Contacts of the strand formed by residues 25 - 32 (chain H) in PDB entry 5IYB


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 VAL 25 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  ARG*     3.1    46.7    -      -       +      +
    552A  ASP*     3.9     6.3    -      -       +      -
    554A  PHE*     3.6    25.1    -      -       +      -
     22H  PHE*     3.9    12.6    +      -       +      +
     23H  ASP*     2.3    40.7    +      -       -      +
     24H  ARG*     1.3    69.1    -      -       -      +
     26H  SER*     1.3    65.6    +      -       -      +
     42H  ASP*     3.8    27.4    -      -       +      +
     43H  VAL      3.3    11.2    -      -       -      +
     44H  ASN*     5.1     0.2    -      -       -      -
    121H  LEU*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 26 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  ARG*     6.1     0.4    -      -       -      +
     15H  ILE*     3.9    22.4    +      -       -      +
     21H  LYS*     5.6     7.1    -      -       -      +
     22H  PHE*     5.8     3.4    -      -       -      +
     25H  VAL*     1.3    78.6    -      -       -      +
     27H  ARG*     1.3    62.2    +      -       -      +
     28H  LEU*     5.2     0.7    -      -       -      -
     42H  ASP*     3.4     5.0    -      -       -      -
     43H  VAL*     3.0    33.2    +      -       -      +
     45H  ILE*     3.6    33.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 27 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  ARG*     3.9    17.2    -      -       -      +
    622A  SER*     3.5    33.3    +      -       -      -
    623A  PRO*     5.0     4.7    -      -       -      +
    625A  ASP*     4.0    23.3    +      -       -      +
     15H  ILE      2.8    26.7    +      -       -      +
     17H  PRO*     3.4    28.2    -      -       +      +
     18H  GLU*     4.8    11.1    +      -       -      -
     26H  SER*     1.3    75.2    +      -       -      +
     28H  LEU*     1.3    64.7    +      -       -      +
     29H  HIS*     4.2     9.2    -      -       +      -
     40H  ILE*     3.7    30.9    -      -       +      +
     41H  LEU      3.6     5.4    -      -       -      +
     42H  ASP*     3.2    30.6    +      -       -      +
    122H  LEU*     4.8    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 28 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12H  VAL*     5.1     4.7    -      -       +      -
     14H  ASP      3.7     2.2    -      -       -      +
     15H  ILE*     3.7    35.4    -      -       +      -
     26H  SER      4.9     0.9    -      -       -      +
     27H  ARG*     1.3    75.3    -      -       -      +
     29H  HIS*     1.3    70.7    +      -       -      +
     30H  CYS*     3.9    15.0    -      -       -      -
     40H  ILE*     3.5     3.5    -      -       -      +
     41H  LEU*     2.7    41.0    +      -       +      +
     43H  VAL*     3.8    38.1    -      -       +      -
     45H  ILE*     5.0     2.5    -      -       +      -
     50H  VAL*     4.5    23.3    -      -       +      -
     56H  PHE*     4.4    21.8    -      -       +      -
    145H  MET*     4.9     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 29 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    622A  SER*     5.9     3.5    +      -       -      -
     12H  VAL*     3.6     1.0    -      -       -      -
     13H  LYS*     2.6    42.1    +      -       +      +
     14H  ASP*     2.7    33.4    +      -       +      +
     17H  PRO*     3.3    39.2    -      -       +      +
     27H  ARG*     4.2     5.6    -      -       -      -
     28H  LEU*     1.3    81.2    +      -       -      +
     30H  CYS*     1.3    56.4    +      -       -      +
     39H  LEU      3.9     1.6    -      -       -      -
     40H  ILE*     3.4    40.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 30 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  PHE*     4.6     6.1    -      -       +      -
     11H  ASP      3.1    13.5    -      -       -      +
     12H  VAL*     4.2     5.6    -      -       -      -
     13H  LYS*     4.0     6.2    -      -       -      +
     28H  LEU*     3.9    18.6    -      -       -      -
     29H  HIS*     1.3    80.3    -      -       -      +
     31H  GLU*     1.3    62.1    +      -       -      +
     38H  ASP*     3.6    11.1    -      -       -      +
     39H  LEU*     2.7    52.2    +      -       +      +
     56H  PHE*     3.7    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 31 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  PHE*     4.6     3.1    -      -       -      -
     11H  ASP*     2.8    50.3    +      -       +      +
     12H  VAL      5.6     0.2    -      -       -      +
     13H  LYS*     2.7    45.3    +      -       +      +
     30H  CYS*     1.3    74.2    -      -       -      +
     32H  SER*     1.3    65.9    +      -       -      +
     35H  PHE*     6.3     0.4    -      -       -      -
     37H  MET      4.0     7.6    -      -       -      +
     38H  ASP*     4.5     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 32 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8H  ASP*     3.5     6.3    -      -       -      -
     10H  PHE*     3.3    33.6    -      -       -      -
     11H  ASP*     5.7     0.2    -      -       -      -
     31H  GLU*     1.3    78.1    -      -       -      +
     33H  GLU*     1.3    59.9    +      -       -      +
     34H  SER*     3.7     4.6    +      -       -      -
     35H  PHE*     2.9    22.2    +      -       -      +
     36H  LYS      3.3     6.8    +      -       -      -
     37H  MET*     2.6    50.3    +      -       -      +
     38H  ASP*     4.7     0.4    -      -       -      +
     39H  LEU*     6.3     0.2    -      -       -      +
----------------------------------------------------------
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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