Contacts of the helix formed by residues 683 - 704 (chain H) in PDB entry 6V3O
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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H GLU* 5.3 2.4 - - + +
115H VAL* 5.9 1.3 - - + -
118H ALA* 3.5 16.3 - - + +
119H HIS* 4.4 6.4 - - + -
194H ARG* 3.8 31.4 - - + +
195H ASN* 5.8 2.6 + - - +
251H THR* 4.2 3.8 - - - -
678H GLU 4.6 0.4 + - - -
681H PHE 3.2 0.2 - - - -
682H GLY* 1.3 79.7 - - - +
684H GLU* 1.3 82.0 + - - +
685H HIS* 2.5 51.4 + - - +
686H LEU* 3.0 30.8 + - + +
687H CYS* 2.8 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 684 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H THR* 4.2 11.4 - - + +
258H LYS* 3.7 30.8 + - + +
683H GLU* 1.3 80.6 - - - +
685H HIS* 1.3 83.4 + - + +
687H CYS* 3.4 7.6 + - - +
688H PHE* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 685 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ALA* 4.0 26.0 - - + +
119H HIS* 4.1 23.1 + + - -
683H GLU* 2.5 38.7 + - - +
684H GLU* 1.3 90.8 + - + +
686H LEU* 1.3 63.9 + - - +
688H PHE* 3.1 10.5 + - + +
689H GLN* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 686 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H GLU* 3.9 37.5 - - + +
117H ILE* 3.6 33.7 - - + -
118H ALA* 4.0 15.9 - - + +
678H GLU 4.9 0.4 - - - +
679H PHE* 3.4 28.0 - - + +
680H CYS 3.5 6.1 - - - +
683H GLU* 3.0 26.5 + - + +
685H HIS* 1.3 75.4 - - - +
687H CYS* 1.3 57.8 + - - +
689H GLN* 3.2 9.9 + - + +
690H THR* 2.9 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 687 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H THR* 4.1 27.6 - - - +
252H VAL* 4.1 16.4 - - - -
255H GLY* 4.4 6.3 - - - -
680H CYS 3.5 10.9 + - - -
681H PHE* 3.7 25.3 - - + -
683H GLU 2.8 11.2 + - - +
684H GLU* 3.4 10.8 - - - +
686H LEU* 1.3 77.6 - - - +
688H PHE* 1.3 61.8 + - - +
690H THR* 3.4 1.7 + - - -
691H LEU* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 688 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H GLY* 4.9 2.7 - - - -
258H LYS* 3.9 23.8 - - + -
259H PHE* 3.5 40.7 - + + -
262H ARG* 3.7 47.8 - - + -
684H GLU 3.2 9.3 + - - +
685H HIS* 3.1 13.4 + - + +
687H CYS* 1.3 81.4 - - - +
689H GLN* 1.3 65.9 + - + +
691H LEU* 3.3 7.8 + - - +
692H GLN* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 689 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ILE* 4.3 19.5 + - - +
118H ALA* 4.6 3.8 + - - +
122H ARG* 6.0 2.4 - - - +
137H ALA* 5.2 8.1 - - - +
140H GLU* 4.6 6.6 - - - +
685H HIS* 3.0 29.0 + - - +
686H LEU* 3.2 15.4 + - + +
688H PHE* 1.3 82.0 - - + +
690H THR* 1.3 64.9 + - - +
692H GLN* 3.8 15.4 + - - +
693H ARG* 3.3 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 690 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H LEU* 5.2 0.2 - - + -
648H GLY 3.8 5.2 + - - +
680H CYS* 2.9 43.4 + - + +
681H PHE* 3.6 27.1 - - + -
686H LEU* 2.9 10.6 + - - +
687H CYS 3.7 2.7 - - - -
689H GLN* 1.3 75.1 - - - +
691H LEU* 1.3 66.7 + - - +
692H GLN 3.2 0.7 + - - -
693H ARG* 3.4 17.9 + - - +
694H PHE* 3.3 47.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 691 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H LEU* 4.4 8.3 - - + -
252H VAL* 5.5 0.4 - - + -
255H GLY 3.9 19.7 - - - +
256H VAL* 3.8 25.8 - - + -
259H PHE* 4.3 14.1 - - + -
283H ILE* 3.7 25.1 - - + +
285H PHE* 4.0 23.3 - - + -
681H PHE* 4.1 14.1 - - + -
687H CYS* 3.0 31.3 + - - +
688H PHE* 3.7 4.5 - - - +
690H THR* 1.3 77.6 - - - +
692H GLN* 1.3 60.7 + - - +
694H PHE* 3.7 5.4 + - - +
695H THR* 3.0 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 692 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H GLU* 5.1 8.3 + - - +
141H SER 5.1 0.8 + - - +
142H ASP* 3.3 22.7 - - - +
143H ILE* 3.2 38.6 + - + +
259H PHE* 3.5 24.9 - - + -
262H ARG* 5.0 5.0 + - - +
688H PHE* 2.9 32.7 + - + +
689H GLN* 3.8 20.9 + - - +
690H THR 3.1 0.6 - - - -
691H LEU* 1.3 78.4 - - - +
693H ARG* 1.3 60.0 + - - +
695H THR* 3.1 4.7 + - - -
696H ALA* 2.8 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 693 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ALA* 4.0 10.7 - - - +
140H GLU* 3.0 43.0 + - - +
141H SER 5.6 0.9 - - - -
648H GLY 2.7 28.8 + - - -
649H GLY* 3.3 22.2 + - - -
650H GLY* 3.6 10.8 - - - -
652H THR* 3.0 27.1 - - - +
653H HIS* 3.6 17.2 - - + +
656H ILE* 5.6 0.4 - - - -
689H GLN* 3.3 28.0 + - - +
690H THR* 3.5 30.5 + - - +
692H GLN* 1.3 76.4 - - - +
694H PHE* 1.3 66.5 + - + +
696H ALA* 4.4 2.0 - - - +
697H ALA* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 694 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H VAL* 4.0 19.8 - - + +
172H LEU* 4.0 31.4 - - + -
283H ILE* 5.8 2.5 - - + -
645H VAL 4.0 17.3 - - - -
646H GLY* 5.8 0.4 - - - -
648H GLY* 4.7 7.6 - - - -
652H THR* 4.1 16.4 - - + -
656H ILE* 3.7 24.0 - - + -
668H ILE* 6.3 0.2 - - + -
670H VAL* 4.0 26.5 - - + -
672H VAL* 5.7 4.3 - - + -
681H PHE* 5.7 0.4 - + - -
690H THR* 3.3 43.3 + - + +
691H LEU* 4.0 4.9 - - - +
692H GLN 3.3 0.4 - - - -
693H ARG* 1.3 82.6 - - + +
695H THR* 1.3 59.4 + - - +
697H ALA* 4.4 0.2 - - - +
698H THR* 2.6 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 695 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H ILE* 3.8 17.9 - - + -
165H LEU* 4.4 6.7 - - + -
168H GLN* 3.0 33.2 + - - +
170H VAL* 4.9 2.4 - - - +
259H PHE* 3.2 23.8 - - + -
263H VAL* 5.0 0.7 - - + -
282H LEU* 4.0 18.7 + - + +
283H ILE* 3.6 15.4 - - - +
691H LEU 3.0 14.0 + - - -
692H GLN 3.1 8.3 + - - -
694H PHE* 1.3 79.2 - - - +
696H ALA* 1.3 61.7 + - - +
699H LEU* 3.2 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 696 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H SER 4.5 2.9 - - - +
143H ILE* 3.8 23.8 - - + +
146H THR* 3.6 28.8 - - - +
653H HIS* 4.0 13.2 - - - +
692H GLN 2.8 20.8 + - - +
693H ARG* 4.2 1.8 - - - +
695H THR* 1.3 71.8 - - - +
697H ALA* 1.3 66.2 + - - +
699H LEU* 3.2 4.6 + - - +
700H GLU* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 697 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653H HIS* 3.5 42.2 - - - +
656H ILE* 3.7 20.4 - - + -
657H LEU* 3.6 10.5 - - + +
693H ARG 2.9 19.3 + - - +
696H ALA* 1.3 75.8 - - - +
698H THR* 1.3 64.3 + - - +
700H GLU* 4.8 0.2 - - - -
701H HIS* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 698 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H GLN* 3.7 24.2 - - + +
170H VAL* 3.4 12.3 - - + +
656H ILE* 3.8 18.1 - - - +
664H ILE* 3.8 28.9 - - + +
666H GLY* 4.8 9.7 + - - -
668H ILE* 4.0 17.1 - - + +
694H PHE 2.6 24.2 + - - -
697H ALA* 1.3 78.4 - - - +
699H LEU* 1.3 64.4 + - - +
701H HIS* 3.5 9.3 + - - +
702H GLY* 3.6 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 699 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H ILE* 4.8 7.2 - - + -
146H THR* 5.2 2.0 - - + -
147H LEU* 3.4 33.7 - - + -
150H LEU* 4.1 7.4 - - + -
161H VAL* 4.4 2.7 - - + +
164H ALA* 3.6 30.7 - - + +
165H LEU* 3.8 29.8 - - + +
168H GLN* 3.1 23.3 + - - +
695H THR 3.2 14.5 + - - +
696H ALA 3.2 3.6 + - - +
698H THR* 1.3 81.3 - - - +
700H GLU* 1.3 64.3 + - - +
702H GLY* 3.4 7.8 + - - -
703H MET* 3.7 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 700 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H THR* 3.5 17.1 + - + +
149H ARG* 2.7 37.7 + - - -
150H LEU* 4.4 16.8 - - + -
653H HIS* 4.6 5.5 - - - -
657H LEU* 3.7 28.8 - - + +
696H ALA 2.9 16.2 + - - +
699H LEU* 1.3 74.4 - - - +
701H HIS* 1.3 56.9 + - - +
703H MET* 3.0 3.8 + - - +
704H HIS* 2.7 66.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 701 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656H ILE 3.4 23.3 - - - +
657H LEU* 3.6 23.1 - - + +
659H GLN* 3.0 24.8 + - + +
660H PRO 3.1 19.1 + - - -
661H PRO* 4.1 1.6 - - + -
662H ASP* 4.0 14.8 + - - -
663H THR* 4.0 2.0 - - - -
664H ILE* 3.6 33.9 - - + +
665H ASN* 5.2 0.8 + - - -
697H ALA 3.0 16.8 + - - +
698H THR 3.9 4.7 - - - +
699H LEU 3.4 0.2 - - - -
700H GLU* 1.3 77.3 - - - +
702H GLY* 1.3 65.6 + - - +
703H MET 3.2 1.0 + - - -
704H HIS 3.4 13.6 + - - -
705H PRO* 3.5 14.0 - - - +
706H PRO* 3.9 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 702 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662H ASP* 5.8 0.7 - - - +
664H ILE* 5.8 0.2 - - - +
665H ASN* 4.7 22.4 - - - +
666H GLY 5.8 1.1 - - - -
698H THR 3.6 6.0 + - - -
699H LEU 3.4 7.4 + - - -
700H GLU 3.2 1.2 - - - -
701H HIS* 1.3 83.9 + - - +
703H MET* 1.3 64.1 + - - +
705H PRO* 5.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 703 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H LEU* 3.6 39.7 - - + -
154H VAL* 4.4 5.2 - - - +
156H LYS* 3.5 48.5 + - + +
160H GLU* 4.5 9.6 - - - +
161H VAL* 4.3 13.7 - - + -
164H ALA* 3.9 29.6 - - + -
699H LEU* 3.7 20.5 + - + +
700H GLU 3.0 2.6 + - - +
702H GLY* 1.3 79.6 - - - +
704H HIS* 1.3 60.9 + - - +
705H PRO* 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 704 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H ARG* 4.6 10.1 - - - -
150H LEU* 4.6 4.9 - - + +
154H VAL* 3.8 30.4 - - + +
657H LEU* 5.2 4.0 - - - +
700H GLU* 2.7 48.8 + - + +
701H HIS* 3.4 9.0 + - - +
703H MET* 1.3 76.4 - - - +
705H PRO* 1.3 77.6 + - + +
706H PRO* 3.9 0.7 - - - +
----------------------------------------------------------
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