Contacts of the strand formed by residues 62 - 70 (chain B) in PDB entry 1LEG


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 PHE 62 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     3.6    24.7    -      -       +      -
     94A  THR*     4.1     0.9    -      -       +      -
     96A  GLN*     3.4    22.0    -      -       -      -
     29B  GLN      2.9    24.3    +      -       -      -
     30B  PHE*     2.8    53.9    +      -       +      +
     31B  HIS*     3.3    30.1    -      +       -      -
     33B  PRO*     3.7    33.9    -      -       +      -
     54B  MET*     3.4    34.5    -      -       +      -
     55B  SER      3.7     2.9    -      -       -      -
     56B  PHE*     3.8    11.2    -      +       -      -
     60B  TRP      3.9     1.1    -      -       -      -
     61B  SER*     1.3    70.7    -      -       -      +
     63B  TYR*     1.3    63.0    +      -       -      +
    990B  PO4      4.3     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  GLU*     2.8    39.6    +      -       +      -
     26B  TYR*     3.4    23.1    -      +       +      +
     27B  VAL      3.4     6.1    -      -       -      -
     28B  THR*     3.3    22.7    -      -       +      -
     29B  GLN*     3.5    23.8    +      -       +      +
     30B  PHE*     4.6     0.7    -      -       -      -
     53B  ASP      4.1     1.3    -      -       -      +
     54B  MET*     3.2     6.9    -      -       -      +
     55B  SER*     2.9    47.9    +      -       -      +
     56B  PHE*     4.5     0.9    -      -       -      -
     57B  SER*     3.6    36.9    -      -       -      -
     61B  SER*     3.6     9.4    -      -       -      -
     62B  PHE*     1.3    81.6    -      -       -      +
     64B  ILE*     1.3    64.1    +      -       -      +
    990B  PO4      5.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  MET*     5.0     4.0    -      -       +      -
     35A  ARG*     6.2     0.9    -      -       -      +
     25B  CYS      4.0     0.7    -      -       -      +
     26B  TYR*     3.2     8.2    -      -       -      -
     27B  VAL*     3.0    38.4    +      -       +      +
     30B  PHE*     4.2    15.3    -      -       +      -
     35B  ILE*     5.2     0.4    -      -       +      -
     37B  ILE*     3.6    28.4    -      -       +      +
     51B  MET*     3.5    31.2    -      -       +      -
     52B  SER*     3.6     9.6    -      -       -      +
     53B  ASP      3.8     6.5    -      -       -      -
     54B  MET*     4.0    22.2    -      -       +      -
     63B  TYR*     1.3    77.5    -      -       -      +
     65B  LEU*     1.3    64.2    +      -       -      +
    990B  PO4      3.9    23.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  PRO*     3.8    11.2    -      -       +      +
    237A  GLY*     3.9    13.0    -      -       -      +
     10B  TYR*     3.7    21.1    -      -       -      +
     24B  ASN*     3.7    25.8    -      -       +      +
     25B  CYS      3.7    15.0    -      -       -      +
     26B  TYR*     3.9    12.1    -      -       +      -
     50B  GLU      3.5     0.5    -      -       -      +
     51B  MET*     3.2    10.6    -      -       -      +
     52B  SER*     2.8    59.1    +      -       -      +
     53B  ASP*     3.6    16.1    +      -       +      +
     64B  ILE*     1.3    75.4    -      -       -      +
     66B  ALA*     1.3    65.1    +      -       -      +
     67B  HIS*     3.7    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ASN*     3.4     0.7    -      -       -      -
     25B  CYS*     2.8    40.8    +      -       +      +
     37B  ILE*     4.0    21.1    -      -       +      +
     39B  MET*     3.8    11.9    -      -       +      +
     49B  VAL*     3.8    12.1    -      -       +      -
     50B  GLU      3.3     5.8    -      -       -      -
     51B  MET*     3.7    18.8    -      -       +      -
     65B  LEU*     1.3    75.4    -      -       -      +
     67B  HIS*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  GLY*     3.4    29.8    +      -       -      -
     22B  ILE*     4.1     9.5    -      -       +      +
     23B  LEU      3.1     7.9    -      -       -      +
     24B  ASN*     3.2    23.8    -      -       -      +
     39B  MET*     4.0     3.5    -      -       -      -
     48B  LYS*     4.1     1.5    +      -       -      -
     49B  VAL*     3.6     0.8    -      -       -      +
     50B  GLU*     2.9    79.3    +      -       -      +
     52B  SER*     3.3    30.5    +      -       -      -
     65B  LEU*     3.7    12.3    -      -       +      -
     66B  ALA*     1.3    72.5    -      -       -      +
     68B  THR*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ILE*     3.4     5.6    -      -       -      -
     23B  LEU*     2.8    43.0    +      -       +      -
     39B  MET*     4.0    17.0    -      -       -      -
     46B  ILE*     3.9    25.0    -      -       +      +
     48B  LYS*     2.7    39.2    -      -       -      +
     49B  VAL*     4.2    12.6    -      -       -      -
     67B  HIS*     1.3    78.1    -      -       -      +
     69B  GLU*     1.3    69.4    +      -       -      +
     70B  PHE*     5.0     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  PRO*     6.5     0.4    -      -       +      -
     21B  ASN      3.4    11.7    -      -       -      +
     22B  ILE*     4.4    10.5    -      -       +      +
     46B  ILE*     5.8     0.3    -      -       -      +
     48B  LYS*     3.0    32.9    +      -       +      +
     50B  GLU*     5.0     0.7    -      -       -      +
     68B  THR*     1.3    87.1    +      -       -      +
     70B  PHE*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  SER*     4.1     2.9    -      -       -      -
     20B  PRO*     3.5     0.6    -      -       -      -
     21B  ASN*     2.7    54.9    +      -       +      +
     22B  ILE      3.4    24.2    -      -       -      -
     23B  LEU*     3.4    33.0    -      -       +      -
     46B  ILE*     6.2     0.4    -      -       +      -
     68B  THR*     4.5     3.8    -      -       +      +
     69B  GLU*     1.3    78.1    -      -       -      +
     71B  THR*     1.3    59.6    +      -       -      +
     72B  PRO*     3.7    19.3    -      -       +      -
     78B  TYR*     3.4    40.6    -      +       +      +
     95B  TRP*     3.5    44.4    -      +       -      -
----------------------------------------------------------
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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