Contacts of the strand formed by residues 100 - 105 (chain A) in PDB entry 1LC7


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 100 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  ARG*     1.3   123.5    -      -       -      +
    101A  ALA*     1.3    61.1    +      -       -      +
    120A  CYS*     3.7     0.9    -      -       -      -
    121A  GLU*     3.3    29.8    +      -       +      +
    123A  ARG*     3.5    24.7    -      -       -      +
    146A  ASP*     2.7    43.7    +      -       -      +
    147A  LEU*     4.1    10.1    -      -       +      -
    148A  ASP*     2.9    36.6    +      -       -      +
    149A  CYS      3.4     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  PRO*     4.1     4.3    -      -       +      -
    100A  ARG*     1.3    75.2    -      -       -      +
    102A  MET*     1.3    60.9    +      -       -      +
    115A  LEU*     4.1    19.3    -      -       +      -
    120A  CYS*     3.4    18.1    -      -       -      -
    121A  GLU      3.0     6.9    +      -       -      -
    122A  ILE*     3.5     5.2    -      -       -      +
    123A  ARG*     2.8    27.4    +      -       -      +
    147A  LEU*     3.9     5.4    -      -       -      +
    149A  CYS*     3.3    24.9    -      -       +      +
    151A  PHE*     4.2     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ALA*     1.3    75.2    -      -       -      +
    103A  ILE*     1.3    77.7    +      -       -      +
    123A  ARG*     3.2    25.4    -      -       +      +
    124A  ARG      5.3     0.9    -      -       -      -
    125A  TRP*     3.9    24.2    -      -       +      +
    139A  ILE*     4.2     7.2    -      -       -      -
    142A  ALA*     3.8    30.3    -      -       +      +
    143A  LEU*     3.9    14.4    -      -       -      -
    147A  LEU*     3.9    16.4    -      -       +      +
    149A  CYS      2.9     9.8    +      -       -      +
    150A  LEU*     3.3    24.3    -      -       +      +
    151A  PHE*     2.9    28.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  MET*     1.3    81.7    -      -       -      +
    104A  VAL*     1.3    60.6    +      -       -      +
    105A  THR*     4.3    11.4    -      -       +      -
    111A  TYR*     4.2    21.1    -      -       +      -
    112A  GLY*     4.6    16.8    -      -       -      +
    115A  LEU*     3.7    28.3    -      -       +      -
    122A  ILE*     4.1    12.8    -      -       +      -
    123A  ARG      3.1     4.0    +      -       -      +
    124A  ARG*     3.5    33.4    -      -       +      +
    125A  TRP*     2.8    30.7    +      -       -      +
    151A  PHE*     3.9    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ILE*     1.3    80.6    -      -       -      +
    105A  THR*     1.3    65.6    +      -       -      +
    106A  PRO      3.5    11.3    -      -       -      +
    107A  GLY*     3.8     7.8    +      -       -      -
    111A  TYR*     5.7     3.5    -      -       -      -
    125A  TRP*     3.2    11.9    -      -       +      +
    127A  LEU*     3.5    40.6    -      -       +      -
    135A  LEU*     4.4     5.2    -      -       +      -
    139A  ILE*     4.0    20.2    -      -       +      -
    150A  LEU*     4.8     1.8    -      -       +      -
    151A  PHE      3.9     6.8    +      -       -      +
    152A  LEU*     3.6    32.1    -      -       +      -
    153A  CYS      6.1     0.7    -      -       -      +
    156A  ASN*     5.0     5.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ILE*     4.3    10.8    -      -       +      -
    104A  VAL*     1.3    77.3    -      -       -      +
    106A  PRO*     1.3    66.3    -      -       +      +
    107A  GLY      5.0     1.3    -      -       -      +
    124A  ARG*     3.9    34.5    -      -       +      +
    125A  TRP      3.0    10.4    +      -       -      -
    126A  SER*     3.8    15.6    +      -       -      -
    127A  LEU*     2.8    33.3    +      -       -      +
    329A  PRO*     3.7    27.2    +      -       +      +
    330A  GLY*     5.4     1.8    -      -       -      -
----------------------------------------------------------
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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