Contacts of the strand formed by residues 25 - 31 (chain B) in PDB entry 2UX2


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 ALA 25 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  LEU*     3.5    11.0    -      -       -      +
      3B  CYS*     3.6     6.8    -      -       -      -
     23B  PHE*     3.7     2.6    -      -       -      +
     24B  ASP*     1.3    87.4    -      -       -      +
     26B  CYS*     1.3    59.9    +      -       -      +
     39B  CYS*     3.8     0.7    -      -       -      -
     40B  TRP      2.8    34.9    +      -       -      +
     41B  LYS      4.2     1.6    -      -       -      -
     42B  PHE*     3.6    31.9    -      -       +      +
     45B  CYS*     4.7     4.9    -      -       -      -
     64B  CYS      3.4    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  LEU*     3.7    10.8    -      -       -      -
      2B  GLN      3.4    13.2    -      -       -      -
      3B  CYS*     2.0    46.2    -      -       -      -
     25B  ALA*     1.3    74.4    -      -       -      +
     27B  LEU*     1.3    60.3    +      -       -      +
     38B  LYS      3.5     2.0    -      -       -      -
     40B  TRP*     4.5     1.8    -      -       -      -
     62B  TYR      3.8     0.5    -      -       -      +
     63B  CYS*     3.2     7.6    -      -       -      +
     64B  CYS*     2.8    29.9    +      -       -      -
     66B  LYS      4.0     0.4    -      -       -      -
     68B  LEU      4.7     0.4    -      -       -      -
     69B  CYS*     3.7    22.2    -      -       -      -
     70B  ASN*     3.5    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  CYS*     1.3    75.0    -      -       -      +
     28B  ILE*     1.3    67.2    +      -       -      +
     29B  THR*     3.3    27.4    -      -       -      +
     36B  TYR*     5.4     1.6    -      -       +      +
     37B  ASN*     3.3     1.6    -      -       -      -
     38B  LYS*     2.8    40.9    +      -       +      +
     40B  TRP*     3.4    57.2    -      -       +      -
     50B  VAL*     4.4     8.5    -      -       +      -
     54B  LEU*     4.6     8.5    -      -       +      -
     61B  TYR*     3.9    12.8    -      -       +      -
     62B  TYR      3.4     5.8    -      -       -      +
     63B  CYS*     3.6    20.2    -      -       -      -
     70B  ASN*     3.0    11.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  LEU*     1.3    75.3    -      -       -      +
     29B  THR*     1.3    67.2    +      -       -      +
     30B  LYS*     5.1     1.1    -      -       +      -
     35B  VAL*     4.2     6.7    -      -       +      -
     36B  TYR      3.3     5.4    -      -       -      +
     37B  ASN*     3.0    13.9    -      -       -      +
     61B  TYR*     3.3     2.6    -      -       -      +
     62B  TYR*     2.9    62.3    +      -       +      +
     70B  ASN*     3.3    10.7    -      -       +      +
     71B  PHE      3.3    11.2    -      -       -      +
     72B  ASN*     2.6    60.6    -      -       -      +
     74B  GLN*     4.4     3.1    -      -       +      -
     75B  LEU*     3.9    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  LEU*     3.3    25.5    -      -       -      +
     28B  ILE*     1.3    79.2    +      -       -      +
     30B  LYS*     1.3    66.3    +      -       -      +
     31B  ALA*     4.0     3.9    +      -       +      +
     34B  GLN      3.9     0.3    -      -       -      +
     35B  VAL*     3.4     5.8    -      -       -      +
     36B  TYR*     2.9    37.2    +      -       +      +
     50B  VAL*     3.8     5.8    -      -       +      +
     54B  LEU*     4.0    14.5    -      -       +      +
     59B  LEU*     3.7    37.0    -      -       +      -
     60B  THR      3.2    17.0    -      -       -      +
     61B  TYR*     3.5     3.3    -      -       -      +
     75B  LEU*     4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  ILE*     5.1     0.9    -      -       +      -
     29B  THR*     1.3    73.9    -      -       -      +
     31B  ALA*     1.3    60.0    +      -       -      +
     32B  GLY      3.8     7.0    +      -       -      +
     34B  GLN      3.6     5.8    -      -       -      +
     35B  VAL*     4.3    19.3    -      -       +      -
     59B  LEU*     3.3     3.4    -      -       -      -
     60B  THR*     3.0    35.4    +      -       -      +
     72B  ASN*     3.0    39.1    +      -       -      +
     75B  LEU*     3.5    26.2    -      -       +      +
     76B  GLU*     2.9    44.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  THR*     4.0     2.4    +      -       +      -
     30B  LYS*     1.3    71.6    -      -       -      +
     32B  GLY*     1.3    63.9    +      -       -      +
     33B  LEU      3.3     0.7    +      -       -      -
     34B  GLN*     2.9    27.6    +      -       -      +
     36B  TYR*     4.4     5.8    -      -       +      -
     56B  GLU*     3.3    39.2    -      -       +      +
     58B  GLU      3.5    19.5    -      -       -      +
     59B  LEU*     3.8    10.1    -      -       +      -
----------------------------------------------------------
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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