Contacts of the strand formed by residues 264 - 268 (chain A) in PDB entry 1L1T


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 264 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  MET*     4.7     2.0    -      -       -      +
    160A  LYS*     5.0     1.3    -      -       -      +
    164A  LEU*     4.5    19.0    -      -       +      +
    174A  ASN*     3.7    26.5    -      -       -      +
    260A  VAL*     3.4     9.7    -      -       -      +
    261A  VAL      3.1    18.1    +      -       -      +
    262A  ALA      4.0     7.4    -      -       -      +
    263A  GLY*     1.3    90.7    -      -       -      +
    265A  GLY*     1.3    67.0    +      -       -      +
    266A  THR*     2.9    13.5    +      -       -      -
     18C  HPD      2.9    37.1    +      -       -      +
     19C    G      2.8    53.1    +      -       -      +
     20C    T      4.1    27.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  LYS*     3.0     9.2    +      -       -      -
    174A  ASN*     3.0    26.7    +      -       -      +
    178A  ASP*     3.9     1.6    -      -       -      +
    258A  LYS*     4.0    18.8    -      -       -      -
    259A  THR      3.6     7.2    -      -       -      -
    260A  VAL*     5.3     2.4    -      -       -      +
    264A  ARG*     1.3    72.4    -      -       -      +
    266A  THR*     1.3    56.9    +      -       -      -
    267A  HIS*     4.1     6.5    -      -       -      -
     17C    A      4.0    15.1    +      -       -      -
     18C  HPD      5.5     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  LYS*     2.9    23.9    +      -       +      +
    178A  ASP*     3.5     7.2    -      -       -      +
    188A  PRO*     3.5    39.0    -      -       +      -
    257A  GLU      3.7     0.5    -      -       -      +
    258A  LYS*     3.2     7.9    -      -       -      +
    259A  THR*     2.9    39.3    +      -       -      -
    261A  VAL*     3.3    25.0    +      -       +      +
    264A  ARG      2.9    12.5    +      -       -      -
    265A  GLY*     1.3    70.5    -      -       -      -
    267A  HIS*     1.3    65.9    +      -       -      +
    268A  TYR*     4.1     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  ASN*     4.8     0.4    -      -       -      -
    178A  ASP*     2.8    31.1    +      -       -      +
    188A  PRO*     5.1     1.0    -      -       -      +
    241A  VAL*     3.3    40.0    -      -       +      +
    242A  TYR*     3.6    31.5    -      +       -      -
    243A  GLY*     3.3    22.6    +      -       -      -
    244A  ARG      4.4     0.2    -      -       -      -
    245A  GLN*     3.3    20.1    +      -       +      -
    256A  ILE*     4.5     1.3    -      -       +      -
    257A  GLU      3.4     6.3    -      -       -      +
    258A  LYS*     3.6    38.4    +      -       +      -
    265A  GLY*     4.1    11.2    -      -       -      -
    266A  THR*     1.3    74.3    -      -       -      +
    268A  TYR*     1.3    64.4    +      -       -      +
    273A  GLN*     4.6     1.4    +      -       -      +
     17C    A      5.4     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  LEU*     3.9    19.3    -      -       +      -
    188A  PRO*     4.1    21.3    -      -       +      -
    241A  VAL*     4.2     5.8    -      -       -      -
    256A  ILE*     3.5     8.0    -      -       -      +
    257A  GLU*     3.0    68.1    +      -       +      -
    259A  THR*     3.8    35.5    -      -       +      +
    266A  THR      4.1     5.8    -      -       -      -
    267A  HIS*     1.3    79.0    -      -       -      +
    269A  CYS*     1.3    67.6    -      -       -      +
    270A  PRO*     3.8    15.3    -      -       +      +
    273A  GLN*     3.2    23.3    -      -       -      +
----------------------------------------------------------
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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