Contacts of the strand formed by residues 954 - 963 (chain B) in PDB entry 3U44


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 GLY 954 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    950B  GLU*     2.8    24.2    -      -       -      +
    951B  SER*     3.0    25.9    +      -       -      -
    952B  SER      3.1     3.2    +      -       -      -
    953B  LYS*     1.3    79.3    -      -       -      +
    955B  LEU*     1.3    63.2    +      -       -      -
    956B  LEU*     4.1     0.2    -      -       -      +
    999B  MET*     4.0    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 955 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    948B  LYS*     3.3    37.7    -      -       +      +
    949B  ALA      4.5     3.4    -      -       -      +
    950B  GLU*     3.3    12.4    +      -       +      +
    953B  LYS      4.8     0.2    -      -       -      +
    954B  GLY*     1.3    73.3    -      -       -      -
    956B  LEU*     1.3    63.4    +      -       -      +
    957B  LEU*     4.4     4.7    -      -       +      -
    993B  SER*     4.1     9.2    -      -       -      +
    997B  LEU*     3.2    44.6    -      -       +      -
    999B  MET*     3.5    30.9    -      -       +      +
   1000B  ARG      4.1     5.1    +      -       -      +
   1001B  ALA*     3.6     8.4    -      -       +      -
   1002B  THR*     3.2    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 956 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909B  PHE*     3.8    18.3    -      -       +      -
    947B  ASP      3.6     0.2    -      -       -      +
    948B  LYS*     3.1     8.0    -      -       -      +
    949B  ALA      2.9    37.8    +      -       -      +
    951B  SER*     3.4    27.4    -      -       -      +
    953B  LYS*     5.6     2.2    -      -       +      -
    954B  GLY      4.1     0.2    -      -       -      +
    955B  LEU*     1.3    75.5    -      -       -      +
    957B  LEU*     1.3    63.6    +      -       -      +
   1002B  THR*     3.3    34.8    -      -       +      +
   1004B  ALA*     4.5     7.0    -      -       +      -
   1042B  LEU*     4.9     2.0    -      -       +      -
   1047B  VAL*     3.9    31.9    -      -       +      -
   1050B  LEU*     3.6    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 957 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    912B  ILE*     3.7    20.2    -      -       +      -
    946B  VAL*     6.2     1.1    -      -       +      -
    947B  ASP      3.2     4.9    -      -       -      +
    948B  LYS*     3.5    24.9    -      -       +      -
    955B  LEU*     4.3     8.3    -      -       +      -
    956B  LEU*     1.3    85.0    -      -       -      +
    958B  ARG*     1.3    61.1    +      -       -      +
    986B  LEU*     4.1     6.5    -      -       +      +
    989B  SER*     3.5    41.1    -      -       -      +
    990B  ILE*     4.4     7.4    -      -       +      -
    993B  SER*     4.0     7.2    -      -       -      +
    996B  TRP*     5.2     2.5    -      -       +      -
    997B  LEU*     4.9     6.7    -      -       +      -
   1001B  ALA*     3.6    24.8    -      -       +      +
   1002B  THR      3.4     6.3    +      -       -      -
   1003B  PRO*     3.7     6.2    -      -       -      +
   1004B  ALA*     2.9    22.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 958 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    907B  SER*     3.7    17.8    +      -       -      -
    909B  PHE*     4.0    24.6    +      -       +      +
    945B  ARG*     4.1    11.9    -      -       -      +
    946B  VAL*     3.4     4.2    -      -       -      +
    947B  ASP*     2.8    64.2    +      -       +      +
    957B  LEU*     1.3    75.7    -      -       -      +
    959B  ILE*     1.3    68.1    +      -       -      +
    960B  VAL*     3.9     4.3    -      -       +      +
    986B  LEU*     4.7     0.9    -      -       -      -
   1004B  ALA*     3.7    13.2    -      -       +      -
   1005B  GLY*     3.4    17.3    -      -       -      +
   1007B  LEU*     3.4    24.3    -      -       -      +
   1037B  MET*     4.9     6.7    -      -       -      +
   1051B  MET*     3.1    48.0    +      -       -      +
   1062B  ILE*     6.2     1.4    -      -       -      +
   1063B  ILE*     4.8     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 959 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    943B  ILE*     4.1    11.7    -      -       +      -
    944B  ASP      5.4     0.7    -      -       -      +
    945B  ARG      3.0    15.3    -      -       -      +
    946B  VAL*     3.5    15.7    -      -       +      -
    958B  ARG*     1.3    78.8    -      -       -      +
    960B  VAL*     1.3    69.2    +      -       -      +
    961B  ALA*     5.6     0.4    -      -       +      -
    982B  MET*     3.5    22.8    -      -       +      +
    985B  TYR*     3.3    48.5    -      -       +      +
    986B  LEU*     3.4    14.8    -      -       +      +
    989B  SER*     3.4    15.5    -      -       -      +
   1005B  GLY      3.3     7.1    +      -       -      +
   1006B  VAL*     3.6     3.3    -      -       +      -
   1007B  LEU*     2.8    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 960 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    944B  ASP*     3.1     2.8    -      -       -      +
    945B  ARG*     2.9    74.2    +      -       +      +
    947B  ASP*     3.6    14.8    -      -       -      +
    958B  ARG*     3.9    15.7    -      -       -      +
    959B  ILE*     1.3    82.3    -      -       -      +
    961B  ALA*     1.3    65.3    +      -       -      +
    962B  TYR*     4.3     6.2    -      -       +      +
   1007B  LEU*     3.4    20.4    -      -       +      +
   1009B  PHE*     4.2    24.2    -      -       +      +
   1037B  MET*     4.5     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 961 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    944B  ASP*     3.4    23.3    -      -       -      +
    959B  ILE*     5.6     0.7    -      -       +      -
    960B  VAL*     1.3    77.7    -      -       -      +
    962B  TYR*     1.3    66.7    +      -       -      +
    963B  LYS*     4.1     2.6    -      -       -      +
    981B  GLN*     5.0     9.0    -      -       -      +
    982B  MET*     3.9    24.9    -      -       +      -
    985B  TYR*     5.8     1.6    -      -       +      -
   1007B  LEU      3.1     8.1    +      -       -      +
   1008B  TYR*     3.6    11.8    -      -       +      +
   1009B  PHE      3.1    19.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 962 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    831B  HIS*     4.1    30.3    -      +       +      -
    834B  LEU*     3.5    36.5    -      -       +      +
    848B  TRP*     6.0     0.7    -      -       -      -
    896B  VAL*     5.6     0.4    -      -       +      -
    900B  LEU*     4.7    21.0    -      -       +      +
    914B  LEU*     5.0     6.5    -      -       +      +
    915B  GLU*     5.1     3.6    -      -       -      -
    944B  ASP*     3.4    29.4    +      -       +      +
    945B  ARG*     3.6    37.9    +      -       +      -
    960B  VAL*     5.3     3.8    -      -       +      -
    961B  ALA*     1.3    75.1    -      -       -      +
    963B  LYS*     1.3    61.1    +      -       -      +
   1009B  PHE*     3.6    27.6    -      +       +      -
   1011B  ILE*     3.5    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 963 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    830B  PHE*     6.3     0.4    -      -       -      -
    961B  ALA*     4.1     5.4    -      -       +      +
    962B  TYR*     1.3    78.2    -      -       -      +
    964B  SER*     1.3    64.7    +      -       -      +
    965B  SER*     3.5    39.8    -      -       -      +
    966B  ASP      5.1     4.0    -      -       -      +
    967B  LYS      5.1     4.3    -      -       -      +
   1008B  TYR*     4.3    26.5    -      -       +      -
   1009B  PHE      2.7    19.1    +      -       -      +
   1010B  HIS*     3.3     3.7    -      -       -      -
   1011B  ILE*     2.7    37.5    +      -       -      +
----------------------------------------------------------
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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