Contacts of the strand formed by residues 245 - 253 (chain B) in PDB entry 4R95


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 TYR 245 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ILE*     4.0    13.0    -      -       +      -
    241B  ASP      3.7     6.5    -      -       -      -
    242B  HIS*     2.9    63.8    +      -       -      +
    243B  SER      3.4     3.0    -      -       -      +
    244B  LEU*     1.3    79.8    -      -       -      +
    246B  THR*     1.3    67.0    +      -       -      +
    247B  GLY      3.3    24.7    -      -       -      -
    248B  SER*     4.8     0.2    -      -       -      -
    249B  LEU*     3.7    25.9    -      -       +      +
    403B  TYR*     3.3    27.4    -      +       +      -
    416B  ALA*     3.5    25.8    -      -       +      -
    417B  VAL      3.3    14.6    -      -       -      +
    419B  ALA*     3.9     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  TYR*     1.3    83.2    -      -       -      +
    247B  GLY*     1.3    68.9    +      -       -      +
    248B  SER      3.9     0.5    +      -       -      +
    416B  ALA*     4.2     0.7    -      -       -      +
    417B  VAL*     3.1    43.2    +      -       -      +
    418B  SER      5.0     1.0    +      -       -      -
    419B  ALA*     5.0    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  TYR*     3.3    17.7    -      -       -      -
    246B  THR*     1.3    78.7    -      -       -      +
    248B  SER*     1.3    59.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 248 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  TYR*     4.8     0.4    -      -       -      -
    246B  THR      4.6     0.5    -      -       -      +
    247B  GLY*     1.3    73.1    -      -       -      -
    249B  LEU*     1.3    66.1    +      -       -      +
    250B  TRP*     3.8    23.1    +      -       -      -
    415B  PHE      3.7     8.1    -      -       -      +
    416B  ALA*     3.7    11.9    -      -       -      +
    431B  VAL*     4.6     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 249 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ILE*     4.1    20.4    -      -       +      -
    242B  HIS*     5.8     0.2    -      -       +      -
    245B  TYR*     3.7    28.7    -      -       +      +
    247B  GLY      4.2     0.4    +      -       -      -
    248B  SER*     1.3    76.3    -      -       -      +
    250B  TRP*     1.3    63.5    +      -       -      +
    251B  TYR*     3.7    34.6    -      -       +      +
    403B  TYR*     4.5     4.9    -      -       +      +
    405B  VAL*     3.7    24.0    -      -       +      -
    414B  GLY*     3.9     3.6    -      -       -      -
    415B  PHE      3.5    18.8    -      -       -      +
    416B  ALA*     3.8    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 250 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  SER*     3.9    21.3    -      -       -      -
    249B  LEU*     1.3    79.3    -      -       -      +
    251B  TYR*     1.3    63.2    +      -       -      +
    355B  GLN*     4.1    20.2    -      -       +      -
    356B  SER      4.8     1.3    -      -       -      -
    357B  PHE*     3.5    50.3    -      +       +      -
    414B  GLY*     3.3     0.7    -      -       -      -
    415B  PHE      2.8    30.0    +      -       -      -
    431B  VAL*     3.8    28.6    +      -       +      -
    432B  GLU*     4.5     0.6    -      -       -      +
    433B  GLY*     3.3    43.7    -      -       -      +
    434B  PRO*     3.4    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ILE*     3.7    24.9    -      -       -      +
    249B  LEU*     3.7    31.2    -      -       +      +
    250B  TRP*     1.3    77.6    -      -       -      +
    252B  THR*     1.3    58.9    +      -       -      +
    350B  GLY*     3.9     0.7    -      -       -      -
    351B  GLU*     3.7    40.6    +      -       +      +
    357B  PHE*     3.4    13.8    -      -       -      -
    405B  VAL*     4.2    13.2    -      -       +      +
    407B  ASP*     4.4     3.4    +      -       +      -
    412B  ARG*     3.5    59.2    +      -       +      -
    413B  ILE      3.3     3.1    -      -       -      -
    414B  GLY*     3.3    32.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  TYR*     1.3    73.7    -      -       -      +
    253B  PRO*     1.3    67.8    +      -       -      +
    262B  VAL*     3.6    29.4    -      -       +      +
    263B  ILE      4.5     3.3    +      -       -      -
    348B  LEU*     3.6    15.2    -      -       +      +
    349B  MET*     2.6    23.9    +      -       -      +
    351B  GLU*     4.9     0.4    -      -       -      -
    357B  PHE*     3.7    11.2    -      -       -      -
    412B  ARG*     3.3     4.0    -      -       -      -
    413B  ILE*     2.8    41.5    +      -       +      +
    415B  PHE*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  THR*     1.3    89.9    +      -       -      +
    254B  ILE*     1.3    66.9    +      -       -      +
    255B  ARG*     3.3     6.4    +      -       -      +
    261B  GLU      3.8     4.3    -      -       -      +
    262B  VAL*     4.1    12.1    -      -       -      +
    263B  ILE      5.0     1.0    +      -       -      -
    349B  MET*     3.4    34.5    -      -       +      +
    350B  GLY      3.6    18.8    -      -       -      +
    351B  GLU*     4.6    11.4    -      -       +      +
    411B  LYS      3.7     9.0    -      -       -      +
    412B  ARG*     4.2     3.4    -      -       +      -
----------------------------------------------------------
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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