Contacts of the strand formed by residues 171 - 174 (chain A) in PDB entry 3DLX


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 PRO 171 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  TYR*     2.7    30.5    +      -       -      +
    133A  VAL      3.3     6.4    -      -       -      +
    135A  LEU*     4.9     2.0    +      -       +      +
    169A  GLY      3.5     5.8    -      -       -      +
    170A  SER*     1.4    92.6    +      -       -      +
    172A  ILE*     1.3    60.3    +      -       -      +
    174A  TYR*     3.3    32.5    -      -       +      +
    180A  VAL*     3.8    27.4    -      -       +      -
    182A  ILE      3.8     4.3    -      -       -      +
    414A  MET*     4.3    23.1    -      -       +      -
    420A  VAL*     4.2     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  ARG*     3.8    31.9    -      -       -      +
    126A  TYR*     3.6     8.2    -      -       -      -
    132A  GLU*     3.3    15.3    -      -       +      -
    133A  VAL      2.8    42.4    +      -       -      +
    134A  GLU*     4.3    19.3    -      -       +      -
    135A  LEU      5.7     0.2    -      -       -      +
    170A  SER*     3.9     7.9    -      -       -      +
    171A  PRO*     1.3    76.7    -      -       -      +
    173A  LYS*     1.3    55.9    +      -       -      +
    182A  ILE*     2.7    28.3    +      -       +      +
    183A  ALA      4.0     4.0    -      -       -      +
    184A  SER*     3.8    30.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  TYR*     5.0     0.2    -      -       -      -
    129A  GLY*     3.4    25.0    +      -       -      +
    130A  GLU      5.5     2.2    -      -       -      -
    131A  LEU      4.4     7.9    -      -       -      +
    132A  GLU*     4.0    28.0    +      -       +      +
    172A  ILE*     1.3    81.7    -      -       -      +
    174A  TYR*     1.3    70.6    +      -       -      +
    180A  VAL*     3.4     7.0    -      -       -      +
    181A  ALA*     2.7    37.6    +      -       +      -
    182A  ILE*     3.0    39.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  TYR*     3.4    51.6    +      +       -      +
    127A  LEU*     3.7    42.8    -      -       +      +
    129A  GLY*     3.2    18.0    -      -       -      +
    171A  PRO*     3.3    25.0    -      -       +      +
    173A  LYS*     1.3    86.8    -      -       -      +
    175A  ASN*     1.3    62.6    +      -       -      +
    178A  GLY*     3.7    17.0    -      -       -      -
    179A  SER      3.3    13.2    -      -       -      +
    180A  VAL*     3.6    21.5    -      -       +      -
    181A  ALA*     4.0     5.4    -      -       -      +
    414A  MET*     4.9     1.6    -      -       -      +
    417A  GLY      5.5     2.4    +      -       -      -
    420A  VAL*     3.7    19.1    -      -       -      +
----------------------------------------------------------
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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