Contacts of the strand formed by residues 116 - 122 (chain D) in PDB entry 3U8M


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 116 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  TYR      5.4     3.4    +      -       -      -
    143C  TRP*     4.0     2.4    -      -       -      -
     36D  ILE*     4.5     0.5    -      -       -      +
     51D  VAL*     3.8    12.1    -      -       -      +
     52D  PHE      3.5     4.0    +      -       -      -
     53D  TRP*     3.4    27.2    +      -       -      -
     97D  VAL*     3.8     1.0    -      -       -      +
     98D  LEU*     2.8    46.5    +      -       -      +
     99D  THR*     2.9    28.0    +      -       -      +
    114D  MET      3.8     1.2    +      -       -      -
    115D  PRO*     1.3    71.8    -      -       -      +
    117D  ILE*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 117 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  VAL      3.6     1.2    -      -       -      +
     51D  VAL*     3.2     4.1    -      -       -      -
     52D  PHE*     2.7    60.4    +      -       +      +
     54D  GLN*     3.9    37.0    -      -       +      +
     95D  PRO*     3.7    31.9    -      -       +      -
     96D  GLU      3.4     7.6    -      -       -      +
     97D  VAL*     4.5    11.4    -      -       +      -
     98D  LEU*     4.4     3.6    -      -       -      -
    115D  PRO*     4.2    20.2    -      -       +      +
    116D  SER*     1.3    78.5    +      -       -      +
    118D  ARG*     1.3    72.6    +      -       -      +
    119D  GLN*     4.1     2.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 118 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47C  GLU*     5.4     3.2    +      -       -      -
     92C  ILE*     2.8    47.2    +      -       -      +
     93C  SER*     5.1     0.2    -      -       -      -
    120C  ARG*     4.2    18.3    -      -       -      +
     39D  LEU*     3.1    30.6    -      -       -      +
     40D  GLU*     5.8     1.8    -      -       -      +
     49D  ASP*     2.9    43.1    +      -       -      +
     50D  VAL      3.3     6.3    -      -       -      +
     51D  VAL*     3.7    10.3    -      -       +      -
     93D  SER*     5.0     0.3    +      -       -      -
     94D  LYS      4.5     0.9    -      -       -      +
     96D  GLU*     2.9    55.9    +      -       +      +
     98D  LEU*     4.2     9.7    -      -       +      +
    117D  ILE*     1.3    72.1    -      -       -      +
    119D  GLN*     1.3    61.0    +      -       -      +
    120D  ARG*     5.2     7.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 119 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  ASP*     4.4     2.9    -      -       -      -
     50D  VAL      3.0    30.3    +      -       -      +
     52D  PHE*     3.9    12.7    -      -       +      -
     54D  GLN*     5.4     1.2    -      -       -      +
     88D  ALA*     4.3     8.8    -      -       -      +
     91D  ALA*     3.2    26.6    -      -       +      +
     93D  SER*     3.0    31.5    +      -       -      +
     95D  PRO*     3.2    35.8    -      -       +      +
    117D  ILE*     4.0     6.5    -      -       +      +
    118D  ARG*     1.3    76.0    -      -       -      +
    120D  ARG*     1.3    67.7    +      -       -      +
    121D  PHE*     3.7    27.1    -      -       +      -
     98E  LEU      5.7     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 120 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  GLU*     6.1     1.6    -      -       -      -
     47D  GLU*     5.7     3.8    -      -       +      -
     48D  VAL      3.1    17.7    -      -       -      +
     49D  ASP*     2.9    37.4    +      -       +      +
     91D  ALA*     3.4     6.9    -      -       -      +
     92D  ILE*     2.8    41.9    +      -       +      +
     93D  SER*     3.0    40.4    +      -       -      +
     94D  LYS      5.6     0.4    +      -       -      -
     96D  GLU*     5.7     3.2    +      -       -      +
    118D  ARG*     5.2     6.5    +      -       -      +
    119D  GLN*     1.3    74.5    -      -       -      +
    121D  PHE*     1.3    61.0    +      -       -      +
    118E  ARG*     5.2     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 121 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47D  GLU*     3.0     7.3    -      -       -      +
     48D  VAL*     2.8    48.5    +      -       +      +
     50D  VAL*     4.2    15.7    -      -       +      -
     52D  PHE*     3.9    22.0    -      +       -      -
     88D  ALA*     3.6    26.7    -      -       +      -
     90D  ASN*     3.5    14.8    -      -       -      +
     91D  ALA*     3.7    21.5    -      -       +      -
     92D  ILE*     4.2     5.4    -      -       -      -
    119D  GLN*     3.7    36.1    -      -       +      -
    120D  ARG*     1.3    74.5    -      -       -      +
    122D  SER*     1.3    61.3    +      -       -      +
    123D  CYS*     3.9     3.6    -      -       -      -
    138D  ILE*     3.6    43.3    -      -       +      -
    140D  ILE*     6.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 122 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  THR      5.8     0.2    -      -       -      -
     46D  ASN      3.3    10.2    +      -       -      -
     47D  GLU*     4.4     4.3    -      -       -      +
     90D  ASN*     3.1    34.3    +      -       -      +
     92D  ILE*     3.9    16.5    -      -       -      +
    121D  PHE*     1.3    70.2    -      -       -      +
    123D  CYS*     1.3    61.3    +      -       -      +
     37E  ASN*     2.9    31.9    +      -       -      -
     39E  LEU*     5.0     1.3    -      -       -      -
    166E  SER*     3.3    13.3    +      -       -      -
    168E  TYR*     4.3    10.2    -      -       -      +
----------------------------------------------------------
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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