Contacts of the strand formed by residues 209 - 216 (chain D) in PDB entry 1MWA


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 HIS 209 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163D  VAL*     3.2    27.8    -      -       -      +
    164D  ASN*     2.9    48.5    +      -       -      +
    208D  ASN*     1.3    80.6    +      -       -      +
    210D  PHE*     1.3    75.9    +      -       -      +
    211D  ARG*     3.1    40.9    +      -       +      +
    240D  GLU*     3.9    14.5    +      -       +      -
    241D  ALA      4.0     6.7    +      -       -      -
    242D  TRP*     5.1    14.2    +      +       +      +
----------------------------------------------------------
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Residues in contact with PHE 210 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145D  LEU*     4.6     8.7    -      -       +      -
    161D  TRP*     4.8     8.3    -      +       +      -
    162D  TRP      3.5     2.2    -      -       -      -
    163D  VAL*     4.8     9.2    -      -       +      -
    196D  LEU*     4.4    19.3    -      -       +      -
    198D  VAL*     3.4    34.5    -      -       +      -
    202D  PHE*     4.8     7.0    -      +       -      -
    203D  TRP*     3.4    31.4    -      +       -      -
    208D  ASN*     3.0    31.2    -      -       -      -
    209D  HIS*     1.3    88.1    +      -       -      +
    211D  ARG*     1.3    74.0    +      -       -      +
    240D  GLU*     3.9     4.9    -      -       -      +
    241D  ALA*     3.6    40.8    +      -       +      +
    242D  TRP      4.1     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 211 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161D  TRP*     3.2    14.1    -      -       -      -
    162D  TRP*     2.7    67.5    +      -       +      +
    164D  ASN      4.2    11.9    -      -       -      -
    209D  HIS*     3.1    33.7    +      -       +      +
    210D  PHE*     1.3    88.7    -      -       -      +
    212D  CYS*     1.3    63.7    +      -       -      +
    213D  GLN*     5.6     7.3    -      -       -      +
    238D  SER*     4.9    14.1    +      -       -      -
    240D  GLU*     4.1    21.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 212 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  VAL*     4.0     8.1    -      -       -      -
    129D  LEU*     4.9     4.0    -      -       +      -
    147D  CYS*     2.0    53.4    -      -       +      -
    148D  LEU      4.5     3.1    -      -       -      -
    159D  LEU*     4.9     4.7    -      -       -      -
    160D  SER      3.2    11.7    -      -       -      +
    161D  TRP*     5.0     7.0    -      -       +      -
    162D  TRP*     4.0     1.6    -      -       -      -
    194D  SER*     5.3     0.2    -      -       -      -
    211D  ARG*     1.3    80.3    +      -       -      +
    213D  GLN*     1.3    68.9    +      -       -      +
    238D  SER*     3.4    20.4    -      -       -      -
    239D  ALA      3.3    21.8    +      -       -      +
    240D  GLU*     5.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 213 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158D  GLU      4.0     0.2    -      -       -      +
    159D  LEU*     3.2     8.3    -      -       -      +
    160D  SER*     3.1    31.2    +      -       -      -
    162D  TRP*     3.1    43.4    -      -       +      +
    211D  ARG*     5.6     6.8    -      -       -      +
    212D  CYS*     1.3    76.0    -      -       -      +
    214D  VAL*     1.3    69.2    +      -       -      +
    215D  GLN*     3.8     3.7    +      -       +      +
    236D  ASN*     3.0    40.4    +      -       +      +
    237D  ILE      4.1     9.6    -      -       -      +
    238D  SER*     4.6     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 214 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125D  PRO*     3.5    31.2    -      -       +      -
    127D  VAL*     3.5    22.7    -      -       +      -
    148D  LEU      3.4    12.3    -      -       -      +
    149D  ALA*     3.2    35.7    -      -       +      -
    157D  VAL*     4.1    17.5    -      -       +      -
    159D  LEU*     4.7     4.9    -      -       +      +
    213D  GLN*     1.3    74.5    -      -       -      +
    215D  GLN*     1.3    51.1    +      -       -      +
    216D  PHE*     2.5    23.2    +      -       -      +
    236D  ASN*     3.8    11.8    -      -       -      -
    237D  ILE      3.2    14.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 215 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40C  ARG*     4.2    14.0    +      -       -      +
    156D  HIS      3.6     6.6    -      -       -      +
    157D  VAL*     3.8     6.9    -      -       -      -
    158D  GLU*     3.2    40.3    +      -       -      +
    162D  TRP*     6.2     2.2    -      -       -      -
    213D  GLN*     3.8     6.1    +      -       +      +
    214D  VAL*     1.3    66.9    -      -       -      +
    216D  PHE*     1.3    59.6    +      -       -      +
    217D  HIS*     3.0    34.7    +      -       +      +
    236D  ASN*     4.2    19.7    -      -       -      +
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Residues in contact with PHE 216 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122D  VAL*     5.3     0.2    -      -       +      -
    123D  THR      3.8     5.6    -      -       -      -
    124D  PRO*     4.2     0.7    -      -       +      -
    125D  PRO*     3.2    39.9    -      -       +      -
    152D  PHE*     3.8     7.6    -      +       -      -
    154D  PRO*     3.3    45.5    -      -       +      -
    157D  VAL*     4.0     6.1    -      -       +      -
    214D  VAL      2.5     9.3    +      -       -      +
    215D  GLN*     1.3    71.0    -      -       -      +
    217D  HIS*     1.3    66.7    +      -       -      +
    218D  GLY*     3.7    13.9    +      -       -      -
    232D  PRO*     3.7    25.6    -      -       +      -
    233D  VAL      3.0    29.2    -      -       -      -
    234D  THR*     4.0    11.8    -      -       -      +
    235D  GLN*     3.1    41.8    +      -       +      +
    236D  ASN*     4.6     0.9    -      -       -      +
----------------------------------------------------------
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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