Contacts of the strand formed by residues 251 - 259 (chain A) in PDB entry 1L0N


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 ALA 251 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  LEU*     1.3    73.4    -      -       -      +
    252A  HIS*     1.3    63.7    +      -       -      +
    253A  VAL*     5.0     2.0    -      -       +      -
    324A  PHE*     3.9     0.5    -      -       -      +
    325A  VAL*     3.3     6.2    -      -       -      -
    326A  CYS*     2.9    36.6    +      -       -      +
    327A  ASP      5.1     0.4    -      -       -      +
    331A  ILE*     3.5    34.1    -      -       +      -
    425A  PHE      3.5     4.9    -      -       -      +
    427A  PRO*     3.4    23.5    -      -       +      +
    428A  ILE*     4.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  MET*     3.5    19.6    -      -       +      +
    146A  ARG*     3.8    21.2    +      -       -      +
    149A  VAL*     3.5    18.8    -      -       +      -
    250A  LEU      3.7     2.8    +      -       -      -
    251A  ALA*     1.3    77.6    +      -       -      +
    253A  VAL*     1.3    65.3    +      -       -      +
    323A  HIS*     3.0    31.5    -      +       -      -
    324A  PHE      3.6     1.8    -      -       -      -
    325A  VAL*     3.3    19.7    -      -       +      +
    424A  GLY*     3.4     0.9    -      -       -      -
    425A  PHE      2.8    36.5    +      -       -      +
    428A  ILE*     4.5     0.5    -      -       -      +
     42I  VAL      3.3    13.0    -      -       -      -
     43I  LEU*     3.2    40.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  VAL*     4.3     1.3    -      -       -      -
    251A  ALA*     5.0     1.8    -      -       +      -
    252A  HIS*     1.3    81.7    -      -       -      +
    254A  ALA*     1.3    70.4    +      -       -      +
    255A  ILE*     4.6     8.7    -      -       +      +
    322A  ALA      4.3     0.2    -      -       -      +
    323A  HIS*     3.2     7.6    +      -       -      -
    324A  PHE*     2.9    70.7    +      -       +      -
    331A  ILE*     4.2    12.3    -      -       +      -
    335A  MET*     5.0     3.8    -      -       -      -
    422A  VAL*     5.0     4.0    -      -       +      -
    423A  ALA      3.3     9.4    -      -       -      +
    424A  GLY*     4.7     2.9    -      -       -      -
    428A  ILE*     5.1     1.6    -      -       +      -
    431A  LEU*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  VAL*     3.8    19.7    -      -       +      +
    150A  PHE*     4.6     7.6    -      -       +      -
    153A  LEU*     3.5    29.7    -      -       +      +
    253A  VAL*     1.3    77.3    -      -       -      +
    255A  ILE*     1.3    60.4    +      -       -      +
    322A  ALA      3.6     7.6    -      -       -      +
    323A  HIS*     4.4    11.9    -      -       +      +
    423A  ALA      2.7    37.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  VAL*     4.7     9.0    -      -       +      -
    254A  ALA*     1.3    76.5    -      -       -      +
    256A  ALA*     1.3    65.7    +      -       -      +
    310A  PHE*     4.1     1.2    -      -       -      -
    321A  GLY*     3.3     1.7    -      -       -      -
    322A  ALA      3.0    38.5    +      -       -      +
    324A  PHE*     5.1     1.6    -      -       +      -
    335A  MET*     3.3    40.6    -      -       +      -
    338A  LEU*     3.8    16.6    -      -       +      -
    339A  GLN*     4.8     1.1    -      -       -      +
    342A  TRP*     3.6    20.2    -      -       +      -
    420A  PRO*     3.7    19.7    -      -       +      -
    421A  ALA      3.4     4.7    -      -       -      +
    422A  VAL*     4.0    10.3    -      -       +      -
    437A  ILE*     3.6    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LEU*     4.4     7.2    -      -       +      +
    236A  PHE*     3.7     1.3    -      -       -      -
    255A  ILE*     1.3    81.4    -      -       -      +
    257A  VAL*     1.3    63.4    +      -       -      +
    310A  PHE*     3.8    15.0    -      -       +      -
    319A  LEU*     4.1    11.2    -      -       +      -
    320A  LEU      3.0    31.4    -      -       -      +
    321A  GLY*     4.0     0.4    -      -       -      -
    342A  TRP*     5.1     1.1    -      -       -      -
    420A  PRO*     3.5     2.1    -      -       -      +
    421A  ALA*     2.8    41.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  PHE*     4.0     7.4    -      -       -      -
    256A  ALA*     1.3    77.1    -      -       -      +
    258A  GLU*     1.3    67.5    +      -       -      +
    318A  GLY      3.6     1.6    -      -       -      +
    319A  LEU*     3.7     1.7    -      -       -      -
    320A  LEU*     2.7    50.9    +      -       +      +
    342A  TRP*     5.5     2.5    -      -       +      -
    414A  TYR*     3.2    31.4    -      -       +      +
    415A  PHE*     4.0    15.3    -      -       +      -
    418A  GLN*     4.6     6.3    -      -       +      +
    419A  CYS      4.4    13.0    -      -       -      +
    420A  PRO*     4.6     4.5    -      -       +      -
    441A  MET*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  CYS      4.7     2.1    -      -       -      +
    236A  PHE*     3.3    51.3    +      -       +      +
    257A  VAL*     1.3    79.9    -      -       -      +
    259A  GLY*     1.3    72.5    +      -       -      +
    316A  ASP      4.9     1.7    -      -       -      +
    317A  THR*     3.0    24.4    +      -       -      +
    318A  GLY      3.2     5.8    -      -       -      +
    414A  TYR*     3.7     6.2    -      -       -      +
    419A  CYS      5.1     0.4    +      -       -      -
     24E  SER*     4.7     9.7    +      -       -      -
     25E  SER*     5.1     2.8    +      -       -      -
     26E  LYS*     3.3    54.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  VAL      3.4     1.8    +      -       -      -
    258A  GLU*     1.3    80.1    -      -       -      +
    260A  PRO*     1.3    72.7    -      -       -      +
    311A  ASN*     5.4     1.3    -      -       -      -
    312A  ILE      5.7     0.2    -      -       -      -
    316A  ASP      4.7     0.2    -      -       -      +
    317A  THR*     3.2     5.4    -      -       -      -
    318A  GLY*     2.6    38.9    +      -       -      -
    320A  LEU*     4.4    14.4    -      -       -      -
    414A  TYR*     4.2     5.8    -      -       -      -
     26E  LYS*     5.3     1.7    -      -       -      -
----------------------------------------------------------
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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