Contacts of the strand formed by residues 257 - 265 (chain B) in PDB entry 6NMY


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 VAL 257 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  PHE*     3.0    13.5    -      -       -      -
    253B  ASP*     2.7    47.2    +      -       -      +
    255B  ALA      3.9     5.2    -      -       -      +
    256B  ALA*     1.3    86.4    -      -       +      +
    258B  LEU*     1.3    64.4    +      -       -      +
    259B  SER*     3.9    19.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  VAL*     4.3    24.7    -      -       +      -
    127A  LEU*     4.7    12.6    -      -       +      -
    250B  CYS*     4.0     7.9    -      -       +      -
    251B  PHE      3.4    35.7    -      -       -      +
    252B  PHE*     3.7    14.1    -      -       +      +
    256B  ALA      4.3     0.2    -      -       -      -
    257B  VAL*     1.3    74.5    -      -       -      +
    259B  SER*     1.3    59.8    +      -       -      +
    260B  CYS*     3.6    22.2    +      -       -      +
    278B  TYR*     6.4     2.2    -      -       +      -
    289B  CYS*     5.9     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  GLU      4.1     0.3    -      -       -      +
    250B  CYS*     3.4     1.2    -      -       -      -
    251B  PHE*     2.9    39.4    +      -       -      +
    253B  ASP*     6.1     0.5    -      -       -      +
    257B  VAL*     3.9    16.6    +      -       -      +
    258B  LEU*     1.3    70.3    -      -       -      +
    260B  CYS*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  LEU*     4.6     1.8    -      -       +      -
    249B  GLU      3.2     3.6    -      -       -      -
    250B  CYS*     2.0    46.4    -      -       -      -
    258B  LEU*     3.6    21.0    +      -       -      +
    259B  SER*     1.3    76.9    -      -       -      +
    261B  SER*     1.3    64.1    +      -       -      +
    262B  TRP*     4.9     1.8    -      -       -      -
    276B  LEU*     3.5    36.6    -      -       +      +
    289B  CYS*     6.4     0.4    -      -       -      -
    304B  HIS      4.5     7.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  ASN*     3.2     6.6    +      -       -      +
    248B  LEU*     3.5     1.5    -      -       -      +
    249B  GLU*     2.9    40.5    +      -       -      +
    259B  SER      5.6     0.2    -      -       -      -
    260B  CYS*     1.3    79.5    -      -       -      +
    262B  TRP*     1.3    67.1    +      -       -      +
    263B  GLU*     5.8     0.3    -      -       -      +
    303B  ARG*     3.6    36.1    +      -       -      +
    304B  HIS      4.1    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  PRO*     3.7    30.9    -      -       +      +
    246B  GLN      3.9     3.8    -      -       -      +
    247B  ASN      3.5     7.2    -      -       -      -
    248B  LEU*     3.9    26.5    -      -       +      -
    260B  CYS      5.1     1.6    -      -       -      -
    261B  SER*     1.3    85.9    +      -       -      +
    263B  GLU*     1.3    67.8    +      -       -      +
    264B  VAL*     4.7     7.7    -      -       -      +
    274B  PHE*     4.4    31.3    -      -       +      +
    275B  GLY      4.6     5.2    -      -       -      -
    276B  LEU*     3.7    42.0    -      -       +      -
    292B  VAL*     3.7    29.2    -      -       +      -
    302B  THR      4.0     0.5    -      -       -      +
    303B  ARG*     3.6     1.0    -      -       -      -
    304B  HIS*     2.9    43.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  PRO*     3.5     2.4    -      -       -      +
    246B  GLN*     3.0    45.9    +      -       +      +
    247B  ASN*     2.7    34.5    +      -       -      +
    261B  SER*     5.8     0.4    -      -       -      +
    262B  TRP*     1.3    77.4    -      -       -      +
    264B  VAL*     1.3    62.9    +      -       -      +
    297B  LEU*     3.8    34.7    -      -       +      +
    301B  HIS*     4.6    17.5    -      -       +      -
    302B  THR      3.4     7.9    -      -       -      +
    303B  ARG*     4.3    18.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  ALA      4.2     9.6    -      -       -      +
    244B  GLN      5.0     0.9    -      -       -      -
    245B  PRO*     4.2    14.6    -      -       +      -
    246B  GLN*     5.9     0.9    -      -       -      +
    262B  TRP*     4.7     8.1    -      -       -      +
    263B  GLU*     1.3    76.2    -      -       -      +
    265B  ARG*     1.3    70.9    +      -       -      +
    268B  VAL*     4.0    13.7    -      -       +      -
    269B  ALA*     4.1    11.2    -      -       +      -
    274B  PHE*     3.7    36.3    -      -       +      -
    294B  ARG*     6.3     0.2    -      -       -      +
    301B  HIS*     4.2     6.5    -      -       -      -
    302B  THR*     2.9    47.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LEU*     3.6    17.1    -      -       +      +
    242B  GLU*     3.2    64.7    +      -       -      +
    244B  GLN      5.6     0.6    +      -       -      -
    246B  GLN*     5.6     0.9    -      -       -      +
    264B  VAL*     1.3    78.8    -      -       -      +
    266B  LYS*     1.3    58.8    +      -       -      +
    267B  GLU*     3.1    31.6    +      -       -      +
    268B  VAL*     3.9    20.2    -      -       +      +
    269B  ALA*     3.0    26.7    +      -       -      +
    300B  LEU*     3.2    43.9    +      -       -      +
    301B  HIS*     3.5    25.9    -      -       +      +
----------------------------------------------------------
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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