Contacts of the helix formed by residues 683 - 704 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 4.2 10.9 - - - +
194A ARG* 3.2 40.7 + - - +
195A ASN* 4.3 17.8 + - - +
251A THR* 3.7 9.0 + - - -
681A PHE 3.3 0.8 - - - +
682A GLY* 1.3 79.9 - - - +
684A GLU* 1.3 79.6 + - + +
685A HIS* 2.9 34.5 - - + +
686A LEU* 3.4 21.1 - - + +
687A CYS* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 4.9 14.4 + - - +
255A GLY* 5.7 4.0 - - - -
258A LYS* 3.6 30.4 + - - +
683A GLU* 1.3 80.5 - - + +
685A HIS* 1.3 76.2 + - + +
687A CYS* 2.8 19.0 + - - +
688A PHE* 3.1 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 5.0 11.2 - - + -
115A VAL* 5.7 1.3 - - - -
118A ALA* 4.1 29.3 - - + +
194A ARG* 5.6 3.0 - - - +
198A THR* 5.7 3.2 + - - -
683A GLU* 2.9 26.5 - - + +
684A GLU* 1.3 82.8 - - + +
686A LEU* 1.3 100.3 + - + +
688A PHE* 3.2 9.4 + - - +
689A GLN* 3.0 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 4.3 29.2 - - + +
194A ARG* 4.2 9.6 - - - +
678A GLU 4.5 1.3 - - - +
679A PHE* 3.4 20.9 - - - +
680A CYS* 3.2 11.6 - - - +
682A GLY* 4.1 3.1 - - - +
683A GLU* 3.4 30.3 - - + +
684A GLU 2.9 0.6 + - - -
685A HIS* 1.3 109.8 + - + +
687A CYS* 1.3 62.6 + - - +
689A GLN* 3.0 16.4 + - - +
690A THR* 3.2 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 3.5 28.7 - - - +
252A VAL* 4.4 8.3 - - - -
255A GLY* 4.9 6.5 - - - -
680A CYS 3.2 10.9 + - - -
681A PHE* 3.9 23.6 - - + -
683A GLU 3.3 10.4 + - - +
684A GLU* 2.8 9.9 + - - +
686A LEU* 1.3 78.7 - - - +
688A PHE* 1.3 66.0 + - - +
689A GLN 3.2 0.9 + - - -
690A THR* 3.2 3.3 + - - -
691A LEU* 3.2 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLY 5.9 0.2 - - - -
258A LYS* 4.6 7.0 - - + -
259A PHE* 4.0 34.7 - + + -
262A ARG* 3.9 37.7 - - + -
684A GLU* 3.1 10.4 + - + +
685A HIS* 3.2 12.8 + - - +
687A CYS* 1.3 83.1 - - - +
689A GLN* 1.3 75.6 + - - +
691A LEU* 4.1 6.3 - - - +
692A GLN* 3.2 49.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 4.1 17.9 + - - +
685A HIS* 3.0 24.6 + - - +
686A LEU* 3.0 10.7 + - - +
688A PHE* 1.3 94.6 + - - +
690A THR* 1.3 56.7 + - - +
692A GLN* 3.1 5.1 + - - +
693A ARG* 2.7 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.7 1.1 - - + -
652A THR* 5.5 1.6 - - - +
680A CYS* 2.9 47.7 + - + +
681A PHE* 3.8 25.1 - - + -
686A LEU 3.2 3.4 + - - -
687A CYS 3.7 6.5 - - - -
689A GLN* 1.3 78.5 - - - +
691A LEU* 1.3 60.7 + - - +
693A ARG* 3.7 5.4 - - - +
694A PHE* 3.0 54.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.8 6.7 - - + -
255A GLY 4.9 0.9 - - - -
256A VAL* 4.5 17.9 - - + +
259A PHE* 3.6 46.1 - - + -
283A ILE* 4.3 18.7 - - + +
285A PHE* 4.0 24.9 - - + -
681A PHE* 4.2 13.5 - - + -
687A CYS* 3.2 30.2 + - - +
688A PHE* 4.1 3.1 - - + +
690A THR* 1.3 75.5 - - - +
692A GLN* 1.3 61.0 + - - +
694A PHE* 3.9 4.0 - - - +
695A THR* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 3.0 26.1 + - - +
142A ASP* 2.7 38.6 + - - +
143A ILE* 2.9 19.5 - - - +
259A PHE* 3.3 21.9 - - - -
262A ARG* 5.3 5.1 - - - +
688A PHE* 3.2 39.2 + - - +
689A GLN* 3.2 11.4 - - - +
691A LEU* 1.3 80.8 - - - +
693A ARG* 1.3 64.6 + - - +
695A THR* 3.2 1.9 + - - -
696A ALA* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.9 12.9 - - - +
141A SER* 3.2 42.3 + - - +
652A THR* 3.5 29.9 - - + +
653A HIS* 3.7 46.8 + - - +
689A GLN* 2.7 32.5 + - - +
690A THR* 3.7 5.8 - - - +
692A GLN* 1.3 73.4 - - - +
694A PHE* 1.3 64.0 + - - +
696A ALA* 3.3 1.6 + - - +
697A ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.6 25.8 - - + -
172A LEU* 3.4 34.1 - - + -
283A ILE* 5.4 2.5 - - + -
652A THR* 3.8 33.7 - - + -
656A ILE* 3.9 12.7 - - + +
668A ILE* 6.1 0.2 - - + -
670A VAL* 4.1 27.1 - - + -
672A VAL* 5.9 3.4 - - + -
680A CYS* 5.9 1.3 - - - -
690A THR* 3.0 46.6 + - + +
691A LEU* 3.9 5.2 - - - +
693A ARG* 1.3 79.3 - - - +
695A THR* 1.3 55.7 + - + +
697A ALA* 3.4 1.7 + - - +
698A THR* 2.7 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.9 8.5 - - - +
165A LEU* 5.5 3.9 - - - +
168A GLN* 3.4 25.1 + - - +
170A VAL* 4.0 2.0 - - + -
259A PHE* 3.2 17.4 - - + -
282A LEU* 3.9 26.2 - - + +
283A ILE* 3.8 27.1 - - + -
691A LEU 2.7 15.5 + - - -
692A GLN 3.2 4.2 + - - -
694A PHE* 1.3 74.8 - - - +
696A ALA* 1.3 60.5 + - - +
699A LEU* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 4.6 12.8 - - - +
142A ASP 4.6 4.0 - - - +
143A ILE* 4.5 15.4 - - + +
146A THR* 3.8 30.3 - - - +
692A GLN 3.0 19.3 + - - +
693A ARG 3.8 3.6 - - - +
695A THR* 1.3 76.6 + - - +
697A ALA* 1.3 62.0 - - - +
699A LEU* 3.8 5.9 - - - +
700A GLU* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A HIS* 4.0 21.3 - - + +
656A ILE* 3.3 35.4 - - + +
693A ARG 3.0 15.7 + - - +
696A ALA* 1.3 75.1 - - - +
698A THR* 1.3 56.2 + - - +
700A GLU* 3.2 5.7 + - - +
701A HIS* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN* 3.6 28.5 - - + +
169A THR 5.8 0.2 - - - +
170A VAL* 3.8 9.7 - - + +
656A ILE* 3.7 18.6 - - - +
664A ILE* 3.4 31.5 - - + +
666A GLY* 4.4 7.8 + - - -
667A SER 4.9 0.2 - - - +
668A ILE* 4.0 15.6 - - + +
694A PHE 2.7 23.4 + - - -
697A ALA* 1.3 76.1 - - - +
699A LEU* 1.3 65.3 + - - +
701A HIS* 3.7 4.1 + - - +
702A GLY* 3.5 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 5.5 3.4 - - + -
146A THR* 4.9 5.6 - - + -
147A LEU* 3.7 31.0 - - + -
150A LEU* 4.2 13.5 - - + -
161A VAL* 4.2 9.4 - - + +
164A ALA* 3.9 27.8 - - + -
165A LEU* 4.2 23.3 - - + +
168A GLN* 3.2 16.3 + - - +
695A THR 2.9 21.2 + - - +
696A ALA* 3.8 4.7 - - - +
697A ALA 3.2 0.2 - - - -
698A THR* 1.3 77.9 - - - +
700A GLU* 1.3 63.2 + - - +
702A GLY* 3.2 9.9 + - - -
703A MET* 3.2 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 3.3 29.3 + - + +
149A ARG* 3.2 39.2 + - - -
150A LEU* 3.9 22.4 - - + -
696A ALA 3.2 12.5 + - - +
697A ALA* 3.8 4.3 - - - +
699A LEU* 1.3 76.1 - - - +
701A HIS* 1.3 54.6 - - - +
702A GLY 2.7 16.1 + - - -
704A HIS* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ILE* 3.3 27.8 + - + -
657A LEU* 4.4 4.1 - - + +
659A GLN* 2.7 31.8 - - + -
660A PRO 3.1 16.3 + - - -
661A PRO* 3.8 5.5 - - - +
662A ASP* 4.1 7.2 + - - -
663A THR 4.4 0.2 + - - -
664A ILE* 3.7 34.8 - - + +
665A ASN 5.4 0.2 - - - -
697A ALA 2.8 21.6 + - - +
698A THR 4.0 4.7 - - - +
700A GLU* 1.3 70.8 - - - +
702A GLY* 1.3 57.1 + - - +
704A HIS 4.5 4.3 - - - -
705A PRO* 3.4 21.3 - - - +
706A PRO* 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ASP* 5.0 5.0 - - - +
664A ILE* 6.1 0.2 - - - -
665A ASN* 5.3 18.5 + - - -
666A GLY 6.0 0.2 - - - -
698A THR 3.5 7.0 + - - -
699A LEU 3.2 7.2 + - - -
700A GLU 2.7 6.5 + - - -
701A HIS* 1.3 76.3 - - - +
703A MET* 1.3 56.8 + - - +
704A HIS 3.2 3.8 - - - -
705A PRO* 3.2 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 4.2 22.2 - - + -
154A VAL* 4.4 2.8 - - - +
156A LYS* 3.3 55.3 + - + +
160A GLU* 3.6 33.2 - - + +
161A VAL* 3.7 17.3 - - + +
164A ALA* 3.9 26.0 - - + -
699A LEU* 3.2 22.2 + - - +
702A GLY* 1.3 73.6 - - - +
704A HIS* 1.3 58.5 + - - +
705A PRO* 3.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 5.9 1.3 - - - -
150A LEU* 3.9 15.3 - - + -
154A VAL* 3.3 35.1 - - + +
657A LEU* 6.0 1.2 - - - +
700A GLU* 2.8 32.6 + - + +
701A HIS* 4.5 1.2 - - - -
703A MET* 1.3 80.8 - - - +
705A PRO* 1.3 77.5 + - + +
706A PRO* 4.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
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