Contacts of the strand formed by residues 420 - 431 (chain A) in PDB entry 5EMV


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 420 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  LEU*     4.9    10.1    -      -       +      +
    292A  GLY      3.6    27.6    -      -       -      +
    293A  PRO*     3.9    19.4    -      -       +      +
    296A  ALA*     4.4     5.1    -      -       +      +
    297A  PHE*     3.6    32.5    -      -       +      -
    411A  VAL*     3.6    26.0    -      -       +      -
    412A  VAL      3.6    14.6    -      -       -      +
    413A  THR*     4.1     6.1    -      -       +      -
    418A  GLN      3.8     2.0    +      -       -      -
    419A  GLU*     1.3    74.6    -      -       -      +
    421A  LEU*     1.3    63.8    +      -       -      +
    422A  LEU      3.8    15.3    -      -       -      +
    423A  CYS*     4.3     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  THR*     3.8    13.6    +      -       -      +
    227A  ARG*     4.0    47.8    -      -       +      +
    228A  LEU*     3.9    20.7    -      -       +      +
    296A  ALA*     3.5    15.7    -      -       -      +
    339A  MET*     3.8    20.6    -      -       +      -
    341A  LEU*     3.6    31.4    -      -       +      -
    412A  VAL*     2.8    15.0    +      -       +      +
    413A  THR      4.1     0.7    -      -       -      -
    414A  ASN*     3.7    24.5    -      -       +      +
    419A  GLU*     3.4     2.0    +      -       +      +
    420A  LEU*     1.3    79.6    -      -       -      +
    422A  LEU*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU*     3.7    23.1    -      -       +      -
    224A  GLY*     3.8    18.6    -      -       -      -
    225A  THR*     4.1     6.1    -      -       +      +
    228A  LEU*     4.4    10.8    -      -       +      +
    230A  LEU*     4.6     8.5    -      -       +      +
    296A  ALA*     3.7     5.8    -      -       -      +
    298A  PHE*     3.6    30.7    -      -       +      -
    333A  TYR*     4.2    24.9    -      -       +      -
    410A  GLN      3.8     1.3    -      -       -      +
    411A  VAL*     3.6     1.4    -      -       -      -
    412A  VAL*     2.7    48.4    +      -       +      +
    420A  LEU*     3.7     4.6    -      -       -      +
    421A  LEU*     1.3    85.3    -      -       -      +
    423A  CYS*     1.3    59.8    +      -       -      +
    424A  THR*     4.2     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  LEU*     4.2     6.5    -      -       -      -
    288A  LEU*     4.5     4.9    -      -       +      -
    296A  ALA      2.9    11.1    +      -       -      +
    297A  PHE*     3.4    39.5    -      -       +      -
    298A  PHE      2.9    25.8    +      -       -      +
    409A  LEU*     3.6    26.2    -      -       -      -
    410A  GLN      3.3     6.3    -      -       -      +
    411A  VAL*     4.1    11.0    -      -       +      -
    420A  LEU*     4.3    11.4    -      -       +      +
    422A  LEU*     1.3    73.9    -      -       -      +
    424A  THR*     1.3    65.3    +      -       -      +
    425A  ALA      5.3     0.2    -      -       -      -
    444A  LEU*     5.3     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU*     3.6    26.2    -      -       +      +
    298A  PHE*     3.3     9.7    -      -       -      +
    300A  VAL*     3.7    24.7    -      -       +      -
    409A  LEU*     3.6     5.0    -      -       -      -
    410A  GLN*     2.8    43.4    +      -       -      -
    422A  LEU*     4.2     7.3    -      -       -      +
    423A  CYS*     1.3    77.0    +      -       -      +
    425A  ALA*     1.3    64.5    +      -       -      +
    426A  TYR*     3.6    35.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ILE*     4.2     9.2    -      -       +      -
    278A  PHE*     3.5    28.9    -      -       +      -
    285A  LEU*     5.0     1.6    -      -       +      -
    298A  PHE      2.9     9.9    +      -       -      +
    299A  LEU*     3.4    17.0    -      -       +      +
    300A  VAL*     2.8    32.1    +      -       -      -
    408A  ILE      3.5     4.3    -      -       -      -
    409A  LEU*     4.2     7.6    -      -       +      +
    423A  CYS*     4.3     0.6    -      -       -      -
    424A  THR*     1.3    75.5    -      -       -      +
    426A  TYR*     1.3    57.4    +      -       -      +
    444A  LEU*     4.6     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU*     5.1     0.3    -      -       -      +
    230A  LEU*     4.9    10.2    -      -       -      +
    233A  PHE*     4.6    19.6    -      +       -      -
    254A  ILE*     5.0     2.2    -      -       +      -
    278A  PHE*     4.6     0.3    -      -       -      -
    300A  VAL*     3.3    19.5    -      -       +      +
    302A  PHE*     3.3    34.3    -      +       +      -
    380A  P1L      6.0     2.0    -      -       +      -
    407A  THR*     3.5    10.4    -      -       -      -
    408A  ILE*     2.7    51.4    +      -       +      +
    410A  GLN*     2.8    41.1    +      -       +      -
    424A  THR*     3.6    32.7    +      -       +      +
    425A  ALA*     1.3    74.0    -      -       -      +
    427A  VAL*     1.3    64.5    +      -       -      +
    428A  PHE*     3.7    22.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ILE*     5.7     2.0    -      -       +      -
    277A  LYS*     4.1    28.0    -      -       +      -
    278A  PHE*     5.5     3.8    -      -       +      -
    299A  LEU*     4.2    23.3    -      -       +      -
    300A  VAL      3.0     4.2    +      -       -      +
    301A  LYS*     3.7    35.4    -      -       +      -
    302A  PHE*     2.8    27.3    +      -       -      +
    406A  PHE      4.6     3.1    -      -       -      +
    407A  THR*     4.3     8.7    -      -       +      -
    425A  ALA      4.3     0.2    -      -       -      -
    426A  TYR*     1.3    79.1    -      -       -      +
    428A  PHE*     1.3    67.3    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    252A  VAL*     4.5     1.6    -      -       +      -
    301A  LYS*     5.1     1.5    -      -       -      +
    302A  PHE*     3.5    33.9    -      +       +      -
    304A  ALA*     5.0     2.2    -      -       +      -
    380A  P1L      3.4    44.6    -      -       +      -
    400A  ASN      5.1     0.7    -      -       -      +
    403A  LEU*     3.4    41.0    +      -       +      +
    404A  GLU*     4.8     0.9    +      -       -      -
    406A  PHE*     3.6    36.3    +      +       +      +
    408A  ILE*     3.9    23.8    -      -       +      -
    426A  TYR*     3.7    35.0    -      +       +      -
    427A  VAL*     1.3    77.1    -      -       -      +
    429A  GLU*     1.3    69.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  LYS*     2.9    34.8    +      -       -      -
    302A  PHE      2.7     9.8    +      -       -      +
    303A  TRP*     3.3    27.3    +      -       +      +
    304A  ALA*     2.9    25.7    +      -       -      +
    400A  ASN*     3.4    31.6    +      -       +      +
    403A  LEU*     3.9     5.9    -      -       -      +
    428A  PHE*     1.3    81.3    -      -       -      +
    430A  VAL*     1.3    66.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  TRP*     4.1    10.9    -      -       -      -
    304A  ALA*     3.6     6.5    -      -       +      +
    306A  LEU*     3.8    22.0    -      -       +      +
    307A  ASN*     5.9     0.9    -      -       -      +
    396A  ARG*     3.8    29.8    -      -       +      +
    399A  MET*     3.6    33.2    -      -       +      -
    400A  ASN*     2.8    19.6    +      -       -      +
    403A  LEU*     3.6    23.8    -      -       +      -
    429A  GLU*     1.3    75.6    -      -       -      +
    431A  SER*     1.3    74.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 431 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  TRP*     3.7    25.6    -      -       -      -
    304A  ALA      2.8    14.3    +      -       -      +
    305A  ASP*     4.5     3.7    -      -       -      -
    306A  LEU      4.8     0.2    +      -       -      -
    307A  ASN*     4.4     7.3    -      -       -      +
    396A  ARG*     4.3     2.2    -      -       -      -
    430A  VAL*     1.3    87.1    -      -       -      +
    432A  THR*     1.3    70.4    +      -       -      +
    435A  ARG*     3.6    14.6    +      -       -      +
    436A  GLY      3.0    27.0    +      -       -      -
    438A  GLN*     5.6     0.7    -      -       -      +
----------------------------------------------------------
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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