Contacts of the strand formed by residues 81 - 89 (chain 8) in PDB entry 4N6V


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 THR 81 (chain 8).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     238  VAL*     4.2     3.8    -      -       -      -
     268  GLN*     3.7     7.2    -      -       -      +
     698  VAL*     3.4     3.3    -      -       -      -
     708  PHE*     2.8    56.0    +      -       +      +
     788  LYS*     6.1     0.9    -      -       +      -
     798  PRO*     3.4    18.4    -      -       +      +
     808  LEU*     1.3    80.7    -      -       -      +
     828  LEU*     1.3    61.7    -      -       -      +
     838  SER*     3.3     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 82 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     238  VAL*     3.9    18.3    -      -       +      +
     268  GLN*     2.8    31.4    +      -       +      +
     278  LEU*     3.8    38.8    -      -       +      +
     308  LYS*     5.4     6.3    -      -       +      +
     678  LEU*     4.1    24.7    -      -       +      -
     688  ARG      3.6     8.7    -      -       -      +
     698  VAL*     4.4     0.7    -      -       +      +
     818  THR*     1.3    71.7    -      -       -      +
     838  SER*     1.3    60.1    +      -       -      +
     848  ASN*     3.4    25.4    -      -       -      +
     858  TYR*     3.9    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 83 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     528  ASN*     5.0     0.9    +      -       -      -
     688  ARG*     2.8    38.8    +      -       -      +
     698  VAL      4.4     0.3    -      -       -      -
     708  PHE*     3.5    28.4    +      -       -      +
     818  THR*     3.3     3.5    +      -       -      -
     828  LEU*     1.3    73.6    -      -       -      +
     848  ASN*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 84 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     308  LYS*     6.2     0.9    -      -       -      +
     688  ARG*     2.9    34.9    +      -       +      +
     828  LEU*     3.4     6.2    -      -       -      +
     838  SER*     1.3    82.1    -      -       -      +
     858  TYR*     1.3    88.0    +      -       -      +
     988  PHE*     3.8    33.3    +      -       +      -
     889  ASN*     3.1    20.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     278  LEU*     3.5    24.7    -      -       +      -
     308  LYS*     3.5    43.9    +      -       +      +
     318  GLU*     2.6    30.3    +      -       -      -
     658  VAL*     4.3     1.1    -      -       +      -
     668  HIS      3.2    13.5    -      -       -      +
     678  LEU*     4.1    16.2    -      -       +      -
     828  LEU*     3.9    12.1    -      -       +      -
     848  ASN*     1.3    88.4    +      -       -      +
     868  GLN*     1.3    70.3    +      -       -      +
     878  THR*     3.7    20.9    -      -       +      -
     988  PHE*     3.7     2.9    -      -       -      -
     879  THR      5.3     0.5    -      -       -      +
     889  ASN*     3.1    54.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 86 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     658  VAL*     3.2     5.1    -      -       -      +
     668  HIS*     2.9    42.2    +      -       +      +
     858  TYR*     1.3    79.4    -      -       -      +
     878  THR*     1.3    64.4    +      -       -      +
     898  LYS*     3.0    36.9    +      -       -      +
     968  THR*     4.6     7.0    +      -       -      -
     988  PHE*     3.3    46.8    -      -       +      +
     869  GLN*     6.0     2.0    -      -       -      +
     879  THR      5.9     1.6    -      -       -      -
     889  ASN*     5.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 87 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     318  GLU*     3.8    21.4    +      -       +      +
     358  PHE*     5.9     1.1    -      -       +      -
     648  PHE      3.9     4.7    -      -       -      -
     658  VAL*     4.2    17.3    -      -       +      -
     858  TYR*     3.7    29.6    -      -       +      -
     868  GLN*     1.3    78.0    -      -       -      +
     888  ASN*     1.3    75.7    +      -       -      +
     898  LYS*     3.3    12.3    +      -       -      +
     319  GLU*     4.4     7.4    +      -       -      -
     859  TYR      5.4     0.5    -      -       -      +
     869  GLN*     5.9     1.4    -      -       -      -
     879  THR*     2.9    31.0    +      -       -      +
     889  ASN*     5.9     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 88 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     638  ASP*     5.7     5.1    -      -       -      +
     648  PHE      3.5     5.2    +      -       -      -
     878  THR*     1.3    81.3    -      -       -      +
     898  LYS*     1.3    64.7    +      -       -      +
     908  ALA      4.4     0.2    +      -       -      -
     938  ASP*     4.6     1.6    -      -       -      +
     309  LYS*     3.1    24.5    +      -       -      +
     319  GLU*     5.0     0.8    +      -       -      +
     849  ASN*     3.0    28.3    +      -       -      +
     859  TYR*     3.0    57.8    +      -       +      +
     869  GLN*     5.8     0.7    -      -       -      -
     879  THR      6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 89 (chain 8). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     628  GLU      3.9     2.8    -      -       -      +
     638  ASP*     3.9     3.1    -      -       -      +
     648  PHE*     3.0    36.7    +      -       +      +
     668  HIS*     3.7    43.4    +      -       +      +
     868  GLN*     3.0    46.0    +      -       -      +
     878  THR      3.7     9.0    -      -       -      +
     888  ASN*     1.3    84.6    -      -       -      +
     908  ALA*     1.3    61.7    +      -       -      +
     938  ASP*     3.5    16.7    +      -       +      +
     948  GLU      5.1     2.4    +      -       -      -
     968  THR*     5.1     5.7    +      -       -      +
----------------------------------------------------------
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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