Contacts of the strand formed by residues 251 - 260 (chain A) in PDB entry 5FWV


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 HIS 251 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  ALA*     4.0     1.6    -      -       -      +
    250A  SER*     1.3   107.4    +      -       -      +
    252A  ILE*     1.4    65.0    +      -       -      +
    253A  HIS*     5.6     0.2    -      -       +      -
    293A  ASN*     3.8    36.2    +      -       +      +
    294A  VAL      3.2    17.7    -      -       -      +
    295A  SER*     3.9    11.2    -      -       -      +
    296A  LEU      3.8     4.9    -      -       -      -
    321A  VAL*     3.1    55.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  ILE*     4.5    17.5    -      -       +      +
    246A  VAL*     4.8     6.5    -      -       +      -
    249A  ALA*     4.4     2.7    -      -       +      -
    251A  HIS*     1.4    76.3    -      -       -      +
    253A  HIS*     1.3    65.7    +      -       -      +
    254A  PHE*     3.5    30.0    -      -       +      -
    293A  ASN*     3.5     3.8    -      -       -      -
    294A  VAL*     2.8    40.4    +      -       +      +
    296A  LEU      3.4    20.0    -      -       -      +
    297A  ASP*     4.0    19.7    -      -       -      +
    298A  PHE      4.4     1.3    -      -       -      +
    299A  VAL*     4.4    11.9    -      -       +      -
    318A  TYR*     4.1    15.0    -      -       +      -
    319A  GLN      3.6    10.5    -      -       -      +
    320A  ALA*     4.2    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  HIS*     5.0     0.4    +      -       -      -
    252A  ILE*     1.3    72.9    -      -       -      +
    254A  PHE*     1.3    65.0    +      -       -      +
    255A  SER*     4.7     9.1    +      -       -      -
    291A  SER*     2.2    36.8    +      -       -      -
    292A  PHE      3.5     4.5    -      -       -      -
    293A  ASN*     3.2    26.5    -      -       -      +
    317A  LEU      3.7     1.1    +      -       -      +
    318A  TYR*     3.2     5.5    -      -       -      -
    319A  GLN*     2.8    64.7    +      -       +      +
    321A  VAL*     5.3     6.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  ILE*     4.1    21.3    -      -       +      -
    252A  ILE*     3.5    34.1    -      -       +      -
    253A  HIS*     1.3    80.0    -      -       -      +
    255A  SER*     1.3    59.6    +      -       -      +
    256A  PHE*     4.7     5.3    -      +       +      -
    270A  LEU*     3.7    32.3    -      -       +      -
    291A  SER*     3.2     6.4    +      -       -      -
    292A  PHE*     2.8    65.7    +      +       +      +
    294A  VAL*     3.9     8.3    -      -       +      -
    299A  VAL*     4.2    16.8    -      -       +      -
    301A  LEU*     5.1     3.1    -      -       +      -
    316A  VAL*     3.8    22.4    -      -       +      -
    317A  LEU      3.5     1.8    -      -       -      -
    318A  TYR*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  HIS*     4.7     9.1    +      -       -      -
    254A  PHE*     1.3    75.2    -      -       -      +
    256A  PHE*     1.3    68.3    +      -       -      +
    257A  PRO*     3.4     5.1    -      -       -      +
    290A  LEU      3.5    20.2    -      -       -      -
    291A  SER*     4.4     4.9    -      -       -      +
    316A  VAL*     3.4     7.1    -      -       -      +
    317A  LEU*     2.9    52.1    +      -       -      +
    319A  GLN*     5.3     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  PHE*     4.7     2.9    -      -       +      -
    255A  SER*     1.3    84.1    -      -       -      +
    257A  PRO*     1.3    59.8    -      -       -      +
    258A  LEU*     2.9    18.8    +      -       -      +
    259A  PHE*     3.9    28.3    +      +       +      +
    268A  VAL*     4.7    14.6    -      -       +      -
    270A  LEU*     5.1     8.3    -      -       +      -
    282A  PHE*     4.0    25.6    -      +       -      -
    288A  PRO*     3.4    36.1    -      -       +      +
    289A  PRO      4.6     6.1    +      -       -      +
    290A  LEU      4.5     3.8    +      -       -      -
    292A  PHE*     4.2    14.6    -      +       -      -
    301A  LEU*     5.4     0.2    -      -       +      -
    314A  PHE*     4.8     4.7    -      +       -      -
    315A  ALA      3.5     6.3    -      -       -      -
    316A  VAL*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  PHE*     3.6    54.6    -      -       +      +
     39A  ASP*     4.6     6.4    -      -       -      +
    224A  VAL*     5.7     0.2    -      -       +      -
    255A  SER*     3.4    16.2    -      -       -      +
    256A  PHE*     1.3    84.7    -      -       -      +
    258A  LEU*     1.3    60.1    +      -       -      +
    315A  ALA      3.2    15.0    -      -       -      +
    316A  VAL      5.2     0.2    -      -       -      -
    317A  LEU*     4.2    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  PHE*     3.7    13.9    -      -       +      +
     34A  THR*     4.6    10.3    -      -       +      -
     39A  ASP*     5.2     9.4    -      -       +      +
    230A  PHE*     3.5    37.7    -      -       +      -
    256A  PHE*     2.9     7.0    +      -       -      +
    257A  PRO*     1.3    82.1    -      -       -      +
    259A  PHE*     1.3    72.5    +      -       -      +
    260A  ASP*     4.7     3.1    -      -       +      +
    312A  GLN*     4.2    27.6    -      -       +      +
    313A  GLY      4.3     3.6    -      -       -      +
    314A  PHE*     3.4    16.8    -      -       -      +
    315A  ALA*     3.0    37.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  PHE*     3.9    20.9    -      +       +      +
    258A  LEU*     1.3    79.9    -      -       -      +
    260A  ASP*     1.3    59.1    +      -       -      +
    261A  ILE*     3.8    24.3    +      -       +      -
    268A  VAL*     3.9    21.8    -      -       +      -
    282A  PHE*     3.6    33.9    -      -       +      -
    283A  HIS      3.7    18.2    -      -       -      -
    286A  SER      3.7     8.5    -      -       -      -
    287A  ARG*     3.4    30.8    +      -       -      +
    288A  PRO*     3.4    34.1    -      -       +      -
    313A  GLY      3.9     2.9    -      -       -      -
    314A  PHE*     3.9     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  LEU*     4.7     2.0    -      -       +      +
    259A  PHE*     1.3    73.5    -      -       -      +
    261A  ILE*     1.3    78.0    +      -       -      +
    262A  ARG*     2.9    35.4    +      -       -      -
    311A  ALA*     3.8     3.1    -      -       -      +
    312A  GLN*     3.1    48.0    -      -       +      +
    313A  GLY      2.7    31.7    +      -       -      +
----------------------------------------------------------
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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