Contacts of the helix formed by residues 683 - 704 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 5.2 2.9 - - + +
115C VAL* 5.9 1.6 - - + -
118C ALA* 3.5 18.0 - - + +
119C HIS* 4.1 7.1 + - - -
194C ARG* 3.7 31.2 - - + +
251C THR* 4.2 3.4 - - - -
678C GLU 4.7 0.2 + - - -
682C GLY* 1.3 77.9 - - - +
684C GLU* 1.3 78.7 + - - +
685C HIS* 2.6 50.2 + - - +
686C LEU* 3.1 31.3 + - + +
687C CYS* 2.8 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 684 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C THR* 4.2 14.8 - - + +
258C LYS* 3.2 41.0 + - - +
683C GLU* 1.3 77.0 + - - +
685C HIS* 1.3 86.6 + - + +
687C CYS* 3.4 3.5 + - - +
688C PHE 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 685 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ALA* 4.0 25.4 - - + +
119C HIS* 3.8 22.7 + + - -
683C GLU* 2.6 34.1 + - - +
684C GLU* 1.3 92.2 + - + +
686C LEU* 1.3 64.9 + - - +
688C PHE* 3.2 10.0 + - - +
689C GLN* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 686 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 3.9 35.2 - - + +
117C ILE* 3.6 34.3 - - + -
118C ALA* 4.0 17.0 - - + +
678C GLU 5.0 0.2 - - - +
679C PHE* 3.3 29.2 - - + +
680C CYS 3.4 5.8 - - - +
683C GLU* 3.1 27.7 + - + +
685C HIS* 1.3 74.8 - - - +
687C CYS* 1.3 62.9 + - - +
689C GLN* 3.1 11.1 + - + +
690C THR* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 687 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C THR* 4.0 27.1 - - - -
252C VAL* 4.2 10.5 - - - -
255C GLY* 4.5 5.6 - - - -
258C LYS* 5.6 0.4 - - - -
680C CYS 3.3 12.9 + - - +
681C PHE* 3.8 25.8 - - + -
683C GLU 2.8 16.1 + - - +
684C GLU* 3.5 6.7 - - - +
686C LEU* 1.3 74.5 - - - +
688C PHE* 1.3 66.4 + - - +
689C GLN 3.2 0.2 + - - -
690C THR* 3.3 2.1 + - - -
691C LEU* 3.0 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 688 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C GLY* 5.0 0.4 - - - -
258C LYS* 3.7 35.4 - - + +
259C PHE* 3.5 36.4 - + + -
262C ARG* 3.6 43.3 - - + -
684C GLU 3.1 11.6 + - - +
685C HIS* 3.2 11.6 + - - +
687C CYS* 1.3 78.9 - - - +
689C GLN* 1.3 67.8 + - + +
691C LEU* 3.6 7.7 - - - +
692C GLN* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 689 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 4.4 18.5 + - - +
118C ALA* 4.7 3.8 + - - +
122C ARG* 6.0 0.7 + - - -
137C ALA* 5.2 7.9 - - - +
140C GLU* 4.5 6.3 - - - +
685C HIS* 3.0 31.9 + - - +
686C LEU* 3.1 15.9 + - + +
688C PHE* 1.3 86.4 - - + +
690C THR* 1.3 58.3 + - - +
692C GLN* 3.8 15.3 + - - +
693C ARG* 2.8 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 690 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C GLY 3.6 9.9 - - - +
649C GLY* 5.2 1.3 - - - -
679C PHE 5.3 0.2 - - - +
680C CYS* 3.3 31.1 + - + +
681C PHE* 3.6 24.1 - - - -
686C LEU* 3.0 17.1 + - + +
687C CYS 3.5 5.5 + - - -
689C GLN* 1.3 76.2 - - - +
691C LEU* 1.3 68.1 + - - +
692C GLN 3.2 0.2 - - - -
693C ARG* 3.3 23.2 - - - +
694C PHE* 3.0 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 691 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 4.5 6.3 - - + -
252C VAL* 5.4 1.3 - - + +
255C GLY* 3.8 31.2 - - - +
256C VAL* 4.1 11.0 - - + +
259C PHE* 4.3 14.6 - - + -
283C ILE* 3.9 26.2 - - + +
285C PHE* 4.0 25.1 - - + -
681C PHE* 4.2 13.5 - - + -
687C CYS* 3.0 29.6 + - - +
688C PHE* 3.6 4.9 - - - +
690C THR* 1.3 81.3 + - - +
692C GLN* 1.3 61.8 + - - +
694C PHE* 3.6 5.0 + - - +
695C THR* 3.1 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 692 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 5.0 7.7 + - - +
141C SER 4.8 2.5 + - - +
142C ASP* 3.3 21.9 - - - +
143C ILE* 3.2 39.4 + - + +
259C PHE* 3.5 25.6 - - + -
262C ARG* 4.8 3.1 + - - +
688C PHE* 2.9 33.8 + - + +
689C GLN* 3.8 20.3 + - - +
690C THR 3.2 0.2 - - - -
691C LEU* 1.3 73.6 - - - +
693C ARG* 1.3 66.2 + - - +
695C THR* 3.2 0.3 + - - -
696C ALA* 3.0 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 693 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ALA* 3.7 13.7 - - - +
140C GLU* 2.8 39.9 + - - +
141C SER 6.0 0.2 - - - -
648C GLY 3.0 19.8 + - - -
649C GLY* 3.5 19.0 + - - -
650C GLY* 3.3 21.4 - - - +
652C THR* 3.4 26.0 - - - +
653C HIS* 3.9 20.5 - - + +
656C ILE* 5.7 0.2 - - - -
689C GLN* 2.8 37.6 + - - +
690C THR* 3.3 34.2 - - - +
692C GLN* 1.3 75.5 - - - +
694C PHE* 1.3 63.0 + - + +
697C ALA* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 694 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 4.0 21.7 - - + +
172C LEU* 4.1 35.7 - - + -
283C ILE* 6.3 1.1 - - + -
645C VAL 3.9 23.1 - - - -
646C GLY* 5.7 0.4 - - - -
648C GLY* 4.6 13.7 - - - -
652C THR* 4.2 16.2 - - + -
656C ILE* 3.7 23.6 - - + -
670C VAL* 4.0 23.1 - - + -
672C VAL* 5.7 4.5 - - + -
681C PHE* 5.8 2.2 - + - -
690C THR* 3.0 32.6 + - - +
691C LEU* 4.1 4.7 - - - +
693C ARG* 1.3 81.9 - - + +
695C THR* 1.3 61.7 + - - +
697C ALA* 4.4 0.2 - - - +
698C THR* 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 695 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 4.2 12.6 - - + -
165C LEU* 4.4 8.1 - - + -
168C GLN* 3.0 32.4 + - - +
170C VAL* 4.9 2.7 - - - +
259C PHE* 3.3 32.9 - - + -
263C VAL* 5.0 0.9 - - + -
282C LEU* 4.0 16.9 + - + +
283C ILE* 3.7 15.8 - - - +
691C LEU 3.1 17.6 + - - -
692C GLN 3.9 0.4 - - - -
694C PHE* 1.3 79.4 - - - +
696C ALA* 1.3 62.7 + - - +
699C LEU* 3.2 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 696 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER 4.6 3.4 - - - +
143C ILE* 4.0 24.4 - - + +
146C THR* 3.5 29.3 - - - +
653C HIS* 4.0 13.5 - - - +
692C GLN* 3.0 16.6 + - + +
695C THR* 1.3 75.6 - - - +
697C ALA* 1.3 65.6 + - - +
699C LEU* 3.3 3.5 + - - +
700C GLU* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 697 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C HIS* 3.6 43.4 - - - +
656C ILE* 3.7 20.9 - - + +
657C LEU* 3.5 12.9 - - + +
693C ARG 3.2 16.9 + - - +
696C ALA* 1.3 78.6 - - - +
698C THR* 1.3 63.3 + - - +
700C GLU 3.4 0.2 + - - -
701C HIS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 698 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C GLN* 3.7 24.5 - - + +
170C VAL* 3.6 12.1 - - + +
656C ILE* 3.8 18.8 - - - +
664C ILE* 3.9 27.8 - - + +
666C GLY* 4.5 9.8 + - - -
668C ILE* 3.9 16.4 - - + +
694C PHE 2.8 22.8 + - - -
697C ALA* 1.3 79.5 - - - +
699C LEU* 1.3 66.3 + - - +
701C HIS* 3.5 8.7 + - - +
702C GLY* 3.6 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 699 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 4.6 11.2 - - + -
146C THR* 5.0 2.2 - - + -
147C LEU* 3.6 31.6 - - + -
150C LEU* 4.4 6.5 - - + -
161C VAL* 4.3 2.2 - - + +
164C ALA* 3.7 30.2 - - + +
165C LEU* 3.8 32.3 - - + +
168C GLN* 3.1 24.5 + - - +
695C THR 3.2 14.8 + - - +
696C ALA 3.3 3.1 + - - +
698C THR* 1.3 80.5 - - - +
700C GLU* 1.3 62.4 + - - +
702C GLY* 3.4 8.3 + - - -
703C MET* 3.7 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 700 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C THR* 4.0 13.9 - - + +
149C ARG* 3.0 42.0 + - - +
150C LEU* 4.3 20.0 - - + -
653C HIS* 4.6 4.7 - - - -
657C LEU* 3.8 26.6 - - + +
696C ALA 3.0 16.1 + - - +
699C LEU* 1.3 74.9 - - - +
701C HIS* 1.3 56.2 + - - +
703C MET* 3.1 3.1 + - - +
704C HIS* 2.7 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 701 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C ILE 3.5 16.8 - - - +
657C LEU* 3.5 31.1 - - + +
659C GLN* 2.9 23.7 + - + +
660C PRO 3.2 17.1 + - - -
661C PRO* 4.1 2.5 - - + -
662C ASP* 4.0 14.4 - - - -
663C THR* 4.2 1.3 - - - -
664C ILE* 3.8 31.7 - - + +
665C ASN* 5.2 0.6 + - - -
697C ALA 3.1 17.4 + - - +
698C THR 3.9 4.7 - - - +
699C LEU 3.4 0.2 - - - -
700C GLU* 1.3 76.8 - - - +
702C GLY* 1.3 66.5 + - - +
703C MET 3.2 1.0 + - - -
704C HIS 3.3 14.4 + - - -
705C PRO* 3.4 14.0 - - + +
706C PRO* 3.8 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 702 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664C ILE* 5.8 0.2 - - - +
665C ASN* 4.5 28.4 + - - -
666C GLY 5.7 0.7 - - - -
698C THR 3.6 6.0 + - - -
699C LEU 3.4 7.1 + - - -
700C GLU 3.2 1.2 - - - -
701C HIS* 1.3 83.3 + - - +
703C MET* 1.3 63.7 + - - +
705C PRO* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 703 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LEU* 3.7 24.9 - - + -
154C VAL* 3.6 16.3 - - - +
156C LYS* 3.7 43.6 + - - +
160C GLU* 4.6 6.3 - - - +
161C VAL* 4.1 22.4 - - + -
164C ALA* 3.9 29.2 - - + -
699C LEU* 3.7 30.2 + - + +
700C GLU 3.1 2.4 + - - -
702C GLY* 1.3 79.1 - - - +
704C HIS* 1.3 60.1 + - - +
705C PRO* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 704 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ARG* 4.9 8.5 - - - -
150C LEU* 4.8 1.8 - - + -
154C VAL* 3.7 30.8 - - + +
657C LEU* 5.2 4.9 - - - +
700C GLU* 2.7 49.3 + - + +
701C HIS* 3.3 8.6 + - - +
703C MET* 1.3 76.8 - - - +
705C PRO* 1.3 77.0 + - + +
706C 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