Contacts of the strand formed by residues 278 - 285 (chain A) in PDB entry 1MHP


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 ILE 278 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  ARG*     3.4    32.8    -      -       +      -
    238A  PHE*     4.2    18.2    -      -       +      -
    250A  LYS*     3.2    27.4    -      -       +      +
    252A  MET*     3.7    36.6    -      -       +      +
    273A  CYS*     3.0    28.9    +      -       +      +
    274A  GLU*     5.0     0.6    +      -       -      +
    276A  GLU*     3.8    15.9    -      -       +      +
    277A  ASN*     1.3    74.9    -      -       -      +
    279A  GLN*     1.3    64.4    +      -       -      +
    280A  ARG*     3.1    26.7    +      -       +      +
    308A  SER*     3.7     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  LYS*     3.0    44.9    -      -       +      +
    250A  LYS      2.9     9.7    +      -       -      +
    251A  VAL*     3.4    14.3    -      -       +      +
    252A  MET*     2.7    33.1    +      -       -      +
    277A  ASN*     3.6     2.4    +      -       -      +
    278A  ILE*     1.3    72.3    -      -       -      +
    280A  ARG*     1.3    55.3    +      -       -      +
    281A  PHE*     4.2    12.6    -      -       +      -
    308A  SER*     3.9     8.5    +      -       -      -
    309A  GLU      5.4     0.9    -      -       -      +
    314A  HIS*     3.7    21.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  ILE*     5.3     0.2    -      -       -      -
    252A  MET*     3.4    15.3    -      -       +      +
    254A  ILE*     4.6     5.2    -      -       +      -
    270A  ILE*     3.7    26.8    -      -       -      +
    273A  CYS*     3.8    19.1    -      -       -      +
    274A  GLU*     3.2    52.9    +      -       -      +
    278A  ILE*     3.1    37.6    +      -       +      +
    279A  GLN*     1.3    75.8    -      -       -      +
    281A  PHE*     1.3    63.4    +      -       -      +
    306A  ILE*     2.8    31.1    +      -       -      +
    307A  ALA*     3.4    16.1    +      -       -      -
    308A  SER*     3.0    44.8    +      -       -      +
    314A  HIS*     3.4    12.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  VAL*     3.9    30.5    -      -       +      -
    252A  MET      2.9     8.0    +      -       -      +
    253A  VAL*     3.3    15.4    -      -       +      +
    254A  ILE*     2.8    28.4    +      -       -      +
    279A  GLN*     4.2    14.1    -      -       +      -
    280A  ARG*     1.3    76.0    -      -       -      +
    282A  SER*     1.3    60.5    +      -       -      +
    283A  ILE*     5.2     0.9    -      -       +      -
    313A  LYS      3.7    11.0    -      -       -      -
    314A  HIS*     3.2    44.6    -      +       -      +
    316A  PHE*     4.4     9.4    -      +       +      -
    331A  LEU*     4.3    20.2    -      -       +      -
    334A  ARG*     4.0    15.5    -      -       +      -
    335A  ILE*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  ILE*     3.4     9.0    -      -       -      -
    280A  ARG      4.1     0.8    +      -       -      -
    281A  PHE*     1.3    74.6    -      -       -      +
    283A  ILE*     1.3    67.8    +      -       -      +
    303A  ILE*     2.9    38.7    +      -       -      +
    306A  ILE*     4.0    18.8    -      -       -      -
    307A  ALA*     3.4    14.9    -      -       -      +
    314A  HIS      3.0     5.0    +      -       -      +
    315A  PHE*     3.4     7.0    -      -       -      -
    316A  PHE*     3.0    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  PHE*     3.6    33.0    -      -       +      -
    253A  VAL*     4.2     5.8    -      -       +      -
    254A  ILE      2.8    15.8    +      -       -      +
    255A  VAL*     3.7    12.1    -      -       +      -
    256A  THR*     3.2    28.4    +      -       -      +
    281A  PHE      5.1     0.7    -      -       -      +
    282A  SER*     1.3    82.4    -      -       -      +
    284A  ALA*     1.3    65.8    +      -       -      +
    285A  ILE*     4.4     1.5    -      -       +      +
    303A  ILE*     4.0     3.2    -      -       -      +
    316A  PHE*     3.3    27.6    -      -       +      +
    318A  VAL*     3.9    24.0    -      -       +      -
    324A  LEU*     4.0    13.7    -      -       +      -
    327A  ILE*     4.6     3.6    -      -       +      -
    331A  LEU*     3.6    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  THR      3.4     3.4    -      -       -      -
    283A  ILE*     1.3    77.0    -      -       -      +
    285A  ILE*     1.3    64.8    +      -       -      +
    286A  LEU*     3.4     9.0    +      -       +      -
    299A  PHE*     3.8    13.0    -      -       +      -
    300A  VAL*     5.3     0.9    -      -       -      -
    303A  ILE*     3.7    30.5    -      -       +      -
    315A  PHE*     3.9    15.7    -      -       +      -
    316A  PHE      3.0     7.3    +      -       -      -
    317A  ASN*     3.7     3.9    -      -       -      +
    318A  VAL      3.0    24.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  ILE*     5.4     2.5    -      -       +      -
    165A  VAL*     6.3     0.4    -      -       +      -
    255A  VAL*     3.6    30.3    -      -       +      -
    256A  THR*     2.9    21.5    +      -       -      +
    257A  ASP*     3.4    31.6    -      -       +      +
    283A  ILE*     4.4     1.8    -      -       +      +
    284A  ALA*     1.3    73.2    -      -       -      +
    286A  LEU*     1.3    62.6    +      -       -      +
    287A  GLY*     3.5    13.0    +      -       -      +
    299A  PHE*     3.6     7.4    -      -       -      -
    318A  VAL*     3.7     5.8    -      -       +      -
    320A  ASP*     3.7     5.8    -      -       -      +
    321A  GLU*     3.5    45.1    -      -       -      +
    324A  LEU*     3.8    28.0    -      -       +      -
----------------------------------------------------------
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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