Contacts of the strand formed by residues 6 - 15 (chain G) in PDB entry 1LNU


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 VAL 6 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  ALA*     5.6     1.8    -      -       +      +
      4G  ASP      3.8     3.1    +      -       -      +
      5G  HIS*     1.3    74.7    -      -       -      +
      7G  GLY*     1.3    69.2    +      -       -      +
      8G  THR*     3.8    11.0    +      -       -      +
     27G  PHE*     2.9    20.0    -      -       -      -
     28G  ASP*     3.1    31.2    +      -       -      +
     29G  GLY      5.2     1.3    -      -       -      +
     40H  GLU*     5.1     3.4    -      -       +      -
     41H  CYS      4.4     4.5    -      -       -      +
     42H  TYR*     3.9    37.7    -      -       +      -
     43H  PHE*     4.0     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 7 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6G  VAL*     1.3    75.7    -      -       -      +
      8G  THR*     1.3    61.4    +      -       -      -
      9G  TYR*     3.3    40.3    -      -       -      -
     27G  PHE*     3.6     5.8    -      -       -      -
     40H  GLU*     3.5     0.5    -      -       -      -
     41H  CYS      3.0    27.3    +      -       -      +
     43H  PHE*     3.2    13.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 8 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6G  VAL*     3.8    14.9    +      -       -      +
      7G  GLY*     1.3    70.1    -      -       -      -
      9G  TYR*     1.3    64.2    +      -       -      +
     11G  ILE*     3.5    24.5    -      -       +      -
     26G  GLU*     2.6    61.9    +      -       -      +
     27G  PHE*     5.2     0.3    -      -       -      -
     28G  ASP      5.5     0.3    +      -       -      -
     29G  GLY      5.9     0.3    +      -       -      -
    140G  VAL*     4.9     4.3    -      -       +      -
     38H  MET*     4.3    20.4    -      -       +      -
     40H  GLU*     4.2    20.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 9 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  GLY*     3.3    36.3    -      -       -      -
      8G  THR*     1.3    80.7    -      -       -      +
     10G  GLY*     1.3    62.6    +      -       -      +
     11G  ILE*     3.0     4.5    +      -       -      +
     25G  PHE*     3.0    36.8    -      +       +      +
     26G  GLU      4.0     1.3    -      -       -      -
     27G  PHE*     3.9     2.3    -      -       -      -
     32G  LEU*     3.8    13.2    -      -       +      -
      4H  GLN      4.7     2.5    -      -       -      +
      6H  ALA*     4.5     7.2    -      -       +      -
     38H  MET*     3.8     0.5    -      -       -      -
     39H  GLY*     2.6    42.6    +      -       -      +
     41H  CYS*     4.0    20.6    -      -       -      -
     43H  PHE*     4.2     9.1    -      +       -      -
    104H  VAL*     4.4     6.1    -      -       +      -
    105H  CYS*     4.7     0.2    -      -       -      -
    108H  ASN*     3.7    28.5    -      -       +      +
    113H  GLU*     2.9    40.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 10 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  TYR*     1.3    71.7    -      -       -      +
     11G  ILE*     1.3    66.4    +      -       -      +
     12G  SER*     2.9    16.8    +      -       -      -
     23G  TYR*     3.0    27.1    -      -       -      -
     24G  THR      3.8     0.2    -      -       -      -
     25G  PHE*     3.0    18.1    -      -       -      -
     63G  ASN*     3.8     0.7    +      -       -      -
      6H  ALA*     4.3    13.2    -      -       -      -
     37H  PHE*     3.5    15.7    -      -       -      -
     38H  MET*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 11 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  THR*     3.5    33.0    -      -       +      +
      9G  TYR      3.0     7.1    +      -       -      +
     10G  GLY*     1.3    72.7    -      -       -      +
     12G  SER*     1.3    59.2    +      -       -      +
     13G  VAL*     4.1    15.2    -      -       +      +
     22G  GLN      3.5     1.6    -      -       -      +
     23G  TYR*     3.3     5.9    -      -       -      -
     24G  THR*     2.8    56.3    +      -       -      +
     26G  GLU*     3.1    37.2    -      -       +      +
    140G  VAL*     3.6    18.6    -      -       +      -
    146G  PHE*     5.8     0.4    -      -       +      -
     36H  GLN*     4.7     4.9    -      -       -      +
     37H  PHE      3.1    13.0    -      -       -      +
     38H  MET*     4.1     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 12 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  GLY      2.9     7.0    +      -       -      -
     11G  ILE*     1.3    70.8    -      -       -      +
     13G  VAL*     1.3    62.1    +      -       -      +
     22G  GLN      3.7     3.8    -      -       -      -
     23G  TYR*     3.2    15.8    -      -       -      -
     63G  ASN*     2.6    27.3    +      -       -      +
     64G  ILE*     4.5     5.4    -      -       -      -
     67G  VAL*     3.1    31.1    -      -       -      +
     35H  TYR      3.8     0.7    -      -       -      +
     36H  GLN*     3.3     2.9    -      -       -      -
     37H  PHE*     2.6    39.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 13 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11G  ILE*     4.7    10.1    -      -       +      -
     12G  SER*     1.3    78.4    -      -       -      +
     14G  TYR*     1.3    70.5    +      -       -      +
     15G  GLN*     4.7     2.9    -      -       -      +
     20G  ILE      5.3     1.1    -      -       -      +
     21G  GLY*     3.3     3.5    -      -       -      -
     22G  GLN*     3.0    52.0    +      -       +      +
     64G  ILE*     4.3     4.0    -      -       -      +
     67G  VAL*     4.2     0.7    -      -       -      -
    116G  PRO*     4.3    16.2    -      -       +      -
    146G  PHE*     3.8    29.4    -      -       +      -
     34H  VAL*     4.2    16.4    -      -       +      -
     35H  TYR      3.3    11.0    -      -       -      +
     36H  GLN*     4.5    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 14 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13G  VAL*     1.3    76.6    -      -       -      +
     15G  GLN*     1.3    71.6    +      -       -      +
     16G  SER*     4.8     4.9    -      -       -      -
     19G  ASP*     2.6    55.2    +      -       -      +
     20G  ILE      3.1    17.3    -      -       -      -
     21G  GLY*     3.9     6.3    -      -       -      -
     64G  ILE*     4.1    17.0    -      -       +      -
     67G  VAL*     3.4    21.1    -      -       +      -
     68G  LYS*     2.7    56.2    -      -       +      +
     71G  LEU*     3.7    16.0    -      -       +      +
     34H  VAL*     3.5     2.1    -      -       -      +
     35H  TYR*     2.8    35.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 15 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13G  VAL*     4.7     3.9    -      -       +      +
     14G  TYR*     1.3    79.1    -      -       -      +
     16G  SER*     1.3    68.8    +      -       -      +
     17G  PRO*     3.5     7.6    -      -       +      +
     19G  ASP*     3.3    17.5    +      -       -      -
     20G  ILE*     2.8    37.7    +      -       +      +
     71G  LEU*     4.1     1.3    -      -       -      -
    115G  PRO*     3.5    25.3    -      -       -      +
    116G  PRO*     3.0    34.1    -      -       -      +
    117G  VAL*     3.3    27.7    -      -       -      +
    169G  TRP*     5.3     0.8    -      -       -      -
     32H  HIS*     5.7     3.0    -      -       -      +
     33H  PHE      3.0     5.4    -      -       -      +
     34H  VAL*     3.4    23.1    -      -       +      +
----------------------------------------------------------
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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