Contacts of the strand formed by residues 56 - 66 (chain A) in PDB entry 5NVL


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 56 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  PRO*     1.3    81.8    -      -       -      +
     57A  GLN*     1.3    66.7    +      -       -      +
     58A  TYR*     3.0    21.2    +      -       -      +
     59A  ASN*     5.6     0.3    -      -       -      +
     60A  TYR*     4.6     3.6    -      -       +      -
     88A  PHE*     3.3    36.3    -      -       +      -
     89A  ALA      2.9    12.7    +      -       -      +
     90A  SER      3.5    24.7    -      -       -      +
     91A  VAL*     3.7    25.6    -      -       +      +
     94A  PHE*     4.6     1.8    -      -       +      -
    156A  LEU*     3.8    38.6    -      -       +      +
     41B  TYR*     4.1     4.8    -      -       -      -
     43B  TYR*     4.4     5.6    -      -       +      -
     48B  MET*     4.6     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LEU*     1.3    74.5    -      -       -      +
     58A  TYR*     1.3    91.6    +      -       +      +
     60A  TYR*     5.4     0.4    -      -       -      -
    156A  LEU      4.8     3.2    +      -       -      -
    158A  GLU*     3.6    28.7    -      -       +      +
     38B  LEU      5.6     0.2    -      -       -      -
     39B  ALA*     3.5     7.0    -      -       +      -
     40B  ASP*     2.6    41.4    +      -       -      +
     41B  TYR*     3.1    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LEU*     3.0    19.7    -      -       -      +
     57A  GLN*     1.3    98.1    -      -       +      +
     59A  ASN*     1.3    71.9    +      -       -      +
     60A  TYR*     3.1    34.1    +      -       +      -
     89A  ALA      4.6     0.2    -      -       -      +
    117A  LYS*     3.5    38.8    -      -       +      -
    158A  GLU*     3.0    30.6    +      -       -      -
    163A  GLY      3.4    12.7    +      -       -      -
    164A  GLU*     3.2    40.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  PRO*     3.8    16.3    -      -       -      +
     49A  MET*     5.7     0.5    -      -       -      +
     56A  LEU      5.6     0.2    -      -       -      +
     58A  TYR*     1.3    79.6    -      -       -      +
     60A  TYR*     1.3    60.1    +      -       -      +
     87A  THR*     3.9     3.8    -      -       +      -
     88A  PHE      3.2     7.9    -      -       -      +
     89A  ALA*     2.9    32.2    -      -       -      +
    117A  LYS*     3.4     6.9    -      -       -      +
    118A  GLU*     2.8    52.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LEU*     4.3     8.1    -      -       +      -
     57A  GLN      5.4     0.2    -      -       -      -
     58A  TYR*     3.1    58.2    -      +       +      -
     59A  ASN*     1.3    72.5    -      -       -      +
     61A  THR*     1.3    64.1    +      -       -      +
     87A  THR*     3.2     3.3    -      -       -      +
     88A  PHE*     2.8    55.3    +      -       +      -
    115A  LEU*     3.9     5.6    -      -       +      -
    116A  PHE      3.3    21.3    -      -       -      +
    117A  LYS*     3.8    21.6    -      -       +      -
    118A  GLU      3.9     0.4    -      -       -      +
    155A  MET*     3.7    38.2    +      -       +      +
    156A  LEU*     3.2    35.9    -      -       +      -
    158A  GLU*     3.5     9.9    +      -       -      -
    166A  ILE*     5.5     1.3    -      -       +      +
    167A  CYS      5.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     1.3    74.5    -      -       -      +
     62A  PHE*     1.3    61.8    +      -       -      +
     63A  TRP*     3.1    39.3    -      -       +      +
     84A  GLN*     3.6    33.8    +      -       +      +
     86A  GLY      3.3    11.4    -      -       -      +
     87A  THR*     2.8    16.6    +      -       -      -
    115A  LEU*     3.4     5.7    -      -       -      -
    116A  PHE      2.7    28.5    +      -       -      -
    117A  LYS      5.0     0.4    -      -       -      -
    118A  GLU*     3.5    19.2    -      -       -      +
    119A  GLY      4.8     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  THR*     1.3    75.1    -      -       -      +
     63A  TRP*     1.3    59.0    +      -       -      +
     85A  ILE*     2.7    49.5    +      -       +      +
     86A  GLY      2.9    11.2    +      -       -      +
     88A  PHE*     3.4    35.4    -      +       -      -
     94A  PHE*     4.1    18.2    -      +       -      -
     97A  PHE*     3.9    27.8    -      +       +      -
     98A  TYR*     4.4    11.4    -      +       +      -
    101A  MET*     3.7    32.5    -      -       +      -
    113A  PHE*     5.3     1.1    -      -       +      -
    114A  HIS      3.3    11.4    -      -       -      -
    115A  LEU*     3.8    24.9    -      -       +      -
    148A  TRP*     4.3    18.8    -      +       -      -
    152A  ILE*     4.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  THR*     3.1    42.5    +      -       +      +
     62A  PHE*     1.3    76.1    -      -       -      +
     64A  TYR*     1.3    63.5    +      -       -      +
     82A  ILE*     3.6    31.6    -      -       +      -
     83A  LYS      3.2     6.7    -      -       -      +
     84A  GLN*     3.5    43.5    -      -       +      -
     85A  ILE*     4.0     4.9    -      -       -      +
    113A  PHE*     3.5     7.8    -      -       -      +
    114A  HIS*     2.8    41.3    +      -       +      +
    116A  PHE*     4.6     3.9    -      -       -      +
    119A  GLY      6.3     1.1    -      -       -      -
    120A  ILE      4.2    12.3    +      -       -      -
    121A  LYS*     4.6    10.3    -      -       +      -
    122A  PRO*     3.4    37.2    -      -       +      +
    123A  MET*     5.2     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TRP*     1.3    76.4    -      -       -      +
     65A  SER*     1.3    74.6    +      -       -      +
     66A  ARG*     3.6    34.0    -      -       +      +
     83A  LYS*     2.8    41.3    +      -       +      +
     85A  ILE*     3.8    20.6    -      -       +      -
    107A  LEU*     4.6     3.2    -      -       +      +
    111A  SER*     4.0    14.6    +      -       -      -
    112A  ASP      3.4    12.8    -      -       -      -
    113A  PHE*     3.6    15.7    -      +       +      -
    114A  HIS*     4.4     1.3    -      -       -      -
     66B  GLU      4.4    11.2    -      -       -      -
     67B  PHE*     3.9    20.2    -      +       +      -
     69B  PRO*     4.1    15.7    -      -       +      +
     70B  ILE*     3.4    29.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  TYR*     1.3    82.0    -      -       -      +
     66A  ARG*     1.3    61.4    +      -       -      +
     80A  GLN*     4.2    10.1    -      -       -      +
     81A  ASN      3.7    18.6    -      -       -      -
     82A  ILE*     3.8    12.2    -      -       -      +
     83A  LYS*     5.6     0.2    -      -       -      -
    110A  HIS      4.6     0.2    -      -       -      -
    111A  SER*     3.3     2.6    -      -       -      -
    112A  ASP*     2.9    50.4    +      -       -      +
    114A  HIS*     3.2    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  TYR*     3.6    25.7    -      -       +      +
     65A  SER*     1.3    75.5    -      -       -      +
     67A  ARG*     1.3    85.5    +      -       -      +
     68A  THR*     3.4    29.6    +      -       -      +
     69A  PRO*     4.7     4.6    -      -       -      +
     79A  GLU      3.7     5.4    +      -       -      -
     80A  GLN*     3.1    15.5    +      -       -      -
     81A  ASN      4.5     3.5    +      -       -      +
    108A  THR*     3.3    32.0    +      -       -      +
    109A  GLY*     3.9    12.9    -      -       -      -
    110A  HIS      3.3     7.0    -      -       -      +
    111A  SER*     3.4    13.2    -      -       -      +
     69B  PRO*     6.0     3.6    -      -       -      -
----------------------------------------------------------
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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