Contacts of the strand formed by residues 229 - 238 (chain H) in PDB entry 5U07


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 GLY 229 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  TYR*     5.1     6.2    -      -       -      -
     11H  THR*     3.5     1.5    -      -       -      -
     12H  LEU*     2.9    32.7    +      -       -      +
    193H  THR*     4.4     7.0    -      -       -      -
    195H  HIS*     3.5    16.4    -      -       -      -
    228H  ALA*     1.3    77.2    -      -       -      +
    230H  THR*     1.3    65.6    +      -       -      -
    231H  PHE*     3.5    12.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 230 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  TYR*     6.4     1.1    -      -       +      -
     31G  GLY*     6.3     0.9    -      -       -      -
    301G  GLU*     5.5     4.0    -      -       +      +
      9H  ILE*     4.6    11.8    -      -       -      +
     11H  THR*     3.6    32.5    -      -       +      +
    193H  THR*     4.7     0.6    -      -       -      +
    194H  VAL*     3.0    40.4    +      -       -      +
    195H  HIS*     3.5    14.4    +      -       +      -
    229H  GLY*     1.3    70.5    -      -       -      -
    231H  PHE*     1.3    65.4    +      -       -      +
    310H  TYR*     4.1    25.1    -      -       +      +
    311H  THR*     4.2     9.2    -      -       +      +
    314H  ALA*     5.1     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 231 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8H  ALA      3.9     0.5    -      -       -      +
      9H  ILE*     3.6     4.9    -      -       -      +
     10H  GLN*     2.9    35.7    +      -       +      +
     12H  LEU*     3.3    35.7    -      -       +      -
     15H  SER*     4.6     9.6    -      -       -      -
     17H  ILE*     4.2     2.5    -      -       +      -
     36H  THR*     3.8    15.7    -      -       -      -
     37H  ARG      5.2     0.4    -      -       -      -
     38H  VAL*     3.3    33.7    -      -       +      -
     43H  TRP*     5.8     3.6    -      +       -      -
    191H  ALA*     4.4    17.0    -      -       +      -
    192H  PHE      3.3     6.1    -      -       -      +
    193H  THR*     3.2    39.3    -      -       +      -
    194H  VAL*     4.8     1.3    -      -       -      -
    227H  SER*     6.0     1.3    -      -       -      -
    228H  ALA      5.3     1.1    -      -       -      -
    229H  GLY*     3.5    12.1    +      -       -      -
    230H  THR*     1.3    73.9    -      -       -      +
    232H  TYR*     1.3    60.3    +      -       -      +
    233H  ARG*     4.1     7.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 232 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  HIS*     3.1    19.9    +      -       +      -
      8H  ALA      3.6     3.4    -      -       -      -
      9H  ILE*     3.6    19.5    -      -       +      -
    190H  HIS      4.5     0.7    -      -       -      +
    191H  ALA*     3.2    23.6    -      -       -      -
    192H  PHE*     2.7    41.6    +      +       +      +
    194H  VAL*     4.2    15.7    -      -       +      -
    230H  THR      3.6     1.6    +      -       -      -
    231H  PHE*     1.3    72.6    -      -       -      +
    233H  ARG*     1.3    73.1    +      -       -      +
    234H  TYR*     4.0    17.4    -      +       +      +
    295H  SER*     5.4     0.4    -      -       -      -
    296H  PHE*     3.0    31.1    +      -       +      +
    297H  ALA*     3.8    20.4    -      -       +      -
    300H  PHE*     3.7    14.6    -      +       +      -
    318H  LEU*     3.8    20.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 233 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  HIS*     3.4     4.2    -      -       -      -
      8H  ALA*     2.9    44.2    +      -       +      +
     10H  GLN*     2.7    45.7    +      -       -      -
     43H  TRP*     3.0    34.7    -      -       -      -
    188H  PHE*     5.2     3.6    -      -       +      -
    189H  ALA      5.8     0.2    -      -       -      -
    191H  ALA*     3.7    20.6    -      -       +      +
    231H  PHE*     4.4     9.0    -      -       +      +
    232H  TYR*     1.3    84.6    -      -       -      +
    234H  TYR*     1.3    62.3    +      -       -      +
    263H  PHE*     2.7    64.8    +      -       +      -
    264H  LEU*     4.6     1.0    +      -       -      +
    281H  PRO*     3.9    13.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 234 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276D  ALA*     3.5    32.3    -      -       +      -
    278D  MET*     4.6     2.7    -      -       +      +
      5H  ASP*     3.7    12.6    -      -       +      +
      6H  ILE      3.3     7.2    -      -       -      -
      7H  HIS*     3.5    35.9    -      +       -      -
    188H  PHE*     4.2     3.8    -      -       -      -
    189H  ALA*     3.2    38.0    +      -       +      +
    232H  TYR*     4.0    15.0    -      -       +      +
    233H  ARG*     1.3    76.8    -      -       -      +
    235H  ALA*     1.3    67.8    +      -       -      +
    236H  ASN*     2.3    39.6    +      -       -      -
    263H  PHE*     4.4     3.8    -      -       -      -
    293H  PRO*     3.4    11.3    -      -       -      +
    294H  ILE      3.6     8.8    +      -       -      -
    295H  SER*     3.5    27.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 235 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5H  ASP*     3.3     4.0    -      -       -      +
      6H  ILE*     2.9    44.2    +      -       +      +
    187H  GLN      3.2    12.8    -      -       -      +
    188H  PHE*     4.2     8.1    -      -       +      -
    234H  TYR*     1.3    81.4    -      -       -      +
    236H  ASN*     1.3    66.5    +      -       -      +
    237H  VAL*     5.6     0.2    -      -       -      -
    259H  PHE*     4.7     9.4    -      -       +      -
    263H  PHE*     3.6    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 236 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276D  ALA*     4.6     0.4    -      -       -      +
    278D  MET*     4.1     4.2    -      -       -      +
      3H  PHE*     5.5     3.8    -      -       +      -
      4H  VAL      3.5     3.1    -      -       -      +
      5H  ASP*     3.1    13.7    -      -       -      +
    186H  VAL*     3.2     9.0    -      -       -      +
    187H  GLN*     2.6    63.8    +      -       +      +
    234H  TYR*     2.3    42.8    +      -       -      -
    235H  ALA*     1.3    71.4    -      -       -      +
    237H  VAL*     1.3    70.9    +      -       -      +
    238H  ASN      4.2     0.9    -      -       -      +
    293H  PRO*     3.2    24.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 237 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3H  PHE*     3.5     2.7    -      -       -      -
      4H  VAL*     2.8    42.9    +      -       +      +
      6H  ILE*     6.3     1.1    -      -       +      -
    169H  LEU*     4.9     0.9    -      -       +      -
    185H  ALA      3.4     9.0    -      -       -      +
    186H  VAL*     3.7     9.2    -      -       +      -
    235H  ALA      5.6     0.4    -      -       -      -
    236H  ASN*     1.3    80.9    -      -       -      +
    238H  ASN*     1.3    61.0    +      -       -      +
    239H  LEU*     3.1    27.7    +      -       +      +
    242H  LEU*     4.1    11.9    -      -       +      -
    256H  VAL*     4.1    15.0    -      -       +      -
    259H  PHE*     3.6    33.0    -      -       +      -
    260H  LEU*     4.5     9.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 238 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2H  THR*     3.8     4.5    +      -       -      +
      3H  PHE*     3.2    41.4    -      -       +      -
    185H  ALA*     2.9    17.7    +      -       -      +
    187H  GLN*     6.1     3.6    -      -       +      +
    236H  ASN*     4.2     1.6    -      -       +      +
    237H  VAL*     1.3    69.0    -      -       -      +
    239H  LEU*     1.3    66.5    +      -       -      +
    240H  ASP*     2.5    29.7    +      -       -      +
    241H  ARG*     3.2    34.8    +      -       +      +
    242H  LEU*     3.1    18.5    +      -       -      +
----------------------------------------------------------
 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