Contacts of the strand formed by residues 17 - 25 (chain C) in PDB entry 1PU5


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 17 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  ASN*     4.6     0.7    -      -       -      +
     15C  ASP*     4.1     1.4    -      -       -      +
     16C  PRO*     1.3    76.1    -      -       +      +
     18C  VAL*     1.3    66.9    +      -       -      +
     42C  SER      3.3     6.1    -      -       -      +
     43C  THR*     3.9    17.5    -      -       -      +
     47C  LEU*     4.5    13.7    -      -       +      -
    145C  LEU*     4.7     8.3    -      -       +      -
    152C  LEU*     2.8    21.8    +      -       +      +
    153C  GLY*     3.4    20.5    -      -       -      -
    154C  CYS      4.5     1.6    +      -       -      -
    155C  ILE*     6.0     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 18 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  ASN*     3.4    22.7    -      -       +      +
     11C  ASP      5.2     0.2    -      -       -      +
     12C  GLU*     4.1    18.4    -      -       +      +
     15C  ASP*     3.3    22.9    -      -       +      +
     16C  PRO      4.7     2.2    -      -       -      +
     17C  ALA*     1.3    81.5    -      -       -      +
     19C  ILE*     1.3    64.8    +      -       -      +
     20C  ARG*     3.5    42.4    -      -       -      +
     41C  GLY*     3.2     2.3    -      -       -      -
     42C  SER*     2.8    41.6    +      -       -      +
    155C  ILE*     5.8     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 19 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  TRP*     3.3    28.0    -      -       +      -
      9C  ASN*     2.9    29.0    +      -       -      +
     18C  VAL*     1.3    74.5    -      -       -      +
     20C  ARG*     1.3    65.5    +      -       -      +
     21C  SER      3.4    26.2    -      -       -      +
     22C  LEU*     4.1    12.6    -      -       +      -
     39C  VAL*     4.0    18.8    -      -       +      -
     40C  VAL      3.6     1.3    -      -       -      +
     41C  GLY*     4.1    11.4    -      -       -      -
    155C  ILE*     3.8    30.1    -      -       +      -
    901C  EPE      5.2     1.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 20 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  TRP*     3.6    12.2    -      -       -      -
      9C  ASN*     6.0     0.8    -      -       -      +
     12C  GLU*     6.1     2.8    -      -       -      +
     18C  VAL*     3.5    21.9    -      -       -      +
     19C  ILE*     1.3    79.9    +      -       -      +
     21C  SER*     1.3    60.3    +      -       -      +
     40C  VAL*     2.6    33.5    +      -       +      +
     41C  GLY*     4.6     3.4    -      -       -      -
     42C  SER*     3.5    24.9    +      -       -      +
    115C  THR*     6.1     0.9    -      -       +      -
    901C  EPE      4.8     8.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 21 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  MET*     4.6     5.2    -      -       -      +
      7C  TRP*     3.7     7.2    -      -       -      -
     19C  ILE*     3.4     4.7    -      -       -      +
     20C  ARG*     1.3    79.3    -      -       -      +
     22C  LEU*     1.3    63.4    +      -       -      +
     23C  THR*     5.8     4.0    -      -       -      -
     38C  SER*     5.6     1.2    +      -       -      -
     39C  VAL*     3.3     2.8    -      -       -      -
     40C  VAL*     2.9    51.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 22 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  PHE*     3.7    28.2    -      -       +      -
      7C  TRP*     3.3    43.4    +      -       +      +
     19C  ILE*     4.1    10.3    -      -       +      -
     21C  SER*     1.3    77.4    -      -       -      +
     23C  THR*     1.3    67.7    +      -       -      +
     24C  LEU*     5.7     0.2    -      -       +      -
     37C  LEU*     3.6    23.3    -      -       +      -
     38C  SER      3.3    18.4    -      -       -      +
     39C  VAL*     3.7    14.4    -      -       +      -
    155C  ILE*     5.5     4.5    -      -       +      -
    157C  ILE*     3.9    24.5    -      -       +      -
    901C  EPE      5.3     0.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 23 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  PHE*     4.1     4.9    -      -       -      -
     21C  SER*     5.8     2.9    -      -       -      -
     22C  LEU*     1.3    82.6    -      -       -      +
     24C  LEU*     1.3    61.8    +      -       -      +
     25C  GLU*     4.6     8.3    +      -       -      -
     36C  THR      4.2     1.7    +      -       -      -
     37C  LEU*     3.4    11.0    -      -       -      +
     38C  SER*     2.6    51.7    +      -       -      +
    120C  LYS*     4.0    20.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 24 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  PHE*     3.6    55.6    -      -       +      +
     22C  LEU*     6.5     0.2    -      -       +      -
     23C  THR*     1.3    77.5    -      -       -      +
     25C  GLU*     1.3    62.9    +      -       -      +
     26C  PRO      3.9     7.4    -      -       -      +
     27C  ASP*     4.9     2.1    -      -       -      +
     29C  ILE*     3.7    28.5    -      -       +      -
     35C  VAL*     3.0    37.0    -      -       +      -
     36C  THR      3.4     4.5    -      -       -      +
     37C  LEU*     4.5    15.3    -      -       +      -
    157C  ILE*     5.4     1.8    -      -       +      -
    159C  ALA*     4.7     4.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 25 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  THR*     4.6     6.7    +      -       -      -
     24C  LEU*     1.3    82.8    -      -       -      +
     26C  PRO*     1.3    73.7    -      -       +      +
     29C  ILE*     5.3     0.4    -      -       -      -
     35C  VAL*     3.3     8.6    -      -       -      +
     36C  THR*     2.7    47.6    +      -       -      +
    120C  LYS*     2.8    42.9    +      -       -      +
----------------------------------------------------------
 Back to top of page


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