Contacts of the strand formed by residues 523 - 531 (chain A) in PDB entry 3V4V


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 ASN 523 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467A  LEU      3.9     1.4    -      -       -      +
    469A  PHE*     2.9    37.2    +      -       -      +
    515A  ILE*     3.2    31.1    -      -       -      +
    516A  GLN      3.1    23.4    +      -       -      +
    517A  VAL*     4.1    19.0    -      -       +      +
    518A  SER      5.1     1.1    -      -       -      +
    521A  GLU*     3.9     9.0    +      -       -      +
    522A  ALA*     1.3    73.3    -      -       -      +
    524A  CYS*     1.3    71.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 524 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466A  THR*     3.8     9.9    -      -       +      -
    467A  LEU      3.0     7.4    -      -       -      +
    468A  CYS*     2.0    63.7    -      -       -      -
    469A  PHE      4.2     0.4    -      -       -      -
    515A  ILE*     5.4     0.2    -      -       -      -
    522A  ALA*     4.2     6.2    +      -       -      -
    523A  ASN*     1.3    87.8    +      -       -      +
    525A  ARG*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 525 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465A  LEU      4.1     0.7    -      -       -      +
    466A  THR*     3.8     1.1    -      -       -      -
    467A  LEU*     3.2    32.5    +      -       +      +
    469A  PHE*     6.2     1.5    -      -       +      -
    484A  TYR*     3.1    37.5    +      -       +      +
    513A  GLY*     5.1     0.2    -      -       -      -
    514A  SER      2.6    37.8    +      -       -      +
    515A  ILE*     3.6    28.6    -      -       +      +
    524A  CYS*     1.3    75.0    -      -       -      +
    526A  THR*     1.3    63.4    +      -       -      +
    527A  HIS*     4.3    11.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 526 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464A  ASP*     4.1    18.8    -      -       +      +
    465A  LEU      3.3    22.0    -      -       -      +
    466A  THR*     2.8    29.6    +      -       -      +
    524A  CYS      5.4     0.2    -      -       -      -
    525A  ARG*     1.3    72.2    -      -       -      +
    527A  HIS*     1.3    79.3    +      -       -      +
    528A  GLN*     5.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 527 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465A  LEU*     2.9    37.6    +      -       -      +
    484A  TYR*     3.0    43.7    +      +       -      -
    486A  MET*     4.7    11.5    -      -       -      -
    502A  PHE*     4.3    17.3    -      -       +      -
    511A  ILE*     3.4    41.1    -      -       +      +
    512A  THR      4.6     2.7    -      -       -      -
    525A  ARG*     4.2    11.8    +      -       +      +
    526A  THR*     1.3    91.6    -      -       -      +
    528A  GLN*     1.3    60.9    +      -       -      +
    529A  ALA      4.0     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 528 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  CYS*     4.6     2.4    -      -       -      +
    462A  CYS*     4.2    16.9    -      -       +      -
    463A  ILE      3.4    10.5    -      -       -      +
    464A  ASP*     4.2    14.1    -      -       -      +
    501A  TYR      4.2     0.9    -      -       -      +
    502A  PHE*     3.4    16.4    -      -       -      +
    503A  SER*     5.0     6.1    +      -       -      +
    526A  THR*     4.3     0.9    -      -       +      -
    527A  HIS*     1.3    73.0    -      -       -      +
    529A  ALA*     1.3    61.2    +      -       -      +
    530A  PHE*     3.3    40.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 529 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462A  CYS*     3.5     3.1    -      -       -      -
    463A  ILE*     2.9    48.0    +      -       +      +
    465A  LEU*     4.5     5.4    -      -       +      -
    488A  LEU*     3.7    36.8    -      -       +      -
    500A  PHE*     3.8     8.4    -      -       +      -
    501A  TYR      3.4     4.5    -      -       -      -
    502A  PHE*     4.2     5.4    -      -       +      -
    527A  HIS      4.0     0.4    +      -       -      -
    528A  GLN*     1.3    72.0    -      -       -      +
    530A  PHE*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 530 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  CYS*     3.4    41.3    -      -       +      -
    455A  GLU*     3.8    28.9    -      -       +      +
    460A  SER*     4.7     2.0    -      -       -      +
    461A  VAL      4.0     4.0    -      -       -      +
    462A  CYS*     4.1     0.7    -      -       +      -
    500A  PHE*     3.1    12.4    -      -       -      -
    501A  TYR*     3.2    44.9    +      +       +      -
    502A  PHE      4.3    13.0    -      -       -      -
    503A  SER*     3.6    31.2    -      -       -      -
    528A  GLN*     3.3    41.1    -      -       +      -
    529A  ALA*     1.3    73.0    -      -       -      +
    531A  MET*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 531 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446A  VAL*     6.4     1.3    -      -       -      -
    448A  ARG*     4.1    21.1    -      -       +      +
    455A  GLU*     4.8     0.2    -      -       -      +
    460A  SER*     4.4     8.7    +      -       -      -
    461A  VAL*     3.1    43.4    +      -       +      +
    499A  ARG*     3.8    14.8    -      -       +      +
    500A  PHE*     3.5    27.4    -      -       +      -
    501A  TYR*     3.7    10.9    +      -       -      -
    529A  ALA      3.8     0.2    +      -       -      -
    530A  PHE*     1.3    73.8    -      -       -      +
    532A  ARG*     1.3    71.5    +      -       -      +
    533A  LYS*     3.4     7.1    +      -       -      +
    535A  VAL*     3.7    38.6    -      -       +      -
    537A  ASP      5.9     0.4    -      -       -      +
    585A  PHE*     4.4    20.2    -      -       +      -
----------------------------------------------------------
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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