Contacts of the strand formed by residues 411 - 421 (chain A) in PDB entry 5VZ7


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 SER 411 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395A  PRO*     3.9     3.3    -      -       -      +
    396A  GLN*     2.9    25.9    +      -       -      +
    397A  PRO      3.2     5.9    -      -       -      -
    410A  GLY*     1.3    82.6    -      -       -      +
    412A  TRP*     1.3    90.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  HIS*     5.2     6.7    -      +       -      -
    285A  ASP*     4.6     5.0    -      -       -      +
    361A  LEU*     3.6    34.8    -      -       +      -
    393A  ARG*     3.0    56.9    -      -       +      +
    394A  LEU      3.1    20.9    -      -       -      +
    395A  PRO*     4.1     1.8    -      -       +      -
    396A  GLN*     3.7    10.4    -      -       -      +
    411A  SER*     1.3    98.3    +      -       -      +
    413A  LYS*     1.3    72.4    +      -       -      +
    414A  ALA*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  ASP*     3.5    19.3    -      -       -      +
    288A  THR*     5.0    15.7    +      -       +      +
    289A  PRO      3.7    19.0    +      -       -      -
    290A  VAL*     4.5     3.6    -      -       -      +
    291A  LEU*     5.1     3.0    -      -       -      +
    294A  ASP*     3.0    27.9    +      -       -      -
    393A  ARG      3.8     0.3    -      -       -      -
    394A  LEU*     2.8    47.3    +      -       +      +
    396A  GLN*     3.5    36.3    +      -       +      +
    412A  TRP*     1.3    82.1    -      -       -      +
    414A  ALA*     1.3    65.0    +      -       -      +
    415A  VAL*     4.1    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  HIS*     3.8    22.0    -      -       +      +
    285A  ASP*     2.9    39.3    +      -       +      +
    286A  LEU*     3.7     9.3    -      -       +      +
    361A  LEU*     3.8     9.2    -      -       +      -
    391A  ILE*     3.7    20.9    -      -       +      -
    392A  PHE      3.3     5.8    -      -       -      -
    412A  TRP*     4.1     2.9    -      -       +      -
    413A  LYS*     1.3    76.4    -      -       -      +
    415A  VAL*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  LEU*     4.1     5.8    -      -       -      -
    290A  VAL*     3.7    28.5    -      -       +      -
    298A  LEU*     4.1    20.9    -      -       +      -
    331A  VAL*     4.5     1.3    -      -       +      -
    391A  ILE*     3.4     2.0    -      -       -      -
    392A  PHE*     2.8    41.0    +      -       +      +
    394A  LEU*     3.6    38.6    -      -       +      -
    413A  LYS*     4.0    13.0    -      -       +      +
    414A  ALA*     1.3    80.6    -      -       -      +
    416A  ARG*     1.3    76.1    +      -       -      +
    417A  VAL*     3.6     2.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  PHE*     3.5    34.8    -      -       +      -
    286A  LEU*     3.8    27.4    -      -       +      +
    290A  VAL*     5.3     0.2    -      -       -      +
    329A  HIS*     3.9    25.3    +      -       +      +
    330A  ASP*     3.2    23.6    +      -       +      +
    331A  VAL      3.0    22.3    +      -       -      -
    389A  PHE*     3.6     3.2    -      -       -      +
    390A  CYS      3.1    32.7    +      -       -      +
    391A  ILE*     4.0    13.5    -      -       -      -
    415A  VAL*     1.3    76.5    -      -       -      +
    417A  VAL*     1.3    72.9    +      -       -      +
    418A  ASP*     2.8    39.3    +      -       -      -
      3P    T      3.7    20.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  LEU*     4.4    13.9    -      -       +      -
    302A  VAL*     5.0     0.4    -      -       +      -
    331A  VAL*     3.3    12.3    -      -       +      +
    333A  PHE*     3.9    25.1    -      -       +      -
    388A  SER      3.9     0.7    -      -       -      +
    389A  PHE*     3.9     0.2    -      -       -      -
    390A  CYS*     2.8    36.0    +      -       -      -
    392A  PHE*     3.6    52.0    -      -       +      -
    415A  VAL*     4.0     9.4    -      -       +      +
    416A  ARG*     1.3    81.6    +      -       -      +
    418A  ASP*     1.3    65.3    +      -       -      +
    419A  LEU*     3.9    11.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330A  ASP*     2.8     5.2    -      -       -      +
    331A  VAL      2.9     7.2    +      -       -      +
    332A  ASP*     3.5    13.9    -      -       +      +
    333A  PHE*     2.9    27.8    +      -       -      +
    388A  SER      3.4     3.6    -      -       -      +
    389A  PHE*     3.4    21.8    -      -       +      -
    416A  ARG*     2.8    35.0    +      -       -      -
    417A  VAL*     1.3    73.4    -      -       -      +
    419A  LEU*     1.3    67.2    +      -       -      +
    702A   MG      2.1    31.9    -      -       -      -
      3P    T      5.4     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  VAL*     4.2    14.1    -      -       +      -
    333A  PHE*     3.6    31.4    -      -       +      -
    335A  ILE*     4.4     9.4    -      -       +      -
    347A  LEU*     4.0    20.7    -      -       +      +
    350A  VAL*     4.3     7.9    -      -       +      -
    351A  MET*     3.7    29.2    -      -       -      -
    354A  LEU*     4.2    15.5    -      -       +      -
    386A  GLU      4.0     0.2    -      -       -      +
    387A  ARG*     3.3     4.5    -      -       -      +
    388A  SER*     2.8    41.0    +      -       -      +
    389A  PHE*     5.8     0.2    -      -       -      -
    390A  CYS*     5.6     2.0    -      -       -      -
    392A  PHE*     5.1     4.9    -      -       +      -
    417A  VAL*     3.9    12.1    -      -       +      +
    418A  ASP*     1.3    83.3    -      -       -      +
    420A  VAL*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  THR*     5.7     0.2    -      -       -      +
    333A  PHE      3.0    16.4    +      -       -      +
    334A  LEU*     3.4    22.2    -      -       +      -
    335A  ILE*     2.8    36.4    +      -       -      +
    386A  GLU*     3.3    13.0    -      -       +      +
    387A  ARG*     4.2    16.2    -      -       +      +
    419A  LEU*     1.3    75.8    -      -       -      +
    421A  VAL*     1.3    71.2    +      -       -      +
    422A  ALA*     5.4     1.6    -      -       +      -
    430A  ALA*     5.7     0.7    -      -       +      -
    434A  TRP*     3.8    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  ILE*     3.3    24.2    -      -       +      +
    343A  GLU*     3.8    39.7    -      -       +      +
    346A  LEU*     4.5     7.9    -      -       +      -
    347A  LEU*     3.9    38.6    -      -       +      +
    386A  GLU*     3.0    31.3    +      -       +      +
    420A  VAL*     1.3    86.8    -      -       -      +
    422A  ALA*     1.3    63.9    +      -       -      +
    423A  PRO*     4.7     1.0    -      -       -      +
----------------------------------------------------------
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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