Contacts of the strand formed by residues 223 - 230 (chain T) in PDB entry 3P71


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 223 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84T  PHE*     4.8     1.6    -      -       -      -
    193T  THR      3.2    13.2    -      -       -      +
    195T  LEU*     4.7     0.9    -      -       +      -
    216T  ALA      4.8     1.3    -      -       -      +
    220T  PHE*     3.7    28.5    -      -       +      +
    221T  GLU      4.2     0.2    -      -       -      -
    222T  ARG*     1.3    76.1    -      -       -      +
    224T  MET*     1.3    62.7    +      -       -      +
    273T  TRP*     3.6    22.0    -      -       +      -
    321T  THR*     3.5     4.7    -      -       -      -
    322T  LYS*     3.1    33.5    +      -       +      +
    329T  LEU*     4.3     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 224 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80T  LEU*     4.1    16.4    -      -       +      +
     84T  PHE*     3.8    37.2    -      -       +      -
    193T  THR      2.8     8.1    +      -       -      +
    194T  LEU*     3.4    10.7    -      -       +      -
    195T  LEU*     2.8    35.4    +      -       -      +
    223T  ALA*     1.3    75.2    -      -       -      +
    225T  PHE*     1.3    60.5    +      -       -      +
    226T  ILE*     3.8    18.2    -      -       +      -
    273T  TRP*     3.7     3.8    -      -       -      -
    319T  TRP*     3.8    35.9    -      -       +      -
    320T  ALA      3.4    13.5    -      -       -      +
    321T  THR*     4.0    10.1    -      -       +      -
    329T  LEU*     5.2     0.7    -      -       +      -
    332T  ILE*     4.1    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 225 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97T  LEU*     4.0    16.8    -      -       +      -
    195T  LEU*     3.4    25.1    -      -       +      -
    197T  ALA*     3.7    24.9    -      -       +      -
    201T  LEU*     4.3    10.1    -      -       +      -
    212T  LEU*     5.4     3.8    -      -       +      -
    213T  LEU*     3.7    36.1    -      -       +      -
    216T  ALA*     4.4    10.8    -      -       +      -
    224T  MET*     1.3    73.8    -      -       -      +
    226T  ILE*     1.3    81.3    +      -       -      +
    227T  ASN*     4.0    12.7    +      -       +      -
    268T  LEU*     4.7     3.8    -      -       +      +
    273T  TRP*     3.7    27.6    -      +       +      -
    319T  TRP*     3.1     7.3    -      -       -      +
    320T  ALA*     2.9    39.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 226 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77T  VAL*     4.2    20.2    -      -       +      -
     80T  LEU*     3.5    33.4    -      -       +      -
     81T  ILE*     4.2    20.0    -      -       +      +
    194T  LEU*     3.6    21.1    -      -       +      -
    195T  LEU      2.9    10.7    +      -       -      +
    196T  ILE*     4.3     9.0    -      -       +      -
    197T  ALA      2.8    29.2    +      -       -      +
    198T  GLU*     6.2     0.4    -      -       -      -
    224T  MET*     3.8    19.3    -      -       +      -
    225T  PHE*     1.3    76.3    -      -       -      +
    227T  ASN*     1.3    63.8    +      -       -      +
    228T  TYR*     4.7     1.3    -      -       +      +
    317T  LEU*     4.2    20.6    -      -       +      -
    318T  CYS      3.5     8.1    -      -       -      +
    319T  TRP*     4.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 227 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197T  ALA      3.5     9.1    -      -       -      +
    201T  LEU*     3.3    23.7    +      -       +      +
    225T  PHE*     4.0    15.4    +      -       +      -
    226T  ILE*     1.3    73.9    -      -       -      +
    228T  TYR*     1.3    62.3    +      -       -      +
    229T  GLU*     3.5    24.6    +      -       -      +
    264T  GLN*     3.9     9.1    +      -       -      -
    267T  ARG*     3.4    21.6    -      -       -      +
    268T  LEU*     5.0    10.5    -      -       +      +
    317T  LEU*     3.8     0.6    -      -       -      -
    318T  CYS*     2.8    57.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 228 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308C  PHE*     3.6    17.8    -      -       -      +
     69T  GLY      4.7     1.4    +      -       -      -
     73T  ARG*     3.4    61.1    -      -       +      +
     77T  VAL*     4.6     2.2    -      -       +      -
    197T  ALA      3.1     8.3    +      -       -      +
    198T  GLU*     4.2    15.0    -      -       +      -
    199T  CYS*     2.7    42.7    +      -       +      -
    200T  VAL      4.5     0.2    +      -       -      -
    226T  ILE*     4.1     1.6    -      -       +      +
    227T  ASN*     1.3    73.0    -      -       -      +
    229T  GLU*     1.3    65.3    +      -       -      +
    281T  MET*     3.6    33.9    -      -       +      +
    315T  TYR*     3.6    31.2    -      +       +      +
    316T  CYS      3.4    16.2    -      -       -      -
    317T  LEU*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 229 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199T  CYS*     4.7     8.1    -      -       -      +
    201T  LEU*     3.3    11.3    +      -       -      +
    202T  VAL*     3.1    29.5    +      -       +      -
    227T  ASN*     3.5    17.3    +      -       -      +
    228T  TYR*     1.3    80.7    -      -       -      +
    230T  GLN*     1.3    69.3    +      -       -      +
    257T  THR*     4.2     2.1    +      -       -      -
    258T  CYS*     3.5    17.0    -      -       -      -
    264T  GLN*     3.0    20.4    +      -       -      +
    267T  ARG*     2.7    28.2    +      -       -      -
    315T  TYR*     3.2    11.1    -      -       -      +
    316T  CYS*     2.8    39.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 230 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308C  PHE      4.0     5.3    +      -       -      -
    309C  LEU*     4.8     2.8    -      -       -      +
    199T  CYS*     4.4     8.2    -      -       -      -
    202T  VAL*     3.3    36.4    -      -       +      +
    203T  TYR*     5.3     0.4    +      -       -      -
    229T  GLU*     1.3    82.4    -      -       -      +
    231T  VAL*     1.3    59.5    +      -       -      +
    233T  MET*     3.7    27.4    -      -       +      -
    241T  MET*     3.0    36.5    -      -       +      +
    252T  LEU*     4.6     8.8    -      -       -      +
    258T  CYS*     3.3    15.0    -      -       -      -
    264T  GLN*     3.2    23.6    +      -       -      -
    314T  HIS      3.2     8.3    -      -       -      +
    315T  TYR*     3.5    22.2    +      -       +      +
----------------------------------------------------------
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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