Contacts of the strand formed by residues 39 - 44 (chain K) in PDB entry 1IBL


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 PRO 39 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    683A    G      4.0     0.4    -      -       -      +
    684A    A      2.6    60.0    +      -       +      +
    685A    G      3.1    24.7    -      -       -      +
    706A    A      4.0    11.2    -      -       +      +
    707A    C      3.7    12.6    -      -       +      +
     31K  THR*     3.9    25.6    -      -       +      -
     32K  ILE      3.5     6.1    -      -       -      +
     33K  THR*     3.3     3.5    -      -       -      +
     37K  GLY      3.4     8.3    -      -       -      +
     38K  ASN*     1.3    82.8    -      -       -      +
     40K  ILE*     1.3    60.3    +      -       -      +
     41K  THR      4.8     2.9    -      -       -      +
     42K  TRP*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 40 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685A    G      3.9    15.4    -      -       -      +
    686A    U      5.0     0.2    +      -       -      -
     14K  VAL*     3.8    27.4    -      -       +      -
     32K  ILE*     2.8    12.4    +      -       +      +
     33K  THR      3.7    23.1    -      -       -      +
     34K  ASP*     4.0     8.7    -      -       +      +
     38K  ASN      3.4     0.6    +      -       -      -
     39K  PRO*     1.3    75.9    -      -       -      +
     41K  THR*     1.3    83.8    +      -       +      +
     72K  ALA*     4.2     7.6    -      -       +      -
     75K  TYR*     3.4    46.6    -      -       +      -
     77K  MET*     3.4    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 41 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685A    G      5.2     4.5    -      -       -      -
    686A    U      5.6     7.2    -      -       -      +
     31K  THR*     3.5     2.8    -      -       -      +
     32K  ILE*     2.7    34.7    +      -       -      +
     39K  PRO*     3.6     2.0    -      -       -      -
     40K  ILE*     1.3   100.7    -      -       +      +
     42K  TRP*     1.3    60.0    +      -       -      +
     68K  ALA*     3.5     9.6    +      -       -      -
     71K  LYS*     3.7    31.9    -      -       +      +
     72K  ALA*     3.4    23.7    +      -       -      +
     75K  TYR*     4.3    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 42 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685A    G      3.5    19.0    +      -       -      -
    686A    U      2.9    37.5    +      -       -      +
    687A    A      3.7    21.5    -      -       -      -
    688A    G      3.6    13.9    -      -       -      -
    704A    A      3.3    30.1    -      -       -      -
    705A    U      3.9    20.2    +      -       -      -
    706A    A      4.7    12.1    -      +       -      +
     29K  ILE*     5.4     5.4    -      -       +      -
     30K  VAL      3.5    11.4    -      -       -      +
     31K  THR*     3.8    18.2    -      -       +      +
     32K  ILE      4.6     0.2    -      -       -      +
     39K  PRO*     6.2     0.4    -      -       +      -
     41K  THR*     1.3    77.3    -      -       -      +
     43K  SER*     1.3    81.0    +      -       -      +
     44K  SER*     4.0     9.6    -      -       -      -
     47K  VAL*     3.1    27.9    -      -       +      +
     68K  ALA*     4.7     5.2    -      -       -      -
     71K  LYS*     3.8    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 43 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  ILE*     3.5     2.8    -      -       -      +
     30K  VAL*     2.9    31.2    +      -       -      +
     42K  TRP*     1.3    81.6    -      -       -      +
     44K  SER*     1.3    73.4    +      -       -      +
     47K  VAL*     3.4    13.4    -      -       -      +
     48K  ILE*     4.4     0.3    -      -       -      +
     64K  ALA*     3.3    31.0    +      -       -      -
     67K  ASP*     3.1    25.6    +      -       -      +
     68K  ALA*     3.6    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 44 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    688A    G      3.4     0.7    +      -       -      -
    689A    C      2.4    30.5    +      -       -      -
     28K  THR      3.6     7.2    -      -       -      -
     29K  ILE*     3.7    18.4    -      -       -      -
     42K  TRP*     4.0     7.4    -      -       -      -
     43K  SER*     1.3    79.3    +      -       -      +
     45K  GLY*     1.3    62.6    +      -       -      +
     46K  GLY      2.6     4.3    +      -       -      -
     47K  VAL*     2.7    30.0    +      -       -      +
     48K  ILE*     3.2    14.9    +      -       -      +
     64K  ALA*     3.6    11.1    -      -       -      +
----------------------------------------------------------
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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