Contacts of the helix formed by residues 683 - 704 (chain B) in PDB entry 1JQO
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 GLU 683 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 4.5 0.2 - - - +
191B ALA* 3.7 14.6 - - - +
194B ARG* 2.7 54.5 + - - +
195B ASN* 5.3 3.5 + - - +
251B THR* 4.0 4.6 - - - +
681B PHE 3.9 3.3 - - - +
682B GLY* 1.3 80.5 - - - +
684B GLU* 1.3 63.8 + - - +
685B HIS* 2.9 37.1 + - + +
686B LEU* 3.1 19.5 - - + +
687B CYS* 3.1 24.9 + - - +
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Residues in contact with GLU 684 (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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250B GLU 5.7 1.8 - - - +
251B THR* 4.2 21.8 - - + +
258B LYS* 4.0 19.2 + - - -
683B GLU* 1.3 76.7 + - - +
685B HIS* 1.3 61.7 + - + +
687B CYS* 3.2 2.4 + - - +
688B PHE* 2.9 31.5 + - - +
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Residues in contact with HIS 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 4.5 14.6 - - + -
118B ALA* 4.3 25.5 - - + +
194B ARG* 5.6 0.6 - - - +
683B GLU* 2.9 39.1 + - + +
684B GLU* 1.3 80.5 - - + +
686B LEU* 1.3 90.0 + - + +
688B PHE* 4.1 6.3 - - - +
689B GLN* 3.2 29.5 + - - +
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Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 3.9 19.7 - - + +
194B ARG* 4.2 1.6 - - - +
678B GLU 4.4 0.9 - - - +
679B PHE* 3.3 27.4 - - - +
680B CYS* 3.7 3.1 - - - +
682B GLY* 3.8 3.6 - - - +
683B GLU* 3.1 45.8 - - + +
684B GLU 3.1 0.2 - - - -
685B HIS* 1.3 92.3 - - + +
687B CYS* 1.3 55.4 + - - +
689B GLN* 3.2 12.4 + - - +
690B THR* 2.7 37.1 + - - +
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Residues in contact with CYS 687 (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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251B THR* 3.6 31.4 - - + -
252B VAL* 4.5 11.2 - - - -
255B GLY* 4.6 10.5 - - - -
680B CYS 3.7 10.5 + - - -
681B PHE* 3.7 22.0 - - + -
683B GLU 3.1 4.6 + - - +
684B GLU 3.6 7.4 - - - +
686B LEU* 1.3 76.5 - - - +
688B PHE* 1.3 68.7 + - - +
690B THR* 3.0 2.9 + - - -
691B LEU* 2.9 46.2 + - - +
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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
----------------------------------------------------------
255B GLY 5.6 0.7 - - - -
258B LYS* 4.8 5.6 - - + -
259B PHE* 3.6 37.5 - + + -
262B ARG* 3.8 37.5 - - + -
684B GLU 2.9 16.3 + - - +
685B HIS* 4.1 7.0 - - - +
687B CYS* 1.3 80.1 - - - +
689B GLN* 1.3 66.4 + - + +
691B LEU* 3.3 7.2 + - - +
692B GLN* 2.9 57.1 + - + +
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Residues in contact with GLN 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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121B ARG* 3.1 41.8 + - - +
141B SER 5.2 2.4 - - - +
685B HIS* 3.2 19.1 + - - +
686B LEU* 3.6 11.2 - - - +
687B CYS 3.2 0.4 - - - -
688B PHE* 1.3 84.3 - - + +
690B THR* 1.3 60.8 + - - +
692B GLN* 3.2 7.7 + - + +
693B ARG* 2.7 56.1 + - - +
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Residues in contact with THR 690 (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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172B LEU* 5.1 1.1 - - + -
652B THR* 5.5 1.6 - - - +
680B CYS* 2.7 36.7 + - + -
681B PHE* 3.7 26.2 - - + -
686B LEU 2.7 19.2 + - - -
687B CYS 3.0 7.2 + - - -
689B GLN* 1.3 72.9 - - - +
691B LEU* 1.3 66.5 + - - +
693B ARG* 3.3 5.1 + - - +
694B PHE* 3.1 52.0 + - + -
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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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172B LEU* 4.4 9.9 - - + -
255B GLY 4.6 9.0 - - - +
256B VAL* 4.8 7.6 - - + +
259B PHE* 3.7 38.9 - - + -
283B ILE* 3.7 36.2 - - + +
285B PHE* 4.0 16.8 - - + -
681B PHE* 4.5 4.3 - - + -
687B CYS* 2.9 38.7 + - - +
688B PHE* 3.6 7.2 - - - +
690B THR* 1.3 75.3 - - - +
692B GLN* 1.3 56.8 + - - +
694B PHE* 3.5 3.1 + - - +
695B THR* 2.6 36.1 + - - +
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Residues in contact with GLN 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER 3.0 29.4 - - - +
142B ASP* 3.3 11.0 - - - +
143B ILE* 2.7 35.5 + - - +
259B PHE* 3.4 18.8 - - - -
262B ARG* 5.0 6.5 - - - +
688B PHE* 2.9 46.4 + - + +
689B GLN* 3.2 14.8 - - + +
691B LEU* 1.3 77.2 - - - +
693B ARG* 1.3 63.6 + - - +
695B THR* 3.4 1.4 + - - -
696B ALA* 3.0 26.6 + - - +
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Residues in contact with ARG 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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121B ARG* 3.8 23.4 - - - +
141B SER* 3.2 53.1 + - - +
652B THR* 4.2 27.4 - - + +
653B HIS* 4.3 29.2 + - + +
689B GLN* 2.7 50.6 + - - +
690B THR* 3.6 8.1 - - - +
692B GLN* 1.3 73.1 - - - +
694B PHE* 1.3 65.4 + - - +
696B ALA* 3.6 2.9 - - - +
697B ALA* 2.9 27.0 + - - +
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Residues in contact with PHE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 3.6 28.9 - - + -
172B LEU* 3.7 27.4 - - + -
283B ILE* 5.6 2.7 - - + -
652B THR* 3.4 32.8 - - + -
656B ILE* 4.2 16.4 - - + -
668B ILE* 6.0 0.7 - - + -
670B VAL* 4.1 27.6 - - + -
672B VAL* 6.1 2.7 - - + -
680B CYS* 5.6 3.6 - - - -
690B THR* 3.1 46.3 + - + +
691B LEU* 4.0 3.6 - - - +
693B ARG* 1.3 78.8 - - - +
695B THR* 1.3 59.8 + - + +
698B THR* 2.8 36.0 + - - -
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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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143B ILE* 3.4 9.1 - - - +
165B LEU* 5.2 3.1 - - - +
168B GLN* 2.9 31.8 + - - +
170B VAL* 4.8 2.2 - - + -
259B PHE* 2.9 17.8 - - + -
282B LEU* 3.5 41.3 - - + +
283B ILE* 3.9 17.0 - - + -
691B LEU 2.6 20.8 + - - -
692B GLN 3.4 5.0 + - - -
694B PHE* 1.3 77.7 - - - +
696B ALA* 1.3 54.9 + - - +
699B LEU* 3.0 19.1 + - - +
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Residues in contact with ALA 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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141B SER 4.3 15.5 - - - +
142B ASP 4.6 1.6 - - - +
143B ILE* 4.3 13.2 - - + +
146B THR* 3.8 26.3 - - + +
692B GLN 3.0 20.1 + - - +
693B ARG 3.6 2.5 - - - +
695B THR* 1.3 73.3 + - - +
697B ALA* 1.3 66.8 + - - +
699B LEU* 2.8 18.4 + - - +
700B GLU* 2.9 17.3 + - - +
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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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653B HIS* 4.0 26.7 - - + +
656B ILE* 3.5 29.2 - - + +
693B ARG 2.9 16.6 + - - +
696B ALA* 1.3 75.4 - - - +
698B THR* 1.3 63.4 + - - +
700B GLU* 3.2 10.6 + - - +
701B HIS* 3.0 24.8 + - - +
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Residues in contact with THR 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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168B GLN* 3.7 26.4 - - + +
169B THR 5.0 0.7 - - - +
170B VAL* 3.7 21.3 - - + +
656B ILE* 3.8 21.3 - - - +
664B ILE* 4.1 23.6 - - + +
665B ASN* 4.5 9.5 - - - +
666B GLY 5.1 0.2 - - - +
668B ILE* 4.1 8.7 - - + +
694B PHE* 2.8 28.8 + - - +
697B ALA* 1.3 75.8 - - - +
699B LEU* 1.3 61.5 + - - +
701B HIS* 3.7 4.3 + - - +
702B GLY* 3.7 12.6 + - - -
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Residues in contact with LEU 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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143B ILE* 5.9 2.7 - - + -
146B THR* 5.0 4.7 - - + -
147B LEU* 4.1 10.5 - - + -
150B LEU* 3.5 28.3 - - + -
161B VAL* 3.9 14.6 - - + +
164B ALA* 4.2 25.6 - - + +
165B LEU* 4.0 24.9 - - + +
168B GLN* 3.3 15.2 + - - +
695B THR 3.0 18.9 + - - +
696B ALA* 2.8 12.4 + - - +
698B THR* 1.3 71.7 - - - +
700B GLU* 1.3 64.4 + - - +
702B GLY* 3.3 8.8 + - - -
703B MET* 3.4 18.8 + - + +
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Residues in contact with GLU 700 (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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146B THR* 3.5 27.2 + - + +
149B ARG* 2.8 41.1 + - - -
150B LEU* 4.4 15.8 - - + +
696B ALA* 2.9 9.8 + - - +
697B ALA* 3.7 11.1 - - - +
699B LEU* 1.3 73.1 - - - +
701B HIS* 1.3 52.9 + - - +
702B GLY 2.6 12.6 + - - -
703B MET 2.8 0.9 + - - +
704B HIS* 2.5 55.7 + - + +
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Residues in contact with HIS 701 (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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656B ILE* 3.2 23.0 + - + -
657B LEU* 4.6 1.6 - - - +
659B GLN 2.9 30.1 - - - -
660B PRO 3.2 17.5 + - - -
661B PRO* 3.6 5.5 - - - +
662B ASP* 3.9 6.7 + - - -
664B ILE* 3.5 42.5 + - + +
665B ASN 4.7 2.0 - - - -
697B ALA 3.0 12.9 + - - +
698B THR 4.0 5.6 - - - +
699B LEU 3.5 0.2 - - - -
700B GLU* 1.3 77.6 - - - +
702B GLY* 1.3 59.9 + - - +
704B HIS 4.5 6.1 - - - -
705B PRO* 3.4 19.5 - - - +
706B PRO* 3.6 24.1 - - + +
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Residues in contact with GLY 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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665B ASN* 4.7 20.2 - - - +
698B THR 3.7 5.8 + - - -
699B LEU 3.3 7.4 + - - -
700B GLU 2.6 6.7 + - - -
701B HIS* 1.3 77.7 - - - +
703B MET* 1.3 58.4 + - - -
705B PRO* 3.4 15.6 - - - +
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Residues in contact with MET 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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150B LEU* 3.8 21.5 - - + -
154B VAL* 4.1 7.1 - - - +
156B LYS* 3.7 53.8 + - + +
160B GLU* 3.6 32.3 - - + +
161B VAL* 4.2 24.0 - - - +
164B ALA* 4.3 14.1 - - + -
699B LEU* 3.4 16.9 + - + +
700B GLU 2.8 4.0 + - - -
702B GLY* 1.3 72.9 - - - +
704B HIS* 1.3 59.5 - - - +
705B PRO* 3.3 8.1 - - - +
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Residues in contact with HIS 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 5.9 2.8 - - - -
150B LEU* 4.6 8.1 - - + -
154B VAL* 3.7 37.5 - - + +
657B LEU* 6.0 0.7 - - - +
700B GLU* 2.5 41.3 + - + +
701B HIS* 4.5 0.9 - - - -
703B MET* 1.3 74.9 - - - +
705B PRO* 1.3 69.8 - - + +
706B PRO* 3.7 3.3 - - - +
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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