Contacts of the helix formed by residues 692 - 714 (chain B) in PDB entry 3QNF
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 MET 692 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687B MET* 4.0 31.0 - - + +
690B ARG* 3.4 33.1 + - + +
691B ASP* 1.3 81.9 - - - +
693B ASN* 1.3 68.2 + - - +
694B GLU* 3.1 3.6 - - - +
695B VAL* 4.4 7.9 - - + +
696B GLU* 3.1 23.9 + - - +
922B MET* 3.2 37.0 - - + -
926B PHE* 3.6 41.1 - - + -
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Residues in contact with ASN 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691B ASP* 4.6 3.7 + - - +
692B MET* 1.3 74.7 - - - +
694B GLU* 1.3 55.7 + - - +
696B GLU* 3.6 14.5 - - - +
697B THR* 2.8 53.1 + - - -
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Residues in contact with GLU 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B MET* 3.1 1.7 - - - +
693B ASN* 1.3 79.5 - - - +
695B VAL* 1.3 65.4 + - + +
697B THR* 4.1 3.0 - - - -
698B GLN* 3.0 39.9 + - - +
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Residues in contact with VAL 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B MET* 3.4 33.2 - - + -
692B MET* 3.6 8.9 + - + +
694B GLU* 1.3 78.5 - - + +
696B GLU* 1.3 66.8 + - - +
698B GLN* 3.4 9.6 + - - +
699B PHE* 2.9 22.9 + - - +
926B PHE* 3.4 37.0 - - + -
929B ILE* 4.5 3.6 - - + -
930B ARG* 3.7 30.1 - - + -
933B LEU* 3.7 13.0 - - + +
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Residues in contact with GLU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B TYR* 5.0 1.1 - - + +
687B MET* 3.5 31.4 - - + +
688B GLU* 3.5 28.9 - - + +
690B ARG 5.3 1.2 - - - +
692B MET 3.1 19.9 + - - +
693B ASN* 3.6 14.6 - - - +
695B VAL* 1.3 79.3 - - - +
697B THR* 1.3 70.0 + - - +
699B PHE* 3.2 2.3 + - - +
700B LYS* 3.0 57.7 + - + +
843B PRO* 6.0 0.9 - - - +
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Residues in contact with THR 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693B ASN* 2.8 39.5 + - - +
694B GLU* 4.1 3.6 - - - -
696B GLU* 1.3 80.2 + - - +
698B GLN* 1.3 59.8 + - + +
700B LYS* 3.4 9.1 + - - +
701B ALA* 2.9 29.7 + - + +
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Residues in contact with GLN 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B GLU* 3.0 37.1 + - - +
695B VAL* 3.8 12.0 - - - +
697B THR* 1.3 77.1 - - + +
699B PHE* 1.3 59.8 + - - +
701B ALA* 3.5 8.3 - - - +
702B PHE* 2.9 28.6 + - - +
930B ARG* 5.8 2.2 + - - +
933B LEU* 3.7 35.0 - - + +
934B GLN* 5.0 3.3 + - - -
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Residues in contact with PHE 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B LEU* 4.5 7.2 - - + -
680B LEU* 3.4 35.7 - - + -
683B MET* 3.6 39.0 - - + -
684B TYR* 3.8 26.5 - + + -
687B MET* 4.0 13.5 - - + -
695B VAL 2.9 18.4 + - - +
696B GLU 3.4 4.5 - - - +
698B GLN* 1.3 74.3 - - - +
700B LYS* 1.3 59.1 + - - +
702B PHE* 3.2 23.6 + + - -
703B LEU* 2.8 29.0 + - + +
929B ILE* 3.9 27.8 - - + -
932B TRP* 5.7 0.7 - + - -
933B LEU* 3.8 12.7 - - + +
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Residues in contact with LYS 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B TYR* 3.4 35.0 - - + -
688B GLU* 2.8 26.5 + - - +
696B GLU* 3.0 43.0 + - + +
697B THR* 3.8 6.7 - - - +
699B PHE* 1.3 71.4 - - - +
701B ALA* 1.3 66.1 + - - +
703B LEU* 3.7 7.5 - - - +
704B ILE* 2.9 29.6 + - - +
737B VAL* 6.3 0.8 - - - +
738B HIS* 3.4 35.5 + - + +
843B PRO* 5.0 6.9 - - - +
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Residues in contact with ALA 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B THR* 2.9 20.6 + - + +
698B GLN* 3.5 10.8 - - - +
699B PHE 3.3 0.2 - - - -
700B LYS* 1.3 77.4 - - - +
702B PHE* 1.3 52.5 + - - +
704B ILE* 3.4 4.6 + - - +
705B ARG* 2.8 37.3 + - - +
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Residues in contact with PHE 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B LEU* 4.5 2.2 - - + -
661B SER* 3.7 19.7 - - - -
662B LEU* 3.6 30.1 - - + -
680B LEU* 4.4 15.9 - - + -
698B GLN 2.9 18.1 + - - +
699B PHE* 3.2 32.1 + + - +
701B ALA* 1.3 73.8 - - - +
703B LEU* 1.3 65.4 + - - +
705B ARG* 3.1 6.0 + - - +
706B LEU* 2.7 60.6 + - + +
932B TRP* 3.7 25.6 - + - -
933B LEU* 4.2 7.4 - - + -
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B LEU* 4.4 4.5 - - + -
680B LEU* 3.8 35.2 - - + -
681B ILE* 4.1 14.6 - - + -
684B TYR* 3.5 35.4 - - + -
699B PHE* 2.8 22.8 + - + +
700B LYS* 3.7 6.7 - - - +
702B PHE* 1.3 79.3 - - + +
704B ILE* 1.3 63.3 + - + +
706B LEU* 3.4 5.9 + - + +
707B LEU* 3.2 40.3 + - + +
734B LEU* 4.5 15.0 - - + -
738B HIS* 5.3 1.6 - - - +
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Residues in contact with ILE 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B LYS 2.9 18.3 + - - +
701B ALA* 3.9 4.5 - - - +
703B LEU* 1.3 76.3 - - + +
705B ARG* 1.3 62.3 + - - +
707B LEU* 3.7 1.0 - - - +
708B ARG* 2.9 28.0 + - + +
711B ILE* 4.6 11.1 - - + +
734B LEU* 5.2 6.7 - - + -
735B ALA* 4.3 9.6 - - - +
738B HIS* 3.2 45.3 - - + +
740B TYR* 3.8 42.4 - - + -
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Residues in contact with ARG 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B LYS* 5.9 0.5 - - - +
701B ALA 2.8 23.0 + - - +
702B PHE* 3.6 7.0 - - - +
704B ILE* 1.3 72.4 - - - +
706B LEU* 1.3 66.0 + - - +
708B ARG* 3.6 19.5 + - - +
709B ASP 5.1 0.2 + - - -
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Residues in contact with LEU 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B SER 3.8 22.4 - - - +
662B LEU* 3.9 17.3 - - + +
664B LEU* 3.8 25.3 - - + +
665B LYS* 3.4 48.7 + - + +
680B LEU* 4.0 21.1 - - + -
702B PHE* 2.7 35.0 + - + +
703B LEU* 3.4 9.0 - - + +
705B ARG* 1.3 80.8 - - - +
707B LEU* 1.3 63.0 + - + +
709B ASP* 4.9 2.6 + - - +
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Residues in contact with LEU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B LEU* 4.8 17.3 - - + +
673B VAL* 4.1 26.9 - - + +
677B LEU* 3.0 35.7 - - + -
703B LEU* 3.2 21.8 + - + +
704B ILE 3.7 0.2 - - - -
706B LEU* 1.3 89.8 - - + +
708B ARG* 1.3 65.2 + - - +
709B ASP 3.3 2.5 - - - -
710B LEU* 2.9 22.5 + - + +
711B ILE* 3.0 27.2 + - + +
731B LEU* 3.7 16.6 - - + -
734B LEU* 3.9 9.6 - - + -
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Residues in contact with ARG 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B ILE* 2.9 19.3 + - - +
705B ARG* 3.6 16.8 - - - +
706B LEU 3.3 2.4 - - - -
707B LEU* 1.3 77.4 - - - +
709B ASP* 1.3 70.2 + - - +
711B ILE* 3.2 9.9 + - - +
712B ASP* 3.2 30.4 + - - +
740B TYR* 3.4 39.3 + - + +
742B PRO* 5.3 5.3 - - - +
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Residues in contact with ASP 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B LYS 4.9 13.2 - - - +
705B ARG 5.1 0.4 + - - -
706B LEU 4.9 2.5 + - - +
707B LEU 3.3 0.6 - - - -
708B ARG* 1.3 85.1 - - - +
710B LEU* 1.3 62.5 + - - +
712B ASP* 3.4 10.2 + - - +
713B LYS* 3.2 20.3 + - - +
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B GLU 3.1 28.0 - - - +
668B THR* 3.8 20.6 - - - +
673B VAL* 4.8 13.9 - - + -
707B LEU* 2.9 17.7 + - + +
709B ASP* 1.3 75.9 - - - +
711B ILE* 1.3 66.5 + - - +
713B LYS* 3.0 19.6 + - + +
714B GLN* 3.1 36.1 + - - +
727B LEU* 4.3 11.4 - - + -
731B LEU* 3.4 18.4 - - + -
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Residues in contact with ILE 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B ILE* 4.6 14.1 - - + +
707B LEU* 3.0 28.6 + - + +
708B ARG* 3.2 11.2 + - - +
710B LEU* 1.3 75.4 - - - +
712B ASP* 1.3 61.8 + - - +
714B GLN* 3.1 22.7 - - - +
716B TRP* 5.4 0.3 + - - -
731B LEU* 3.9 32.3 - - + +
732B LEU* 4.3 12.6 - - + +
734B LEU* 5.0 6.1 - - + -
735B ALA* 3.7 35.9 - - + +
740B TYR* 4.4 8.3 - - + -
743B CYS* 3.8 19.0 - - - -
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Residues in contact with ASP 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B ARG* 3.2 21.2 + - - +
709B ASP* 3.7 11.7 - - - +
710B LEU 3.2 0.2 - - - -
711B ILE* 1.3 72.1 - - - +
713B LYS* 1.3 60.1 + - - +
714B GLN 3.1 9.1 + - - +
740B TYR* 2.6 36.3 + - - -
742B PRO* 4.7 6.2 - - - +
743B CYS* 5.0 1.6 - - - -
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Residues in contact with LYS 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B ASP 3.2 12.1 + - - +
710B LEU* 3.0 19.8 + - + +
712B ASP* 1.3 75.3 - - - +
714B GLN* 1.3 62.2 + - - +
715B THR* 3.3 9.9 + - - +
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Residues in contact with GLN 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B LEU* 3.1 34.4 + - - +
711B ILE* 3.1 17.9 - - - +
712B ASP 3.1 6.0 - - - +
713B LYS* 1.3 76.6 + - - +
715B THR* 1.3 65.7 + - - +
716B TRP* 3.3 17.2 + - - -
724B GLU 4.4 4.0 + - - -
727B LEU* 4.6 5.1 - - - +
728B ARG* 3.5 62.4 - - + +
731B LEU* 3.6 9.4 - - + +
732B LEU* 4.0 10.8 - - + -
746B ARG* 4.9 1.4 + - - -
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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
------------------------------------------------------------
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