Contacts of the strand formed by residues 246 - 253 (chain A) in PDB entry 5IWM


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 ARG 246 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  GLY*     4.4     2.2    +      -       -      -
    223A  LEU*     3.5    29.6    -      -       +      +
    244A  ARG      3.9     0.2    +      -       -      -
    245A  SER*     1.3    71.1    -      -       -      +
    247A  ALA*     1.3    63.6    +      -       -      +
    248A  VAL*     5.4     7.3    -      -       +      +
    260A  VAL      3.9     0.2    -      -       -      +
    261A  VAL*     3.4     4.5    -      -       -      +
    262A  THR*     3.0    37.2    +      -       -      +
    263A  GLU*     2.8    55.4    +      -       +      +
    485A  ARG      5.4     3.0    +      -       -      -
    487A  GLU*     2.8    37.8    +      -       -      +
    489A  GLN*     5.5     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  SER*     3.5     5.9    +      -       -      +
    246A  ARG*     1.3    77.3    -      -       -      +
    248A  VAL*     1.3    68.4    +      -       -      +
    259A  ILE*     4.2     4.5    -      -       +      -
    260A  VAL      3.3     5.4    -      -       -      +
    261A  VAL*     3.8    21.5    -      -       +      -
    318A  LEU*     3.9    34.0    -      -       +      +
    322A  TYR*     3.9    10.1    +      -       +      +
    327A  LEU*     5.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  ARG*     5.4     8.7    -      -       +      +
    247A  ALA*     1.3    79.1    -      -       -      +
    249A  ILE*     1.3    68.5    +      -       -      +
    250A  GLU*     4.1    10.2    +      -       +      +
    258A  ARG      3.8     0.2    -      -       -      +
    259A  ILE*     3.4     7.0    -      -       -      +
    260A  VAL*     2.9    56.5    +      -       +      +
    262A  THR*     6.1     2.5    -      -       +      -
    318A  LEU*     6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  VAL*     1.3    80.4    -      -       -      +
    250A  GLU*     1.3    63.5    +      -       -      +
    257A  GLN*     4.0    24.6    +      -       +      +
    258A  ARG      3.5     7.6    -      -       -      +
    259A  ILE*     4.5    10.1    -      -       +      -
    314A  ALA*     3.8    24.9    -      -       +      +
    315A  SER*     3.3    43.5    -      -       -      +
    318A  LEU*     4.6    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  VAL*     5.1     9.0    -      -       +      +
    249A  ILE*     1.3    74.4    -      -       -      +
    251A  GLU*     1.3    64.1    +      -       +      +
    257A  GLN*     3.4     8.7    -      -       -      +
    258A  ARG*     2.8    80.7    +      -       +      +
    260A  VAL*     3.5    15.2    -      -       +      +
    303A  ARG*     3.3    14.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  GLU*     1.3    83.4    -      -       +      +
    252A  ARG*     1.3    60.3    +      -       -      +
    253A  GLY      3.7     3.6    -      -       -      +
    256A  ARG      3.6     9.0    -      -       -      +
    257A  GLN*     4.3     7.8    -      -       +      +
    258A  ARG*     4.3     7.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  GLU*     1.3    73.7    -      -       -      +
    253A  GLY*     1.3    59.1    +      -       -      +
    256A  ARG*     2.9    54.6    +      -       +      +
    257A  GLN      3.3    16.0    +      -       -      -
    258A  ARG*     3.7    28.2    +      -       -      +
    290A  THR*     3.4    15.2    +      -       -      +
    291A  ASP*     5.6     0.2    -      -       -      +
    307A  ASP*     3.3    39.8    +      -       -      +
    308A  VAL      2.7    26.3    +      -       -      -
    309A  ARG*     4.7     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  GLU*     3.7     4.6    -      -       -      +
    252A  ARG*     1.3    80.4    -      -       -      +
    254A  GLY*     1.3    63.7    +      -       -      -
    255A  GLY      3.4     2.9    -      -       -      -
    256A  ARG*     3.4    33.2    +      -       -      +
----------------------------------------------------------
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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