Contacts of the helix formed by residues 789 - 794 (chain D) in PDB entry 2BKU
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.
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 ASP 789 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747D GLN* 5.0 3.6 - - - +
748D ILE* 4.6 6.4 - - - +
751D LEU* 5.7 1.9 - - - +
785D GLN* 2.9 18.0 + - + +
786D VAL 3.3 2.3 - - - +
788D GLU* 1.3 72.8 - - + +
790D PRO* 1.3 69.9 - - - +
791D GLN* 2.8 46.2 + - - +
792D LEU* 3.0 23.7 + - + +
793D TYR* 3.1 14.8 + - - -
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Residues in contact with PRO 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788D GLU 3.3 9.6 - - - +
789D ASP* 1.3 90.4 - - - +
791D GLN* 1.3 57.3 + - + +
793D TYR* 3.2 32.5 - - + +
794D SER* 2.5 44.1 + - - +
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Residues in contact with GLN 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744D LEU* 3.3 34.8 - - - +
747D GLN* 5.0 0.4 + - - -
748D ILE* 3.4 44.2 - - + +
752D GLU* 5.1 1.0 - - - +
789D ASP* 2.8 30.7 + - - +
790D PRO* 1.3 75.0 - - + +
792D LEU* 1.3 61.7 + - - +
794D SER* 4.3 3.1 - - - -
795D GLU* 4.0 17.3 - - - +
798D THR* 5.2 0.2 + - - -
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Residues in contact with LEU 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D ILE* 4.5 10.3 - - + -
751D LEU* 3.9 40.4 - - + -
752D GLU* 4.7 12.1 - - + +
782D PHE* 5.1 4.5 - - + -
785D GLN* 3.7 17.9 - - + +
786D VAL* 3.6 38.6 - - + +
789D ASP* 3.0 20.1 + - + +
791D GLN* 1.3 78.3 - - - +
793D TYR* 1.3 66.2 + - - +
794D SER 3.3 1.1 - - - -
795D GLU* 3.1 12.8 + - - +
798D THR* 3.2 34.1 - - + -
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Residues in contact with TYR 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D VAL* 3.2 13.9 - - - +
787D ALA 3.1 25.6 - - - -
788D GLU 3.6 6.5 - - - -
789D ASP 3.1 20.2 + - - -
790D PRO* 3.2 36.9 - - + +
792D LEU* 1.3 78.6 - - - +
794D SER* 1.3 69.9 + - - +
795D GLU 3.4 1.4 + - - +
799D SER* 2.4 30.2 + - - +
830D TYR* 4.0 15.7 - - + +
833D ARG* 4.0 17.0 - - - -
840D PHE* 3.1 24.2 - + + -
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Residues in contact with SER 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790D PRO* 2.5 32.2 + - - +
791D GLN* 4.3 3.8 + - - -
793D TYR* 1.3 87.7 - - - +
795D GLU* 1.3 66.6 + - - +
796D ASP* 3.4 2.4 + - - -
839D LEU* 5.8 4.2 - - - +
840D PHE* 4.3 10.5 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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