Contacts of the helix formed by residues 686 - 705 (chain F) in PDB entry 1XFV
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 686 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684F ASP* 2.8 2.1 - - + -
685F LYS* 1.3 81.7 - - - +
687F GLU* 1.3 66.8 + - - +
689F ALA* 3.2 18.4 - - - +
690F LYS* 3.3 13.4 + - - +
738F SER* 5.3 1.6 + - - -
739F LYS* 3.3 52.7 + - + +
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Residues in contact with GLU 687 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677F GLY 5.3 0.3 - - - +
679F TYR* 3.7 4.4 - - - +
680F LYS* 2.7 59.8 + - + +
682F SER* 3.9 14.8 - - - +
684F ASP* 3.0 16.3 + - + +
686F ASP* 1.3 75.4 - - - +
688F PHE* 1.3 56.7 + - - +
689F ALA 3.0 0.7 - - - -
690F LYS* 2.5 58.9 + - - +
691F LYS* 2.7 11.0 + - - -
739F LYS* 4.7 9.2 + - - +
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Residues in contact with PHE 688 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679F TYR* 6.0 0.4 - - - -
684F ASP 3.6 8.6 + - - +
685F LYS* 4.7 24.5 - - + +
687F GLU* 1.3 78.3 - - - +
689F ALA* 1.3 60.4 + - + +
691F LYS* 2.8 21.7 + - + +
692F GLU* 2.6 68.9 + - + -
21T LYS* 4.6 26.2 - - + -
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Residues in contact with ALA 689 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685F LYS 3.7 13.5 + - - +
686F ASP* 3.2 16.9 + - - +
687F GLU 3.0 0.2 - - - -
688F PHE* 1.3 84.8 - - - +
690F LYS* 1.3 64.3 + - + +
692F GLU* 3.5 4.5 + - - +
693F SER* 2.9 25.0 + - - -
738F SER* 5.7 3.1 - - - +
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Residues in contact with LYS 690 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678F VAL* 3.8 22.1 + - + +
679F TYR* 4.4 1.6 - - + -
686F ASP 3.3 6.7 + - - +
687F GLU* 2.5 56.9 + - - +
689F ALA* 1.3 71.4 - - - +
691F LYS* 1.3 68.0 + - - +
693F SER* 3.0 13.1 + - - -
694F VAL* 3.0 19.4 + - + +
735F VAL* 4.3 13.0 - - + +
738F SER* 4.0 19.1 - - - +
739F LYS* 4.5 12.9 - - + +
740F GLN 3.0 26.4 + - - +
741F ILE* 3.4 27.4 - - + +
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Residues in contact with LYS 691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679F TYR* 3.7 51.4 - - + +
687F GLU 2.7 9.1 + - - -
688F PHE* 2.8 27.3 + - + +
690F LYS* 1.3 71.2 - - - +
692F GLU* 1.3 63.5 + - - +
693F SER 2.5 13.9 + - - -
694F VAL* 2.5 21.1 + - - +
695F LYS* 3.2 8.4 + - + -
17T SER* 3.7 19.3 + - - -
18T LEU* 4.0 15.3 - - + +
20T ASP* 3.0 28.6 + - - +
21T LYS* 4.1 10.9 + - - +
23T GLY* 4.2 9.5 - - - -
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Residues in contact with GLU 692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688F PHE* 2.6 49.0 + - + +
689F ALA* 3.8 4.9 - - - +
691F LYS* 1.3 79.9 - - - +
693F SER* 1.3 56.7 + - - +
695F LYS* 3.6 25.4 + - - +
696F LYS* 3.0 37.3 + - + +
21T LYS* 5.1 12.6 - - - +
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Residues in contact with SER 693 (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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689F ALA 2.9 17.7 + - - -
690F LYS* 3.4 7.0 - - - -
691F LYS 2.5 7.9 + - - -
692F GLU* 1.3 73.3 - - - +
694F VAL* 1.3 62.9 + - - -
696F LYS* 3.1 20.7 - - - +
697F ILE* 3.2 13.6 + - - +
731F GLU* 2.4 33.2 + - - -
734F ASN* 4.8 1.7 + - - +
735F VAL* 3.1 21.3 + - - +
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Residues in contact with VAL 694 (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 PHE* 4.2 13.0 - - + -
667F LEU* 4.7 7.0 - - + -
678F VAL* 4.0 29.2 - - + -
679F TYR* 4.6 5.4 - - + -
690F LYS 3.0 14.8 + - - +
691F LYS* 2.5 20.3 + - - +
693F SER* 1.3 69.4 - - - +
695F LYS* 1.3 69.0 + - - +
696F LYS 2.9 1.6 - - - -
697F ILE* 2.7 22.1 + - - +
698F ALA* 2.7 15.3 + - - +
735F VAL* 5.4 5.6 - - + -
749F PHE* 4.5 11.2 - - + -
18T LEU* 3.1 35.2 - - + -
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Residues in contact with LYS 695 (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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691F LYS* 3.2 4.0 + - + +
692F GLU* 3.6 27.6 + - - +
694F VAL* 1.3 82.4 - - - +
696F LYS* 1.3 62.0 + - - +
698F ALA* 3.2 4.4 + - - +
699F GLY* 3.0 19.6 + - - -
18T LEU* 3.5 34.3 + - + +
19T PHE* 3.6 55.9 + - + +
21T LYS* 4.1 19.8 - - - +
31T GLU* 6.0 0.4 - - - +
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Residues in contact with LYS 696 (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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692F GLU* 3.0 26.8 + - + +
693F SER* 3.1 17.9 - - - +
694F VAL 2.9 0.4 - - - -
695F LYS* 1.3 78.0 - - - +
697F ILE* 1.3 58.4 + - - +
699F GLY* 3.3 1.8 + - - -
700F TYR* 3.2 61.8 + - + -
730F ASN* 5.2 2.4 + - - -
731F GLU* 2.8 39.5 + - + +
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Residues in contact with ILE 697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663F PHE* 4.0 11.9 - - + -
693F SER 3.4 15.3 - - - +
694F VAL* 2.7 17.3 + - - +
696F LYS* 1.3 67.9 - - - +
698F ALA* 1.3 52.2 + - - +
699F GLY 2.7 14.6 + - - -
700F TYR* 3.2 6.2 + - - +
701F LEU* 2.8 54.8 + - + +
728F ALA* 4.7 6.5 - - + +
731F GLU* 3.9 16.8 - - + +
732F ILE* 3.0 56.5 - - + +
735F VAL* 4.5 3.6 - - + -
749F PHE* 3.9 17.9 - - + -
752F LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 698 (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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660F SER* 3.8 23.4 + - - +
663F PHE* 4.3 17.2 - - + -
664F ILE* 4.8 5.2 - - + -
694F VAL 2.7 18.4 + - - +
695F LYS* 3.4 12.6 - - - +
697F ILE* 1.3 71.4 - - - +
699F GLY* 1.3 60.4 + - - +
701F LEU* 4.5 4.5 - - - -
702F SER* 3.8 8.5 + - - -
18T LEU* 4.2 10.1 - - + -
19T PHE* 4.1 21.2 - - + -
38T SER* 5.3 1.2 - - - -
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Residues in contact with GLY 699 (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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695F LYS 3.0 10.8 + - - -
696F LYS* 3.3 4.9 + - - -
697F ILE 2.7 3.0 - - - -
698F ALA* 1.3 77.2 - - - +
700F TYR* 1.3 67.3 + - - +
702F SER* 3.0 7.5 + - - -
703F ASP* 2.9 32.5 + - - +
19T PHE* 6.4 0.4 - - - -
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Residues in contact with TYR 700 (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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657F ILE* 5.7 0.2 - - - -
696F LYS* 3.2 43.9 + - + -
697F ILE* 3.2 5.3 + - - +
699F GLY* 1.3 72.4 - - - +
701F LEU* 1.3 57.8 + - - +
703F ASP* 2.5 40.9 + - + +
704F TYR* 2.9 11.5 + - - +
724F ARG* 4.1 11.2 - - - +
727F GLN* 3.3 61.4 + - + -
728F ALA* 3.3 18.2 - - + -
730F ASN* 5.6 1.1 - - + -
731F GLU* 4.2 13.7 - - + -
786F GLU* 4.9 4.2 + - - -
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Residues in contact with LEU 701 (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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657F ILE* 3.2 38.1 - - + -
658F PRO* 3.4 30.8 - - + +
659F THR 3.8 2.0 - - - +
660F SER* 4.1 12.0 + - - +
663F PHE* 3.7 37.5 - - + -
697F ILE* 2.8 36.4 + - + +
698F ALA* 4.6 0.9 - - - -
700F TYR* 1.3 73.5 - - - +
702F SER* 1.3 59.7 + - - +
704F TYR* 3.4 16.9 - - - +
705F TYR* 3.8 13.2 - - - -
728F ALA* 4.4 6.5 - - + +
732F ILE* 6.4 0.2 - - + -
752F LEU* 5.3 1.8 - - + -
756F ILE* 4.3 4.7 - - + -
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Residues in contact with SER 702 (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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660F SER* 3.5 26.9 - - - +
698F ALA 3.8 6.3 + - - -
699F GLY* 3.0 13.3 + - - -
700F TYR 2.8 0.6 + - - -
701F LEU* 1.3 75.1 - - - +
703F ASP* 1.3 73.5 + - - +
704F TYR 3.0 2.0 - - - -
705F TYR* 3.0 28.0 + - - +
706F ASN* 3.7 1.4 + - - +
37T ARG 5.8 2.0 - - - -
38T SER* 5.7 2.7 - - - -
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Residues in contact with ASP 703 (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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699F GLY* 2.9 28.6 + - - +
700F TYR* 2.5 27.2 + - - +
702F SER* 1.3 78.2 + - - +
704F TYR* 1.3 60.8 + - - +
706F ASN* 3.5 16.0 - - - +
724F ARG* 3.2 39.4 + - - +
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Residues in contact with TYR 704 (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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657F ILE* 3.4 50.5 - - + -
700F TYR 2.9 7.9 + - - +
701F LEU 3.4 13.9 - - - +
703F ASP* 1.3 79.8 - - - +
705F TYR* 1.3 86.4 + + - +
706F ASN 3.1 6.1 + - - -
709F ASN* 4.0 6.4 - - - +
721F SER* 4.0 23.6 + - - -
724F ARG* 4.1 15.5 + - + +
725F GLY* 4.2 13.2 - - - +
759F GLN* 2.4 32.6 + - + -
760F VAL* 6.3 1.1 - - + -
763F LEU* 3.5 5.9 - - + +
130T ILE* 3.9 10.7 - - - +
131T ASP* 3.0 31.1 + - + +
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Residues in contact with TYR 705 (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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656F THR* 3.0 33.1 - - - +
657F ILE* 3.1 24.9 + - + +
658F PRO 3.8 5.8 - - - -
659F THR* 3.8 24.0 - - + -
701F LEU 3.8 11.2 - - - -
702F SER* 3.0 15.0 + - - +
704F TYR* 1.3 100.9 - + - +
706F ASN* 1.3 60.1 + - - +
707F SER 3.9 1.9 + - - -
759F GLN* 5.3 0.2 + - - -
130T ILE* 4.3 20.4 - - + -
131T ASP* 5.9 0.7 - - - -
137T ASN* 4.6 7.9 + - - -
139T GLU* 3.6 26.0 - - + +
140T GLU* 4.6 12.3 - - + -
143T GLN* 4.4 24.5 + - + +
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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
------------------------------------------------------------
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