Contacts of the helix formed by residues 686 - 705 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684E ASP* 2.8 1.5 - - + -
685E LYS* 1.3 81.9 - - - +
687E GLU* 1.3 67.2 + - - +
689E ALA* 3.2 18.4 - - - +
690E LYS* 3.2 13.3 + - - +
738E SER* 5.3 0.9 + - - -
739E LYS* 3.3 52.7 + - + +
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Residues in contact with GLU 687 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677E GLY 5.2 0.5 - - - +
679E TYR* 3.7 4.4 - - + +
680E LYS* 2.7 59.8 + - + +
682E SER* 3.9 15.3 - - - +
684E ASP* 3.0 15.8 + - + +
686E ASP* 1.3 75.3 - - - +
688E PHE* 1.3 57.9 + - - +
689E ALA 3.0 1.3 - - - -
690E LYS* 2.5 60.0 + - - +
691E LYS* 2.7 11.2 + - - -
739E LYS* 4.7 9.2 + - - +
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Residues in contact with PHE 688 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679E TYR* 6.0 0.4 - - - -
684E ASP 3.6 8.4 + - - +
685E LYS* 4.8 24.2 - - + +
687E GLU* 1.3 78.3 - - - +
689E ALA* 1.3 60.4 + - - +
691E LYS* 3.1 21.2 - - + +
692E GLU* 2.6 68.2 + - + -
21S LYS* 4.5 27.4 - - + -
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Residues in contact with ALA 689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685E LYS 3.7 13.5 + - - +
686E ASP* 3.2 17.1 + - - +
687E GLU 2.9 0.4 + - - -
688E PHE* 1.3 84.8 - - - +
690E LYS* 1.3 64.6 + - + +
692E GLU* 3.5 5.2 + - - +
693E SER* 2.9 25.7 + - - -
738E SER* 5.8 2.7 - - - +
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Residues in contact with LYS 690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678E VAL* 3.8 22.6 + - + +
679E TYR* 4.4 1.3 - - + -
686E ASP 3.8 7.4 - - - +
687E GLU* 2.5 56.6 + - - +
689E ALA* 1.3 72.3 - - - +
691E LYS* 1.3 68.5 + - - +
693E SER* 3.0 12.8 + - - -
694E VAL* 3.0 19.4 + - + +
735E VAL* 4.3 13.8 - - + +
738E SER* 4.1 18.8 - - - +
739E LYS* 4.5 11.8 - - + +
740E GLN 3.0 25.6 + - - +
741E ILE* 3.4 28.0 - - + +
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Residues in contact with LYS 691 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679E TYR* 3.7 50.5 - - + +
687E GLU 2.7 10.7 + - - -
688E PHE* 2.8 26.9 + - + +
690E LYS* 1.3 70.0 - - - +
692E GLU* 1.3 62.0 + - - +
693E SER 2.5 13.7 + - - -
694E VAL* 2.5 20.0 + - - +
695E LYS* 3.2 9.1 + - + -
17S SER* 3.7 20.0 + - - -
18S LEU* 4.0 15.7 - - + +
20S ASP* 2.9 29.7 + - - +
21S LYS* 4.1 10.3 + - - +
23S GLY* 4.2 9.5 - - - -
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Residues in contact with GLU 692 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688E PHE* 2.6 48.8 + - + +
689E ALA* 3.8 5.4 - - - +
691E LYS* 1.3 78.6 - - - +
693E SER* 1.3 56.7 + - - +
695E LYS* 3.5 23.8 + - - +
696E LYS* 3.0 37.4 + - + +
21S LYS* 5.1 13.7 - - - +
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Residues in contact with SER 693 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689E ALA 2.9 18.5 + - - -
690E LYS* 3.4 6.5 - - - -
691E LYS 2.5 8.5 + - - -
692E GLU* 1.3 72.7 - - - +
694E VAL* 1.3 62.4 + - - -
696E LYS* 3.1 20.2 - - - +
697E ILE* 3.2 14.3 + - - +
731E GLU* 2.3 33.6 + - - +
734E ASN* 4.8 1.2 + - - +
735E VAL* 3.1 20.2 - - - +
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Residues in contact with VAL 694 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663E PHE* 4.2 13.4 - - + -
667E LEU* 4.8 7.6 - - + -
678E VAL* 4.0 29.6 - - + -
679E TYR* 4.6 6.1 - - + -
690E LYS* 3.3 14.8 - - - +
691E LYS* 2.5 16.7 + - - +
693E SER* 1.3 69.1 - - - +
695E LYS* 1.3 70.2 + - - +
696E LYS 2.8 1.1 - - - -
697E ILE* 2.7 22.7 + - - +
698E ALA* 2.7 15.0 + - - +
735E VAL* 5.4 5.4 - - + -
749E PHE* 4.5 10.8 - - + -
18S LEU* 3.1 34.5 - - + -
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Residues in contact with LYS 695 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691E LYS* 4.1 3.4 - - + +
692E GLU* 3.5 27.4 + - - +
694E VAL* 1.3 82.6 - - - +
696E LYS* 1.3 62.5 + - - +
698E ALA* 3.2 5.2 + - - +
699E GLY* 3.0 19.6 + - - -
18S LEU* 3.5 34.3 + - + +
19S PHE* 3.5 57.0 + - + +
21S LYS* 4.2 19.2 - - - +
31S GLU* 6.0 0.8 - - - +
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Residues in contact with LYS 696 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692E GLU* 3.0 26.5 + - + +
693E SER* 3.1 16.6 - - - +
694E VAL 2.8 0.2 - - - -
695E LYS* 1.3 78.0 - - - +
697E ILE* 1.3 58.2 + - - +
699E GLY* 3.3 1.8 + - - -
700E TYR* 3.2 61.1 + - + -
730E ASN* 5.2 2.4 + - - -
731E GLU* 2.8 39.3 + - + +
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Residues in contact with ILE 697 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663E PHE* 4.0 12.6 - - + -
693E SER 3.4 15.0 - - - +
694E VAL* 2.7 17.4 + - - +
696E LYS* 1.3 68.9 - - - +
698E ALA* 1.3 53.2 + - - +
699E GLY 2.7 14.4 + - - -
700E TYR* 3.2 6.2 + - - +
701E LEU* 2.8 53.9 + - + +
728E ALA* 4.7 7.2 - - + +
731E GLU* 3.9 17.3 - - + +
732E ILE* 3.0 55.6 - - + +
735E VAL* 4.6 3.4 - - + -
749E PHE* 3.9 17.9 - - + -
752E LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 698 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660E SER* 3.8 22.0 + - - +
663E PHE* 4.3 16.8 - - + -
664E ILE* 4.8 4.9 - - + -
694E VAL 2.7 18.0 + - - +
695E LYS* 3.5 12.3 - - - +
697E ILE* 1.3 71.7 - - - +
699E GLY* 1.3 60.0 + - - +
701E LEU* 4.5 4.5 - - - -
702E SER* 3.7 9.8 + - - -
18S LEU* 4.2 9.4 - - + -
19S PHE* 4.1 21.3 - - + -
38S SER* 5.2 1.2 - - - -
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Residues in contact with GLY 699 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695E LYS 3.0 10.6 + - - -
696E LYS* 3.7 4.7 - - - -
697E ILE 2.7 2.8 - - - -
698E ALA* 1.3 78.7 - - - +
700E TYR* 1.3 66.2 + - - -
702E SER* 3.0 7.9 + - - -
703E ASP* 2.8 31.1 + - - +
19S PHE* 6.4 0.4 - - - -
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Residues in contact with TYR 700 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657E ILE* 5.7 0.4 - - - -
696E LYS* 3.2 44.3 + - - -
697E ILE* 3.2 5.5 + - - +
699E GLY* 1.3 72.9 - - - +
701E LEU* 1.3 57.8 + - - +
703E ASP* 2.5 42.4 + - - +
704E TYR* 2.9 12.0 + - - +
724E ARG* 4.1 10.2 - - - +
727E GLN* 3.3 60.9 + - + -
728E ALA* 3.3 17.9 - - + -
730E ASN* 5.7 0.4 - - + -
731E GLU* 4.2 13.2 - - + -
786E GLU* 4.9 4.7 + - - -
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Residues in contact with LEU 701 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657E ILE* 3.2 39.3 - - + -
658E PRO* 3.3 28.6 - - + +
659E THR 3.9 2.0 - - - +
660E SER* 4.1 13.8 + - - +
663E PHE* 3.7 37.9 - - + -
697E ILE* 2.8 35.5 + - + +
698E ALA* 4.6 0.9 - - - -
700E TYR* 1.3 73.1 - - - +
702E SER* 1.3 60.8 + - - +
704E TYR* 3.3 16.5 - - - +
705E TYR* 3.8 12.3 - - - -
728E ALA* 4.4 5.6 - - + +
732E ILE* 6.3 0.2 - - + -
752E LEU* 5.3 1.8 - - + -
756E ILE* 4.3 4.5 - - + -
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Residues in contact with SER 702 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660E SER* 3.5 27.3 - - - +
698E ALA 3.7 5.8 + - - -
699E GLY* 3.0 15.9 + - - -
700E TYR 2.8 0.6 + - - -
701E LEU* 1.3 74.2 - - - +
703E ASP* 1.3 72.1 + - - +
704E TYR 3.0 2.0 - - - -
705E TYR* 3.0 28.4 + - - +
706E ASN* 4.3 1.2 - - - -
37S ARG 5.8 2.0 - - - -
38S SER* 5.7 2.2 - - - -
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Residues in contact with ASP 703 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699E GLY* 2.8 29.8 + - - +
700E TYR* 2.5 30.6 + - - +
702E SER* 1.3 77.1 + - - +
704E TYR* 1.3 62.4 + - - +
706E ASN* 3.5 15.8 - - - +
724E ARG* 3.2 40.1 + - - +
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Residues in contact with TYR 704 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657E ILE* 3.4 48.9 - - + -
700E TYR 2.9 8.1 + - - +
701E LEU 3.3 13.2 - - - +
702E SER 3.0 0.2 - - - -
703E ASP* 1.3 77.5 - - - +
705E TYR* 1.3 84.2 - + - +
706E ASN 3.1 6.4 + - - -
709E ASN* 4.0 6.6 - - - +
721E SER* 4.0 23.6 + - - -
724E ARG* 4.2 15.2 + - + +
725E GLY* 4.2 12.8 - - - -
759E GLN* 2.4 33.8 + - + -
760E VAL* 6.3 1.3 - - + -
763E LEU* 3.4 6.0 - - + +
130S ILE* 3.9 11.6 - - + +
131S ASP* 3.0 32.3 + - + +
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Residues in contact with TYR 705 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656E THR* 3.0 33.3 - - - +
657E ILE* 3.1 24.9 + - + +
658E PRO 3.8 6.3 - - - -
659E THR* 3.8 23.6 - - + -
701E LEU 3.8 11.2 - - - -
702E SER* 3.0 14.9 + - - +
704E TYR* 1.3 101.8 - + - +
706E ASN* 1.3 59.8 + - - +
707E SER 3.9 1.4 + - - -
759E GLN* 5.3 0.3 + - - -
130S ILE* 4.3 20.6 - - + -
131S ASP* 5.8 0.7 - - - -
137S ASN* 4.6 7.3 + - - -
139S GLU* 3.6 26.3 - - + +
140S GLU* 4.6 13.2 - - + -
143S GLN* 4.4 23.0 + - + +
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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