Contacts of the strand formed by residues 29 - 36 (chain B) in PDB entry 2FBW


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 ARG 29 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  TYR*     3.5     5.9    -      -       -      -
     18B  ARG*     2.8    60.1    +      -       +      +
     26B  ASP*     6.0     4.1    -      -       -      +
     27B  LYS      4.0     8.0    +      -       -      +
     28B  PRO*     1.3    76.5    -      -       -      +
     30B  MET*     1.3    69.9    +      -       -      +
     31B  GLN*     3.0    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  SER*     3.4    44.9    -      -       -      +
     16B  ILE      3.4     1.8    -      -       -      -
     17B  TYR*     3.6    27.4    -      -       -      +
     29B  ARG*     1.3    84.8    +      -       -      +
     31B  GLN*     1.3    59.9    +      -       -      +
     32B  THR*     4.4     1.0    +      -       -      -
     98B  LYS*     4.4     5.6    -      -       +      +
     99B  ILE      4.0     2.0    -      -       -      +
    100B  TYR*     3.6    47.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE      3.4     2.6    -      -       -      +
     15B  SER*     4.2     0.7    -      -       -      -
     16B  ILE      2.8    34.8    +      -       -      +
     18B  ARG*     3.2    31.0    +      -       +      -
     29B  ARG*     3.0    27.3    +      -       -      +
     30B  MET*     1.3    75.4    -      -       -      +
     32B  THR*     1.3    68.4    +      -       -      +
     33B  TYR*     3.2    41.0    +      -       +      +
     56B  ASP*     3.9     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  LYS*     4.1    33.0    -      -       +      +
     14B  PHE      3.1    10.8    -      -       -      +
     15B  SER*     4.4    11.7    +      -       -      +
     30B  MET      4.4     1.4    +      -       -      -
     31B  GLN*     1.3    81.8    +      -       -      +
     33B  TYR*     1.3    75.3    +      -       -      +
     34B  GLU*     5.2     2.7    -      -       +      -
     96B  THR*     5.5     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LYS      3.5     0.9    -      -       -      +
     13B  LYS*     3.3     5.5    -      -       -      -
     14B  PHE*     2.8    33.3    +      -       +      +
     16B  ILE*     3.8    31.0    -      -       +      -
     18B  ARG*     2.9    19.7    +      -       -      -
     31B  GLN*     3.2    44.7    -      -       +      -
     32B  THR*     1.3    77.1    -      -       -      +
     34B  GLU*     1.3    63.6    +      -       -      +
     35B  VAL*     4.0     0.6    +      -       +      -
     51B  ILE*     3.6    45.3    -      -       +      -
     55B  LEU*     4.4    13.7    -      -       +      -
     56B  ASP*     2.8    32.3    +      -       +      -
     59B  LEU*     4.3     7.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ILE*     3.6    25.4    -      -       +      +
     12B  LYS      3.4     4.7    -      -       -      -
     13B  LYS*     3.4    32.2    +      -       +      -
     32B  THR*     5.2     3.6    -      -       +      -
     33B  TYR*     1.3    74.6    -      -       -      +
     35B  VAL*     1.3    59.7    +      -       -      +
     55B  LEU*     3.5    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ARG      3.4     1.0    -      -       -      +
     11B  ILE*     4.3     3.4    -      -       -      -
     12B  LYS*     2.7    42.8    +      -       -      +
     14B  PHE*     4.1    17.9    -      -       +      -
     33B  TYR      4.7     0.9    -      -       -      +
     34B  GLU*     1.3    79.6    -      -       -      +
     36B  ASP*     1.3    64.0    +      -       -      +
     37B  LEU*     3.4     7.0    +      -       +      +
     40B  CYS*     4.1    19.1    -      -       +      -
     47B  ALA*     4.6     6.7    -      -       +      +
     50B  LYS*     4.0    28.5    -      -       +      +
     51B  ILE*     3.6    37.7    -      -       +      +
     55B  LEU*     4.7     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  THR      4.9     1.4    -      -       -      +
      9B  SER*     3.5    20.9    -      -       -      -
     10B  ARG      3.2    19.2    +      -       -      -
     11B  ILE*     3.7    14.9    -      -       +      +
     34B  GLU      4.3     0.2    -      -       -      -
     35B  VAL*     1.3    71.8    -      -       -      +
     37B  LEU*     1.3    61.2    +      -       -      +
     38B  ASN*     3.1    17.3    +      -       -      +
     39B  LYS*     3.0    56.1    +      -       +      +
     40B  CYS*     3.7     3.5    +      -       -      +
     50B  LYS*     4.1     7.6    -      -       -      +
----------------------------------------------------------
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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