Contacts of the strand formed by residues 241 - 247 (chain E) in PDB entry 5HMG


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 ASP 241 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169E  PRO*     3.6     2.1    -      -       -      +
    170E  ASN      2.8    23.9    +      -       -      -
    206E  THR*     3.4    13.6    +      -       -      -
    207E  ARG*     2.9    49.3    +      -       -      +
    208E  ARG*     3.7    23.1    +      -       -      +
    237E  VAL*     3.8    10.7    -      -       +      -
    238E  LYS*     3.1    27.2    +      -       +      +
    239E  PRO      3.2     1.6    +      -       -      +
    240E  GLY*     1.3    79.9    -      -       -      +
    242E  VAL*     1.3    76.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 242 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221C  PRO*     4.2    12.2    -      -       +      +
    167E  THR*     3.1    28.3    -      -       +      +
    168E  MET      3.9     2.5    -      -       -      -
    169E  PRO*     4.0    20.2    -      -       +      -
    206E  THR*     3.1    29.3    -      -       -      +
    207E  ARG*     3.6    29.2    -      -       -      +
    237E  VAL*     4.1     4.0    -      -       -      -
    240E  GLY      4.7     0.4    -      -       -      +
    241E  ASP*     1.3    86.4    +      -       -      +
    243E  LEU*     1.3    60.1    +      -       -      +
    244E  VAL*     4.5     0.7    -      -       +      -
      2I  NAG      3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 243 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125E  PHE*     4.4     6.1    -      -       +      -
    167E  THR*     3.1     7.6    +      -       -      -
    168E  MET*     2.9    41.7    +      -       +      +
    178E  TYR*     3.7    40.8    -      -       +      -
    180E  TRP*     6.3     0.4    -      -       +      -
    204E  VAL*     3.5    29.4    -      -       +      -
    205E  SER      3.5     8.1    -      -       -      +
    206E  THR*     4.3     0.9    -      -       +      -
    235E  THR*     3.9    18.8    -      -       +      -
    237E  VAL*     4.0    13.6    -      -       +      +
    242E  VAL*     1.3    73.7    -      -       -      +
    244E  VAL*     1.3    60.3    +      -       -      +
    245E  ILE*     3.8    29.2    -      -       +      -
    254E  PRO*     5.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 244 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219C  SER*     3.3    30.7    -      -       -      +
    220C  ARG      4.6     0.7    -      -       -      -
    221C  PRO*     3.6    35.0    -      -       +      -
    165E  ASN*     4.3    13.2    -      -       -      +
    166E  VAL      3.3     9.0    -      -       -      +
    167E  THR*     3.4    24.2    -      -       -      +
    203E  THR      3.8     0.3    -      -       -      +
    204E  VAL*     3.5     2.9    -      -       -      +
    205E  SER*     2.9    33.8    +      -       -      +
    242E  VAL*     4.5     1.8    -      -       +      -
    243E  LEU*     1.3    71.7    -      -       -      +
    245E  ILE*     1.3    66.0    +      -       -      +
      1I  NAG      4.2    14.1    -      -       -      +
      2I  NAG      4.8     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 245 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125E  PHE*     4.1    14.4    -      -       +      -
    127E  TRP*     4.2     7.9    -      -       +      -
    164E  LEU*     3.9     2.4    -      -       +      +
    165E  ASN*     3.5     1.7    +      -       -      -
    166E  VAL*     2.9    40.6    +      -       +      +
    180E  TRP*     5.9     1.3    -      -       +      -
    202E  VAL*     4.9     0.9    -      -       +      -
    203E  THR      3.7     2.5    -      -       -      +
    204E  VAL*     4.1    21.5    -      -       +      +
    243E  LEU*     3.8    26.9    -      -       +      -
    244E  VAL*     1.3    76.6    -      -       -      +
    246E  ASN*     1.3    62.3    +      -       -      +
    251E  LEU*     3.9    34.8    -      -       +      -
    254E  PRO*     3.5    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 246 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218C  GLY*     4.0     8.6    -      -       -      -
    219C  SER*     3.5    33.0    +      -       -      +
    163E  VAL*     3.9    17.0    -      -       -      +
    164E  LEU      3.1    11.0    +      -       -      +
    165E  ASN*     2.9    28.4    +      -       -      +
    201E  ARG*     4.0    15.9    +      -       -      -
    202E  VAL*     3.7     0.7    -      -       -      +
    203E  THR*     2.8    41.5    +      -       -      +
    244E  VAL*     4.0     0.6    -      -       +      -
    245E  ILE*     1.3    74.1    -      -       -      +
    247E  SER*     1.3    67.4    +      -       -      +
      1I  NAG      6.0     0.4    -      -       -      +
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Residues in contact with SER 247 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161E  TYR*     4.2     1.8    +      -       -      -
    162E  PRO      3.7     0.9    -      -       -      +
    163E  VAL*     3.4     2.3    -      -       -      -
    164E  LEU*     2.7    45.8    +      -       -      +
    201E  ARG*     2.9    16.7    +      -       -      +
    202E  VAL*     3.8     3.9    -      -       -      +
    246E  ASN*     1.3    81.6    +      -       -      +
    248E  ASN*     1.3    56.6    +      -       -      +
    249E  GLY*     2.9    25.8    +      -       -      -
    251E  LEU*     3.7    33.6    -      -       -      +
----------------------------------------------------------
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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