Contacts of the helix formed by residues 680 - 698 (chain B) in PDB entry 5J3V
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 680 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B LYS* 3.7 32.2 - - + +
639B ASP* 5.7 1.3 - - - +
642B ILE* 4.1 14.6 - - - -
678B ASP* 2.8 19.1 + - - +
679B LYS* 1.3 77.5 - - - +
681B PRO* 1.3 74.8 - - + +
682B GLU* 3.8 17.3 - - - +
683B VAL* 3.1 28.2 + - + +
684B ARG* 3.3 9.4 + - - -
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Residues in contact with PRO 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LYS 3.4 6.1 - - - +
680B MET* 1.3 85.8 - - + +
682B GLU* 1.3 68.9 + - - +
684B ARG* 3.3 22.5 + - - +
685B GLN* 2.9 26.1 + - - +
721B PHE* 4.4 24.2 - - + -
724B VAL* 3.2 23.8 - - + +
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Residues in contact with GLU 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ILE* 3.6 24.7 - - + +
680B MET* 3.3 17.1 - - + +
681B PRO* 1.3 85.8 - - - +
683B VAL* 1.3 60.0 + - - +
685B GLN* 3.6 17.3 + - - +
686B SER* 3.1 28.2 + - - -
18D LYS* 4.2 32.2 - - + +
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Residues in contact with VAL 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LYS* 4.1 3.1 - - + -
641B MET* 3.7 34.1 - - + -
642B ILE* 4.1 15.0 - - + -
645B LEU* 4.1 3.2 - - + +
675B CYS* 3.7 26.5 - - + +
678B ASP* 3.6 25.4 - - + +
680B MET* 3.1 29.5 + - + +
682B GLU* 1.3 74.3 - - - +
684B ARG* 1.3 65.9 + - - +
686B SER* 3.3 4.8 + - - -
687B SER* 3.1 22.2 + - - -
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Residues in contact with ARG 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B CYS 3.6 7.0 - - - +
676B MET 3.3 26.5 - - - +
677B GLN 4.8 0.4 - - - -
678B ASP 3.0 26.3 + - - +
679B LYS* 3.5 17.6 + - - +
680B MET 3.3 2.6 + - - +
681B PRO* 3.3 22.2 + - - +
683B VAL* 1.3 77.9 - - - +
685B GLN* 1.3 61.0 + - - +
687B SER* 2.7 20.4 + - - -
688B PHE* 3.1 23.8 + - + -
716B ASN* 3.1 24.7 + - - +
721B PHE* 3.4 37.1 - - - -
724B VAL* 3.4 25.1 - - + +
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Residues in contact with GLN 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B PRO 2.9 16.1 + - - +
682B GLU* 3.7 20.5 - - - +
684B ARG* 1.3 78.4 - - - +
686B SER* 1.3 65.4 + - - +
688B PHE* 3.9 2.3 - - - +
689B ALA 3.2 8.8 + - - -
723B SER* 3.3 33.8 + - - +
724B VAL* 4.1 16.9 - - + +
727B ASN* 2.8 35.3 + - - +
15D ALA* 4.2 12.5 + - - +
16D PRO 3.7 22.0 + - - -
17D ARG* 4.8 5.3 - - - +
18D LYS* 5.0 4.5 - - - +
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Residues in contact with SER 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ILE* 3.3 20.2 - - - +
645B LEU* 3.9 23.0 - - - +
646B ASP* 3.1 27.3 + - - +
649B SER* 5.4 0.5 - - - -
682B GLU 3.1 17.0 + - - -
683B VAL 3.8 3.6 - - - -
685B GLN* 1.3 83.3 - - - +
687B SER* 1.3 61.8 + - - +
689B ALA* 3.5 6.5 + - - +
690B LEU* 3.1 21.5 + - - +
727B ASN* 5.0 0.2 - - - +
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Residues in contact with SER 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B LEU* 4.0 7.8 - - - +
672B MET* 3.5 18.2 - - - +
675B CYS* 3.7 25.3 + - - -
676B MET* 3.6 19.7 - - - +
683B VAL 3.1 13.4 + - - -
684B ARG* 2.7 26.9 + - - -
686B SER* 1.3 75.4 - - - +
688B PHE* 1.3 60.8 + - - +
690B LEU* 3.2 6.5 + - - +
691B LEU* 3.0 22.9 + - - +
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Residues in contact with PHE 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B MET* 3.6 40.2 - - + -
684B ARG* 3.1 18.9 + - + +
685B GLN* 4.8 0.7 - - - -
687B SER* 1.3 77.9 + - - +
689B ALA* 1.3 66.4 + - - +
691B LEU* 3.1 6.6 + - + +
692B GLY* 3.1 18.9 + - - -
712B ILE* 4.0 9.0 - - + -
713B LEU* 3.6 28.7 - - + -
716B ASN* 3.5 49.1 - - + -
724B VAL* 3.8 25.6 - - + -
727B ASN* 3.9 22.4 - - + +
728B ALA* 4.2 5.8 - - + -
730B TRP* 4.4 1.0 - - - -
731B ALA* 4.1 7.1 - - - +
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Residues in contact with ALA 689 (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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646B ASP* 5.4 2.9 - - - +
649B SER* 4.4 4.7 - - - +
685B GLN 3.2 4.1 + - - +
686B SER* 3.6 11.9 - - - +
687B SER 3.2 0.2 - - - -
688B PHE* 1.3 79.0 - - - +
690B LEU* 1.3 61.7 + - - +
692B GLY 3.6 0.3 + - - -
693B ASP* 3.2 30.5 + - - +
727B ASN* 3.4 23.9 - - - +
730B TRP* 3.7 9.5 - - - -
14D LYS* 3.6 22.9 - - + -
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B LEU* 3.8 27.6 - - + +
648B LEU* 3.5 44.0 - - + +
649B SER* 3.6 8.7 - - - +
652B ALA* 4.7 2.2 - - + -
668B ILE* 3.7 31.4 - - + -
672B MET* 3.7 14.4 - - + -
686B SER 3.1 14.5 + - - +
687B SER* 3.2 10.0 + - - +
689B ALA* 1.3 74.3 - - - +
691B LEU* 1.3 64.6 + - - +
693B ASP* 4.5 0.7 - - - -
694B LEU* 3.1 37.4 + - + +
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Residues in contact with LEU 691 (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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669B LEU* 5.7 0.4 - - + -
672B MET* 3.7 8.7 - - + -
676B MET* 3.8 22.2 - - + -
687B SER 3.0 13.2 + - - +
688B PHE* 3.1 10.7 + - + +
690B LEU* 1.3 77.4 - - - +
692B GLY* 1.3 53.4 + - - +
694B LEU* 3.4 3.9 + - + +
695B THR* 2.5 39.3 + - - +
702B VAL* 3.8 18.6 - - + -
709B PHE* 3.6 37.7 - - + -
713B LEU* 4.0 37.7 - - + -
731B ALA* 4.4 6.7 - - + -
735B ILE* 4.5 6.1 - - + -
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Residues in contact with GLY 692 (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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688B PHE 3.1 8.4 + - - -
689B ALA 3.6 0.4 + - - -
691B LEU* 1.3 79.9 - - - +
693B ASP* 1.3 60.6 + - - +
695B THR* 3.3 17.6 + - - -
696B LYS* 3.3 19.6 + - - +
730B TRP* 3.5 27.4 - - - -
731B ALA* 4.5 12.3 - - - +
734B GLU* 4.6 3.8 - - - +
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Residues in contact with ASP 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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649B SER* 2.3 40.2 + - - +
652B ALA* 3.7 24.0 - - + +
653B GLU* 4.2 12.4 - - - +
689B ALA 3.2 14.6 + - - +
690B LEU* 3.9 4.7 - - - +
691B LEU 3.3 0.6 - - - -
692B GLY* 1.3 76.6 - - - +
694B LEU* 1.3 61.8 + - - +
696B LYS* 3.5 13.4 + - - +
697B ALA* 3.3 23.4 + - - +
730B TRP* 3.5 14.8 - - - -
14D LYS* 3.3 19.6 + - - +
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Residues in contact with LEU 694 (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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652B ALA* 3.7 20.9 - - + -
659B ILE* 4.1 8.7 - - + -
663B VAL* 3.9 25.1 - - + -
668B ILE* 4.9 9.4 - - + -
669B LEU* 4.6 12.1 - - + -
672B MET* 3.6 29.2 - - + -
690B LEU* 3.1 27.5 + - + +
691B LEU* 3.9 4.0 - - + +
693B ASP* 1.3 74.8 - - - +
695B THR* 1.3 59.8 + - - +
697B ALA* 3.7 1.6 - - - +
698B CYS* 2.8 54.1 + - - +
702B VAL* 3.8 12.3 - - + +
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Residues in contact with THR 695 (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 LEU* 2.5 23.7 + - - +
692B GLY* 3.4 12.6 - - - -
693B ASP 3.2 0.4 - - - -
694B LEU* 1.3 78.7 - - - +
696B LYS* 1.3 59.0 + - - +
697B ALA 3.7 0.2 + - - -
699B PHE* 3.3 43.2 + - + +
702B VAL* 4.2 11.2 - - - +
734B GLU* 3.8 12.8 - - + +
735B ILE* 3.8 38.4 - - + +
738B GLN* 3.4 12.3 - - + +
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Residues in contact with LYS 696 (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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653B GLU* 6.0 7.4 - - - +
692B GLY 3.3 14.2 + - - +
693B ASP* 3.5 13.7 + - - +
694B LEU 3.3 0.2 - - - -
695B THR* 1.3 77.8 - - + +
697B ALA* 1.3 60.8 + - - +
730B TRP* 4.8 11.1 - - - -
734B GLU* 3.2 39.9 + - + +
738B GLN* 4.5 13.3 + - + +
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Residues in contact with ALA 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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652B ALA* 3.8 10.3 - - + +
656B GLY* 3.2 33.0 - - - +
657B GLY* 3.5 18.4 - - - +
659B ILE* 4.1 11.0 - - + -
660B GLU* 3.8 6.9 - - - +
693B ASP 3.3 17.8 + - - +
694B LEU* 4.2 2.7 - - - +
696B LYS* 1.3 80.2 - - + +
698B CYS* 1.3 61.7 + - - +
699B PHE 4.0 1.1 - - - -
700B GLN* 4.8 0.3 - - - +
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Residues in contact with CYS 698 (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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659B ILE* 3.8 15.3 - - - -
660B GLU* 3.6 22.2 - - + -
663B VAL* 3.9 18.8 - - - -
694B LEU* 2.8 47.6 + - - +
697B ALA* 1.3 74.1 - - - +
699B PHE* 1.3 62.2 + - - +
700B GLN* 3.2 15.5 - - - +
701B HIS* 3.3 18.0 + - + +
702B VAL* 3.5 8.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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