Contacts of the strand formed by residues 616 - 622 (chain B) in PDB entry 3H44


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 LEU 616 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530B  PHE*     4.0    20.4    -      -       +      +
    608B  ALA      4.7     0.5    -      -       -      +
    611B  ALA*     2.9    31.9    +      -       +      +
    612B  GLU*     3.3     6.9    +      -       -      +
    614B  ALA*     3.3     4.2    -      -       +      +
    615B  GLY*     1.3    79.2    -      -       -      +
    617B  SER*     1.3    60.9    +      -       -      +
    631B  VAL*     3.8    11.2    -      -       +      -
    632B  LYS      3.7    13.0    -      -       -      +
    634B  TYR*     4.0    14.4    -      -       +      +
    637B  LYS*     3.8    29.2    -      -       +      +
    638B  GLN*     3.8    29.8    -      -       +      +
    641B  LEU*     3.9    21.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 617 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612B  GLU*     3.2    32.8    +      -       -      -
    615B  GLY      4.1     1.7    +      -       -      -
    616B  LEU*     1.3    76.0    -      -       -      +
    618B  TYR*     1.3    64.8    +      -       -      +
    630B  SER      3.8     0.2    -      -       -      +
    631B  VAL*     3.3     7.5    -      -       -      +
    632B  LYS*     2.9    44.8    +      -       -      +
    641B  LEU*     4.6     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 618 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601B  LYS*     3.5    39.2    +      -       +      +
    604B  LEU*     3.4    39.3    -      -       +      +
    605B  ASN*     4.8     2.2    +      -       -      -
    608B  ALA*     3.7    27.2    -      -       +      +
    612B  GLU*     6.2     2.9    -      -       +      -
    617B  SER*     1.3    81.1    -      -       -      +
    619B  ASP*     1.3    64.3    +      -       -      +
    620B  LEU*     4.1    21.3    -      -       +      -
    629B  LEU*     4.2     5.4    -      -       +      -
    630B  SER      3.1     9.4    -      -       -      +
    631B  VAL*     4.3     4.3    -      -       +      -
    641B  LEU*     4.4     8.1    -      -       +      -
    645B  ILE*     3.6    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 619 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601B  LYS*     6.0     0.2    +      -       -      -
    618B  TYR*     1.3    75.4    -      -       -      +
    620B  LEU*     1.3    62.0    +      -       -      +
    621B  GLN*     4.3    14.0    +      -       -      +
    628B  TYR*     3.7    20.7    +      -       +      +
    629B  LEU*     3.2     6.3    +      -       -      +
    630B  SER*     2.8    48.7    +      -       -      +
    632B  LYS*     6.1     2.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 620 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578B  PHE*     5.8     0.9    -      -       +      -
    597B  LEU*     3.8    23.9    -      -       +      +
    600B  LEU*     3.7    29.8    -      -       +      -
    601B  LYS*     2.6    55.7    +      -       +      +
    604B  LEU*     6.0     0.2    -      -       +      -
    618B  TYR*     4.1    19.1    -      -       +      -
    619B  ASP*     1.3    77.1    +      -       -      +
    621B  GLN*     1.3    57.5    +      -       -      +
    627B  MET*     4.9     6.5    -      -       +      -
    628B  TYR      3.3    15.0    -      -       -      +
    629B  LEU*     4.0    21.5    -      -       +      -
    645B  ILE*     4.9     3.6    -      -       +      -
    649B  MET*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 621 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597B  LEU*     3.5    10.3    -      -       -      -
    601B  LYS*     4.6     6.6    +      -       -      +
    619B  ASP*     4.7    12.8    +      -       -      +
    620B  LEU*     1.3    75.6    -      -       -      +
    622B  ASN*     1.3    71.6    +      -       -      +
    623B  THR*     5.2     2.0    -      -       +      +
    628B  TYR*     2.8    63.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 622 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    590B  SER*     4.1     5.4    -      -       -      +
    593B  ALA*     4.1    17.1    -      -       +      +
    594B  TYR*     3.3    54.0    +      -       -      +
    597B  LEU*     3.2    19.6    -      -       +      +
    621B  GLN*     1.3    83.7    -      -       -      +
    623B  THR*     1.3    65.1    +      -       -      +
    626B  GLY      3.5    11.0    -      -       -      +
    627B  MET*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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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