -      -       +      -
    349C  ARG*     3.6    43.3    -      -       +      +
    352C  VAL*     4.5    25.1    -      -       +      -
    353C  LEU*     3.8    24.3    -      -       +      +
    513C  LEU*     1.3    78.3    -      -       -      +
    515C  THR*     1.3    63.4    +      -       -      +
    527C  TYR*     3.2     3.8    -      -       -      -
    528C  ARG*     2.9    35.8    +      -       +      +
    530C  LEU*     4.5    13.0    -      -       +      -
    537C  GLU*     5.5     1.3    -      -       +      +
    540C  ASN      5.0     0.2    -      -       -      +
    541C  GLY*     4.6     8.7    -      -       -      -
    542C  ASP*     3.5     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 515 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349C  ARG*     3.0    25.6    +      -       -      +
    353C  LEU*     4.1     9.8    -      -       -      +
    513C  LEU*     3.7    18.2    -      -       +      -
    514C  VAL*     1.3    75.4    -      -       -      +
    516C  LYS*     1.3    59.0    +      -       -      +
    517C  THR*     3.9    17.5    +      -       -      +
    524C  ILE*     3.7    16.8    -      -       +      -
    526C  ASP      3.5     6.3    -      -       -      -
    527C  TYR*     3.9    11.0    -      -       +      -
    542C  ASP*     2.8    26.3    +      -       -      +
    563C  LEU*     3.5    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 516 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353C  LEU*     4.1    21.7    -      -       +      +
    515C  THR*     1.3    74.1    -      -       -      +
    517C  THR*     1.3    65.4    +      -       -      +
    524C  ILE*     3.7     2.4    -      -       -      -
    525C  GLU*     2.8    59.5    +      -       +      +
    526C  ASP*     2.9    20.9    +      -       +      +
----------------------------------------------------------
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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