Contacts of the helix formed by residues 788 - 798 (chain F) in PDB entry 4OQB
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 788 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662F LYS* 4.3 13.5 - - + +
663F SER* 3.5 40.6 - - - +
787F LYS* 1.3 74.6 - - - +
789F PRO* 1.4 78.6 - - + +
790F ILE 3.3 0.2 - - - -
791F ASP* 3.1 12.7 + - - +
792F VAL* 3.0 25.4 + - - +
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Residues in contact with PRO 789 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F LYS* 5.8 3.8 - - + -
787F LYS 4.7 0.9 - - - +
788F ASP* 1.4 89.2 - - + +
790F ILE* 1.3 64.7 + - + +
792F VAL* 3.4 11.1 + - + +
793F ASN* 3.4 27.9 + - - +
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Residues in contact with ILE 790 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F SER* 4.2 16.2 - - - +
665F LEU* 4.5 6.7 - - + -
670F GLN* 4.0 47.8 - - + +
673F ILE* 3.4 32.0 - - + +
674F LYS* 4.4 19.7 - - + +
788F ASP* 3.3 1.0 - - - +
789F PRO* 1.3 80.9 - - + +
791F ASP* 1.3 59.1 + - - +
793F ASN* 3.4 7.2 + - - +
794F TYR 3.0 22.5 + - - -
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Residues in contact with ASP 791 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663F SER* 3.3 30.6 - - - -
664F LYS* 3.5 7.3 + - - +
665F LEU* 3.2 31.2 - - - +
787F LYS* 4.6 7.2 - - + -
788F ASP* 3.1 20.5 + - - +
790F ILE* 1.3 76.2 - - - +
792F VAL* 1.3 64.2 + - - +
794F TYR* 3.6 6.9 - - - +
795F GLU* 3.1 36.1 + - + +
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Residues in contact with VAL 792 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780F GLY 5.2 1.8 - - - +
781F GLY* 5.9 1.8 - - - -
782F SER 5.8 5.4 - - - +
787F LYS* 4.3 16.6 - - + +
788F ASP 3.0 22.5 + - - +
789F PRO* 3.6 11.2 - - + +
790F ILE 3.3 0.2 - - - -
791F ASP* 1.3 77.5 - - - +
793F ASN* 1.3 63.1 + - - +
795F GLU* 3.6 9.8 + - - +
796F LYS* 3.3 50.1 + - - +
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Residues in contact with ASN 793 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673F ILE* 4.0 23.0 - - + +
677F PHE* 3.9 20.6 - - + +
778F LEU* 3.4 32.1 - - - +
789F PRO* 3.4 14.9 + - - +
790F ILE* 3.4 8.9 + - - +
792F VAL* 1.3 76.8 - - - +
794F TYR* 1.3 63.4 + - - +
796F LYS* 3.5 22.1 + - - +
797F LEU* 3.4 23.9 + - - +
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Residues in contact with TYR 794 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665F LEU* 4.1 22.0 - - + -
669F VAL* 3.9 24.7 - - + -
673F ILE* 3.5 28.0 - - + +
790F ILE 3.0 10.8 + - - +
791F ASP* 3.6 11.7 - - - +
792F VAL 3.3 0.2 - - - -
793F ASN* 1.3 75.8 - - - +
795F GLU* 1.3 72.8 + - + +
797F LEU* 3.2 22.6 + - + +
798F LYS 3.8 2.8 + - - -
799F THR* 3.6 20.2 + - - +
800F ASP* 3.7 6.0 + - - -
801F ILE* 2.8 54.9 + - + -
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Residues in contact with GLU 795 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787F LYS* 5.4 8.4 - - - +
791F ASP* 3.1 26.4 + - + +
792F VAL* 4.0 8.6 - - - +
793F ASN 3.4 0.2 - - - -
794F TYR* 1.3 83.4 - - + +
796F LYS* 1.3 60.9 + - + +
798F LYS* 3.4 21.3 + - - +
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Residues in contact with LYS 796 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677F PHE* 5.2 2.7 - - + -
777F LEU* 3.2 54.1 + - + +
778F LEU* 2.8 29.3 + - - -
780F GLY 3.2 27.6 + - - -
781F GLY* 4.3 6.7 - - - +
792F VAL* 3.3 36.1 + - + +
793F ASN* 3.6 22.8 + - - +
794F TYR 3.2 0.6 - - - -
795F GLU* 1.3 76.4 - - + +
797F LEU* 1.3 62.1 + - - +
798F LYS* 3.2 12.0 + - - +
874F SER* 4.5 0.9 - - - -
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Residues in contact with LEU 797 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672F LEU* 6.2 0.4 - - + -
673F ILE* 4.2 17.3 - - + -
676F ILE* 4.0 25.4 - - + -
677F PHE* 3.6 21.1 - - + -
777F LEU* 5.3 0.7 - - + -
793F ASN 3.4 14.3 + - - +
794F TYR* 3.2 14.6 + - + +
796F LYS* 1.3 75.0 - - - +
798F LYS* 1.3 71.1 + - - +
799F THR* 3.4 11.9 - - - +
801F ILE* 4.6 17.7 - - + -
870F ALA 3.9 15.3 - - - +
873F LEU* 3.5 27.5 - - + +
874F SER* 3.4 22.6 - - - +
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Residues in contact with LYS 798 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777F LEU* 5.8 0.4 - - + -
794F TYR 3.8 1.8 + - - -
795F GLU* 3.4 16.8 + - - +
796F LYS* 3.2 16.7 - - - +
797F LEU* 1.3 79.2 - - - +
799F THR* 1.3 63.8 + - - +
841F ARG* 4.9 1.4 + - - +
842F GLU* 3.2 50.6 + - + +
873F LEU 4.6 0.7 - - - +
874F SER* 4.8 15.4 + - - +
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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