Contacts of the strand formed by residues 23 - 29 (chain B) in PDB entry 1UIR


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 23 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  MET*     3.8     9.9    -      -       -      -
     21B  MET*     3.4     1.2    -      -       -      -
     22B  GLU*     1.3    82.5    -      -       +      +
     24B  VAL*     1.3    71.8    +      -       -      +
     25B  ILE*     3.8    34.8    -      -       +      +
     38B  PHE*     3.4     4.4    -      -       -      +
     39B  GLU*     2.9    46.0    +      -       +      +
     45B  LYS*     5.8     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  MET*     4.6    12.2    -      -       -      +
     21B  MET*     3.9    32.8    -      -       +      -
     23B  ARG*     1.3    84.5    +      -       -      +
     25B  ILE*     1.3    65.1    +      -       -      +
     26B  ALA      3.9    18.4    -      -       -      +
     27B  SER*     4.4    11.7    -      -       -      +
     36B  PHE*     6.0     2.2    -      -       +      -
     37B  LEU      3.9    11.2    -      -       -      +
     38B  PHE*     4.1     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  ARG*     3.8    30.7    +      -       -      +
     24B  VAL*     1.3    75.7    -      -       -      +
     26B  ALA*     1.3    60.9    +      -       -      +
     37B  LEU*     2.8    32.4    +      -       +      +
     38B  PHE*     4.4     9.0    -      -       -      -
     39B  GLU*     4.1    11.7    -      -       -      +
     45B  LYS*     3.5    46.2    -      -       +      +
    120B  HIS*     3.8    30.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  VAL*     3.7     6.1    -      -       -      +
     25B  ILE*     1.3    84.7    -      -       +      +
     27B  SER*     1.3    61.7    +      -       -      +
     35B  TYR*     4.2    14.8    -      -       +      +
     37B  LEU*     2.7    38.1    +      -       +      +
    116B  VAL*     5.0     1.6    -      -       +      -
    120B  HIS*     4.0    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  VAL*     4.4    12.6    -      -       -      +
     26B  ALA*     1.3    77.6    -      -       -      +
     28B  GLY*     1.3    58.8    +      -       -      +
     35B  TYR*     3.2    24.2    +      -       -      -
     36B  PHE*     3.9    20.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  SER*     1.3    76.0    -      -       -      +
     29B  LYS*     1.3    62.4    +      -       -      +
     34B  ASP*     3.5     5.7    -      -       -      +
     35B  TYR*     2.9    44.3    +      -       -      +
     36B  PHE*     5.3     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  GLY*     1.3    76.9    -      -       -      +
     30B  THR*     1.3    76.2    +      -       -      +
     31B  PRO*     5.5     3.4    -      -       -      -
     33B  GLN      3.6     6.3    -      -       -      +
     34B  ASP*     3.4    21.3    -      -       -      +
     35B  TYR*     3.6     4.3    -      -       -      -
    112B  GLU*     4.2     3.3    -      -       -      +
----------------------------------------------------------
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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