Contacts of the strand formed by residues 423 - 430 (chain A) in PDB entry 4UHW


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 GLU 423 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329A  GLU*     4.2     2.9    -      -       -      +
    332A  GLN*     3.6    14.0    -      -       -      +
    376A  ASN*     4.7     2.8    -      -       -      +
    418A  TYR      4.5     1.6    -      -       -      +
    419A  SER*     3.4    14.9    -      -       -      -
    420A  ARG*     2.7    62.4    +      -       -      +
    422A  TRP*     1.3    78.3    -      -       -      +
    424A  PHE*     1.3    75.3    +      -       -      +
    425A  VAL*     5.0     2.2    -      -       +      -
    446A  ARG*     2.7    43.1    +      -       +      +
    447A  VAL      3.4    11.7    -      -       -      +
    448A  PHE*     3.9     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329A  GLU*     3.2    28.7    -      -       +      -
    332A  GLN*     3.7    17.7    -      -       -      +
    422A  TRP*     3.7    17.7    -      +       -      -
    423A  GLU*     1.3    81.2    -      -       -      +
    425A  VAL*     1.3    64.1    +      -       -      +
    445A  MET      4.0     0.2    -      -       -      +
    446A  ARG*     3.4     4.9    -      -       -      +
    447A  VAL*     3.1    40.0    +      -       +      +
    449A  PHE*     3.8    23.6    -      +       -      -
    526A  PHE*     4.3     3.2    -      -       +      -
    530A  VAL*     3.2    34.3    -      -       +      -
    533A  ILE*     3.5    32.1    -      -       +      -
    534A  LEU*     4.0    10.3    -      -       +      -
    537A  MET*     3.8    13.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332A  GLN*     3.2    43.9    +      -       +      +
    333A  MET*     3.9    31.2    -      -       +      -
    336A  ALA*     4.0    21.2    -      -       +      +
    371A  ILE*     4.7     4.7    -      -       +      -
    374A  VAL*     4.7     7.0    -      -       +      -
    419A  SER*     5.5     1.1    -      -       -      -
    423A  GLU*     5.0     3.4    -      -       +      -
    424A  PHE*     1.3    81.8    -      -       -      +
    426A  SER*     1.3    67.6    +      -       -      +
    445A  MET      3.4     9.4    -      -       -      +
    446A  ARG*     3.9    23.8    -      -       +      -
    526A  PHE*     4.6     0.7    -      -       -      -
    529A  GLU*     4.6     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  ALA*     4.7     2.2    -      -       -      -
    339A  LYS*     5.3     1.0    +      -       -      -
    425A  VAL*     1.3    80.0    -      -       -      +
    427A  ALA*     1.3    60.6    +      -       -      +
    428A  PHE*     3.4    14.3    -      -       -      -
    443A  SER      4.1     0.2    -      -       -      +
    444A  GLY*     3.5     1.9    -      -       -      -
    445A  MET*     2.9    35.1    +      -       -      +
    526A  PHE*     3.4    29.1    -      -       -      -
    529A  GLU*     2.7    36.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  ALA*     4.0    13.6    -      -       +      +
    339A  LYS*     2.7    39.6    +      -       +      +
    340A  HIS*     3.6    11.2    -      -       +      +
    371A  ILE*     3.3    38.1    -      -       +      -
    426A  SER*     1.3    76.1    +      -       -      +
    428A  PHE*     1.3    58.1    +      -       -      +
    443A  SER      3.1    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 428 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  LYS*     3.8    16.2    -      -       -      +
    340A  HIS*     3.2    12.3    -      -       -      -
    426A  SER*     3.4    33.4    -      -       -      -
    427A  ALA*     1.3    78.8    -      -       -      +
    429A  ARG*     1.3    61.6    +      -       -      +
    442A  ASN*     3.2     1.6    -      -       -      -
    443A  SER*     2.9    30.7    +      -       -      +
    445A  MET*     4.6     8.1    -      -       +      -
    522A  PHE*     3.4    51.1    -      +       +      -
    525A  LYS*     3.9    29.8    -      -       +      -
    526A  PHE*     3.8    23.8    -      +       +      -
    529A  GLU*     3.5    16.6    -      -       -      -
    553A  LEU      6.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  LYS*     5.9     0.8    -      -       -      +
    340A  HIS*     3.8    20.6    +      -       +      +
    343A  THR*     3.5    33.6    +      -       +      -
    367A  ASP*     2.9    39.2    +      -       -      -
    428A  PHE*     1.3    78.5    -      -       -      +
    430A  GLN*     1.3    67.9    +      -       -      +
    431A  ALA*     4.0    13.3    -      -       -      +
    434A  GLN      4.1    16.4    +      -       -      -
    435A  GLU*     5.2     0.4    -      -       -      +
    437A  ALA      3.1    26.9    +      -       -      -
    439A  ALA*     3.6    18.9    -      -       +      +
    441A  VAL      3.5     7.6    -      -       -      +
    442A  ASN*     3.8    11.9    -      -       +      -
    522A  PHE*     3.8     7.6    -      -       -      -
   1177A  THR*     5.5     0.7    -      -       -      +
   3006A  FAD      3.9     4.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429A  ARG*     1.3    80.9    -      -       -      +
    431A  ALA*     1.3    78.4    +      -       -      +
    432A  GLN      5.4     0.6    -      -       -      -
    433A  ARG      5.6     1.8    +      -       -      -
    439A  ALA*     3.7     2.4    -      -       -      -
    440A  ILE*     2.7    36.1    +      -       +      +
    441A  VAL      3.0     8.7    +      -       -      -
    514A  PHE*     4.1    14.6    -      -       +      -
    518A  LEU*     3.8    19.3    -      -       +      -
    522A  PHE*     4.1     6.7    -      -       +      -
   1177A  THR*     3.3    43.1    +      -       -      +
   1179A  ASP*     3.6    25.1    +      -       -      +
   1308A  PRO*     3.9    14.3    -      -       +      +
----------------------------------------------------------
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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