Contacts of the strand formed by residues 220 - 227 (chain A) in PDB entry 4C02


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 220 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  LYS*     4.2     0.3    -      -       -      +
    217A  GLY      3.1    29.0    +      -       -      +
    218A  ARG      3.1     6.1    +      -       -      -
    219A  TYR*     1.3    83.7    -      -       -      +
    221A  GLU*     1.3    68.3    +      -       -      +
    236A  ILE      3.3     8.3    -      -       -      -
    237A  PHE      4.2     0.2    -      -       -      -
    238A  SER*     3.5    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  CYS*     4.3     5.6    -      -       -      -
    215A  GLY      3.4     9.0    -      -       -      +
    216A  LYS*     3.7    29.2    -      -       +      +
    219A  TYR*     3.9     2.8    -      -       -      -
    220A  GLY*     1.3    79.7    -      -       -      +
    222A  VAL*     1.3    62.8    +      -       -      +
    223A  TRP*     3.1    35.0    +      -       +      +
    234A  VAL      3.8     0.5    -      -       -      +
    235A  LYS*     3.3     4.7    -      -       -      +
    236A  ILE*     2.8    46.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  CYS*     3.7     2.8    -      -       -      -
    214A  VAL*     2.8    33.8    +      -       +      -
    215A  GLY*     2.9    18.2    +      -       -      +
    219A  TYR*     3.9    20.2    -      -       +      +
    221A  GLU*     1.3    76.2    -      -       -      +
    223A  TRP*     1.3    68.6    +      -       -      +
    233A  ALA*     4.4     4.3    -      -       +      -
    234A  VAL      3.4     7.6    -      -       -      +
    235A  LYS*     4.2    18.4    -      -       +      -
   1507A  TAK      3.7    53.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  LEU*     3.9    39.0    -      -       +      -
    211A  LEU      3.9     6.5    -      -       -      -
    212A  GLU*     3.2    34.8    -      -       -      -
    213A  CYS*     3.7    25.0    -      -       +      +
    214A  VAL*     4.3     4.0    -      -       -      -
    221A  GLU*     3.1    37.0    +      -       +      +
    222A  VAL*     1.3    81.7    -      -       -      +
    224A  ARG*     1.3    62.5    +      -       -      +
    233A  ALA*     3.4     5.5    -      -       -      +
    234A  VAL*     2.7    39.0    +      -       +      +
    236A  ILE*     3.8    24.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  LEU      3.9     0.3    -      -       -      -
    211A  LEU*     2.9    43.0    +      -       +      +
    212A  GLU*     2.7    53.6    +      -       +      +
    214A  VAL*     4.2     5.4    -      -       +      +
    223A  TRP*     1.3    75.7    -      -       -      +
    225A  GLY*     1.3    61.6    +      -       -      +
    231A  ASN*     2.9    28.7    +      -       -      +
    232A  VAL      3.7     3.4    -      -       -      -
    285A  TYR*     3.4    43.1    -      -       +      +
   1515A  EDO      4.3    11.7    +      -       -      -
   1516A  EDO      4.2    21.2    +      -       -      -
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Residues in contact with GLY 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  ILE*     4.4     4.5    -      -       -      -
    209A  THR      3.1    14.6    -      -       -      -
    210A  LEU*     4.2     4.7    -      -       -      -
    211A  LEU*     4.2     5.6    -      -       -      -
    223A  TRP      3.8     1.0    +      -       -      -
    224A  ARG*     1.3    74.1    -      -       -      +
    226A  SER*     1.3    60.1    +      -       -      -
    231A  ASN*     3.3    10.7    -      -       -      +
    232A  VAL*     2.9    40.4    +      -       -      -
    234A  VAL*     4.9     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  GLN      4.0     1.4    -      -       -      +
    208A  ILE*     3.4     7.1    -      -       -      +
    209A  THR*     2.7    41.3    +      -       -      -
    211A  LEU*     3.8    20.0    -      -       -      -
    225A  GLY*     1.3    75.8    -      -       -      -
    227A  TRP*     1.3    60.6    +      -       -      +
    228A  GLN      4.1     0.7    +      -       -      -
    229A  GLY*     3.5    25.5    +      -       -      -
    230A  GLU      3.5     8.3    +      -       -      -
    231A  ASN*     5.2     1.6    -      -       -      -
    232A  VAL*     4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  SER      3.4    23.1    -      -       -      -
    180A  LEU*     3.5    43.1    -      -       +      -
    183A  LEU*     3.7    26.7    -      -       +      -
    204A  VAL*     3.7    31.4    -      -       +      +
    207A  GLN*     2.8    46.9    +      -       +      +
    208A  ILE*     4.1     9.6    -      -       +      -
    226A  SER*     1.3    72.4    +      -       -      +
    228A  GLN*     1.3   103.9    +      -       +      +
    229A  GLY      3.2     1.1    -      -       -      -
    230A  GLU*     2.9    36.8    +      -       -      +
    232A  VAL*     4.6     4.4    -      -       +      +
   1110B  EDO      4.3     4.7    -      -       -      -
----------------------------------------------------------
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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