Contacts of the strand formed by residues 113 - 117 (chain L) 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 SER 113 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137H  SER*     5.3     7.0    -      -       -      -
    111L  ALA      3.8     2.3    +      -       -      -
    112L  PRO*     1.3    73.3    -      -       -      +
    114L  VAL*     1.3    60.0    +      -       -      +
    115L  PHE*     3.6    24.1    -      -       -      -
    134L  LEU      3.3     2.1    -      -       -      +
    135L  LEU*     3.6     0.2    -      -       -      -
    136L  ASN*     2.9    39.7    +      -       -      +
    137L  ASN*     6.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137H  SER*     3.7     4.1    +      -       -      -
    112L  PRO*     3.7    10.7    +      -       +      +
    113L  SER*     1.3    76.7    -      -       -      +
    115L  PHE*     1.3    76.7    +      -       -      +
    133L  CYS*     5.3     2.9    -      -       -      -
    134L  LEU      2.8     9.9    -      -       -      +
    135L  LEU*     4.5     4.7    -      -       +      -
    193L  CYS      5.5     0.7    -      -       -      +
    195L  VAL*     3.6    39.9    -      -       +      -
    200L  LEU*     5.5     0.2    -      -       +      -
    204L  VAL*     4.0    20.0    -      -       +      -
    206L  LYS*     3.0    51.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 115 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134H  LYS      3.5     8.3    -      -       -      +
    135H  SER*     3.6    24.9    -      -       -      -
    136H  THR      4.2     0.9    -      -       -      -
    137H  SER*     4.0    21.8    -      -       -      -
    140H  THR*     4.5    14.1    -      -       -      -
    142H  ALA*     3.4    33.2    -      -       +      -
    188H  THR*     4.6     7.9    -      -       +      -
    113L  SER*     3.6    35.9    -      -       -      -
    114L  VAL*     1.3    83.2    -      -       -      +
    116L  ILE*     1.3    60.1    +      -       -      +
    117L  PHE*     4.4     6.7    -      -       +      -
    132L  VAL      3.8     0.3    -      -       -      +
    133L  CYS*     3.4     3.5    -      -       -      +
    134L  LEU*     2.7    64.4    +      -       +      +
    136L  ASN*     4.0    12.1    -      -       +      -
    206L  LYS*     4.4     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 116 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134H  LYS*     3.3    39.0    +      -       +      +
    135H  SER*     3.6    10.2    +      -       -      -
    115L  PHE*     1.3    75.4    -      -       -      +
    117L  PHE*     1.3    64.0    +      -       -      +
    118L  PRO*     4.0     0.7    -      -       -      +
    131L  VAL*     4.3     5.2    -      -       +      -
    132L  VAL      3.4     7.9    -      -       -      +
    147L  TRP*     3.8    23.8    -      -       +      -
    191L  TYR      3.9     5.8    -      -       -      +
    192L  ALA*     4.1     0.7    -      -       -      -
    193L  CYS*     3.9    10.8    -      -       -      -
    206L  LYS*     3.5    37.8    -      -       +      +
    207L  SER      4.1     4.9    -      -       -      +
    208L  PHE*     3.7    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 117 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  LEU*     3.3    56.0    -      -       +      +
    130H  ALA      3.6    13.0    -      -       -      -
    135H  SER*     3.0    28.9    -      -       -      -
    142H  ALA*     3.7    24.0    -      -       +      -
    143H  LEU*     3.8    13.0    -      -       -      -
    186H  VAL*     4.9     4.9    -      -       +      -
    115L  PHE*     4.4    12.6    -      -       +      -
    116L  ILE*     1.3    74.2    -      -       -      +
    118L  PRO*     1.3    69.5    -      -       +      +
    130L  SER      4.2     0.3    -      -       -      +
    131L  VAL*     3.5     8.3    -      -       -      +
    132L  VAL*     2.7    52.0    +      -       +      +
    134L  LEU*     4.5    15.5    -      -       +      -
    208L  PHE*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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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