Contacts of the strand formed by residues 469 - 475 (chain K) in PDB entry 1LWU


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 GLN 469 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276K  ARG*     3.6     6.5    -      -       -      +
    277K  VAL*     3.4    28.9    -      -       +      +
    333K  ASP      4.3     0.9    -      -       -      +
    334K  MET*     2.9     8.1    -      -       -      +
    335K  SER*     2.7    56.9    +      -       -      +
    467K  MET*     3.3     4.5    -      -       -      +
    468K  ARG*     1.3   114.3    +      -       -      +
    470K  MET*     1.3    60.3    +      -       -      +
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Residues in contact with MET 470 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274K  GLN*     3.9     6.1    -      -       -      +
    275K  ASN*     3.3     0.6    -      -       -      -
    276K  ARG*     2.5    44.9    +      -       +      +
    332K  PHE*     4.5     9.4    -      -       -      -
    333K  ASP      3.4     7.4    +      -       -      +
    334K  MET*     4.0    27.4    -      -       -      -
    432K  PRO*     3.5    36.3    -      -       +      -
    455K  VAL*     3.5    29.8    -      -       +      -
    456K  VAL      4.4     7.4    -      -       -      +
    457K  TRP*     3.8    25.6    -      -       +      -
    467K  MET*     4.0     9.6    -      -       +      -
    469K  GLN*     1.3    75.1    -      -       -      +
    471K  ALA*     1.3    69.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 471 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272K  VAL*     4.8     2.0    -      -       +      -
    274K  GLN*     3.1    16.2    -      -       -      +
    275K  ASN*     3.2    18.8    -      -       +      +
    331K  LEU      3.7     0.9    -      -       -      +
    332K  PHE*     3.3    10.0    -      -       -      +
    333K  ASP*     3.0    34.4    +      -       +      +
    470K  MET*     1.3    83.2    -      -       -      +
    472K  MET*     1.3    61.3    +      -       -      +
    473K  LYS*     4.4    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 472 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272K  VAL*     3.5     3.5    -      -       -      -
    273K  VAL*     2.8    34.7    +      -       +      -
    274K  GLN*     2.8    31.4    +      -       +      +
    313K  TRP*     4.4    12.3    -      -       -      -
    330K  VAL*     3.6    24.7    -      -       +      -
    331K  LEU      3.9     2.7    -      -       -      -
    332K  PHE*     3.3    34.8    -      -       +      -
    349K  PHE*     3.6    29.2    -      -       +      -
    422K  TRP*     4.1    20.6    -      -       +      -
    423K  TRP*     4.3     8.1    -      -       +      -
    432K  PRO*     5.4     1.3    -      -       +      -
    471K  ALA*     1.3    73.2    -      -       -      +
    473K  LYS*     1.3    60.7    +      -       -      +
    474K  LEU*     4.5     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 473 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262K  ASP*     2.7    35.0    +      -       -      +
    265K  SER*     3.9     4.0    +      -       -      -
    270K  TRP*     3.4    30.2    -      -       +      -
    271K  THR      3.4     4.9    -      -       -      +
    272K  VAL*     3.8    21.3    -      -       +      -
    330K  VAL*     3.2     6.7    -      -       -      +
    331K  LEU*     2.9    43.4    +      -       +      +
    333K  ASP*     3.2    43.8    +      -       +      +
    471K  ALA*     4.4    13.2    -      -       +      +
    472K  MET*     1.3    79.9    -      -       -      +
    474K  LEU*     1.3    64.5    +      -       -      +
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Residues in contact with LEU 474 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231K  HIS*     2.8    18.8    +      -       +      -
    270K  TRP*     3.4     3.3    -      -       -      -
    271K  THR*     2.8    28.8    +      -       -      +
    273K  VAL*     3.4    24.5    -      -       +      -
    319K  VAL*     3.7    19.3    -      -       +      -
    322K  LEU*     3.7    21.5    -      -       +      -
    323K  THR*     4.6     1.3    -      -       +      -
    328K  GLN*     4.0    20.6    -      -       +      +
    329K  GLN      3.5     1.6    -      -       -      -
    330K  VAL*     3.9    14.6    -      -       +      -
    349K  PHE*     3.6    33.0    -      -       +      -
    472K  MET*     4.5     3.1    -      -       +      -
    473K  LYS*     1.3    81.6    -      -       -      +
    475K  ARG*     1.3    63.8    +      -       -      +
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Residues in contact with ARG 475 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231K  HIS*     3.1     1.1    -      -       -      -
    233K  GLU*     3.3    21.6    +      -       -      +
    266K  HIS*     3.2    24.2    +      -       -      +
    267K  GLY*     4.4     4.9    +      -       -      -
    268K  GLY      3.6    18.8    +      -       -      -
    269K  GLY      3.9     7.2    -      -       -      +
    270K  TRP*     3.3    33.7    -      -       +      +
    328K  GLN*     3.4     5.3    -      -       -      -
    329K  GLN*     2.6    67.6    +      -       +      +
    345K  GLN*     4.7     3.4    +      -       -      -
    474K  LEU*     1.3    77.0    -      -       -      +
    476K  PRO*     1.3    77.0    -      -       +      +
    477K  LYS      4.7     4.8    +      -       -      +
----------------------------------------------------------
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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