Contacts of the strand formed by residues 619 - 627 (chain A) in PDB entry 6UMW


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 VAL 619 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614A  ILE*     3.9    15.9    -      -       +      -
    615A  ASP      4.2     4.0    -      -       -      +
    616A  VAL*     3.1    24.4    +      -       +      +
    617A  SER      3.3     2.6    -      -       -      +
    618A  PHE*     1.3    82.7    -      -       -      +
    620A  LYS*     1.3    65.1    +      -       -      +
    621A  ILE*     4.1    12.8    +      -       +      +
    637A  ARG      3.4     6.7    -      -       -      +
    638A  LEU*     3.8    19.7    -      -       +      -
    648A  VAL*     5.2     1.3    -      -       +      -
    650A  ILE*     3.6    34.8    -      -       +      -
    687A  VAL*     5.0     3.6    -      -       +      -
    694A  MET*     5.2     2.9    -      -       -      -
    696A  ILE*     4.4    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617A  SER      5.5     5.8    -      -       -      +
    618A  PHE      5.3     2.7    -      -       -      +
    619A  VAL*     1.3    78.4    -      -       -      +
    621A  ILE*     1.3    62.3    +      -       -      +
    622A  GLU*     3.7     5.9    +      -       +      +
    636A  GLY*     3.0     5.9    -      -       -      -
    637A  ARG*     2.9    49.7    +      -       +      +
    645A  GLU*     6.1     0.2    -      -       -      +
    650A  ILE*     4.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616A  VAL*     5.8     2.9    -      -       +      -
    619A  VAL*     4.1     8.7    -      -       +      +
    620A  LYS*     1.3    74.7    -      -       -      +
    622A  GLU*     1.3    62.7    +      -       -      +
    634A  TYR*     3.4    49.8    -      -       +      -
    650A  ILE*     3.8    19.7    -      -       +      -
    652A  THR*     5.8     1.8    -      -       +      -
    694A  MET*     4.0    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620A  LYS*     4.2    13.1    -      -       +      +
    621A  ILE*     1.3    79.9    -      -       -      +
    623A  GLU*     1.3    81.4    +      -       -      +
    624A  VAL*     3.7     0.5    +      -       -      +
    634A  TYR*     3.6    13.3    -      -       -      -
    635A  LYS*     2.8    25.8    +      -       -      +
    636A  GLY*     4.3     2.2    -      -       -      -
    637A  ARG*     2.4    44.4    +      -       -      -
    647A  PTR      4.1    12.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 623 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    622A  GLU*     1.3    88.7    -      -       -      +
    624A  VAL*     1.3    64.7    +      -       -      +
    625A  ILE*     3.9    17.1    -      -       +      +
    634A  TYR*     3.3     1.8    -      -       -      -
    635A  LYS*     2.8    58.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 624 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    622A  GLU      5.1     0.7    -      -       -      +
    623A  GLU*     1.3    81.6    -      -       -      +
    625A  ILE*     1.3    64.2    +      -       -      +
    626A  GLY      3.7    18.6    -      -       -      +
    627A  ALA*     6.0     0.7    -      -       +      -
    632A  GLU*     4.1    15.5    -      -       +      -
    633A  VAL      3.6    13.0    -      -       -      +
    634A  TYR*     3.5    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 625 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    623A  GLU*     3.7    20.4    -      -       +      +
    624A  VAL*     1.3    80.2    -      -       -      +
    626A  GLY*     1.3    58.0    +      -       -      +
    633A  VAL*     2.9    31.8    +      -       +      +
    634A  TYR      3.9     5.4    -      -       -      +
    635A  LYS*     3.8    24.7    -      -       +      +
    649A  ALA*     4.6     0.4    -      -       +      -
    699A  PHE*     3.9    15.3    -      -       +      -
    901A  CTC      3.8    59.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 626 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    624A  VAL*     3.6    12.6    -      -       -      +
    625A  ILE*     1.3    82.2    -      -       -      +
    627A  ALA*     1.3    60.2    +      -       -      -
    628A  GLY      3.8     2.2    -      -       -      -
    632A  GLU*     3.5     3.1    -      -       -      +
    633A  VAL*     2.8    32.0    +      -       -      +
    901A  CTC      4.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 627 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    624A  VAL*     6.0     0.4    -      -       +      -
    626A  GLY*     1.3    72.3    -      -       -      -
    628A  GLY*     1.3    66.1    +      -       -      +
    631A  GLY      3.5     4.7    -      -       -      -
    632A  GLU*     3.8    21.5    -      -       +      +
    654A  LYS*     4.2     8.1    -      -       -      +
----------------------------------------------------------
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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