Contacts of the helix formed by residues 683 - 704 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F GLU* 4.7 10.3 - - + +
115F VAL* 5.7 1.5 - - + -
118F ALA* 3.5 19.1 - - + +
119F HIS* 4.4 5.9 + - - -
194F ARG* 3.7 31.0 - - - +
251F THR* 4.2 3.4 - - - -
682F GLY* 1.3 79.0 - - - +
684F GLU* 1.3 77.7 + - - +
685F HIS* 2.6 52.9 + - - +
686F LEU* 3.0 25.8 + - + +
687F CYS* 2.9 22.2 + - - +
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Residues in contact with GLU 684 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250F GLU 5.7 0.4 - - - +
251F THR* 3.7 17.4 + - - +
254F LYS* 4.1 25.0 + - - +
682F GLY 4.4 0.2 + - - -
683F GLU* 1.3 76.8 + - - +
685F HIS* 1.3 77.3 + - + +
687F CYS* 3.3 4.3 + - - +
688F PHE* 3.1 20.1 + - - +
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Residues in contact with HIS 685 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ALA* 3.9 26.9 - - + +
119F HIS* 4.0 21.4 - + - -
683F GLU* 2.6 38.0 + - - +
684F GLU* 1.3 85.1 - - + +
686F LEU* 1.3 56.9 + - + +
688F PHE* 3.1 11.2 + - - +
689F GLN* 3.0 30.0 + - + +
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Residues in contact with LEU 686 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU* 4.0 35.4 - - + +
117F ILE* 3.5 35.9 - - + +
118F ALA* 3.8 18.4 - - - -
679F PHE* 3.8 21.5 - - + +
680F CYS 3.4 9.6 - - - +
683F GLU* 3.0 20.7 + - + +
685F HIS* 1.3 73.6 - - + +
687F CYS* 1.3 61.3 + - - +
689F GLN* 3.1 13.0 + - + +
690F THR* 2.8 33.1 + - - -
693F ARG* 5.1 0.3 + - - -
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Residues in contact with CYS 687 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F THR* 3.9 36.8 - - + +
252F VAL* 4.2 6.5 - - - -
255F GLY* 4.5 6.1 - - - -
680F CYS 3.3 10.8 + - - -
681F PHE* 3.7 27.1 - - + -
683F GLU 2.9 12.5 + - - +
684F GLU 3.5 9.0 - - - +
686F LEU* 1.3 77.4 - - - +
688F PHE* 1.3 61.8 + - - +
690F THR* 3.4 1.6 + - - -
691F LEU* 3.1 45.3 + - - +
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Residues in contact with PHE 688 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F GLY* 5.1 4.5 - - - -
258F LYS* 3.7 36.3 - - + -
259F PHE* 3.5 37.6 - + + -
262F ARG* 3.6 43.1 - - + -
684F GLU 3.1 12.9 + - - +
685F HIS* 3.1 13.4 + - - +
687F CYS* 1.3 79.8 - - - +
689F GLN* 1.3 74.6 + - - +
691F LEU* 3.5 7.9 + - - +
692F GLN* 3.1 38.1 + - + +
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Residues in contact with GLN 689 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG* 5.1 12.5 - - - +
137F ALA* 5.4 7.1 + - - +
140F GLU* 4.5 11.2 + - - +
685F HIS* 3.0 21.2 + - + +
686F LEU* 3.1 16.1 + - + +
688F PHE* 1.3 84.8 - - + +
690F THR* 1.3 65.1 + - - +
692F GLN* 3.0 30.0 + - - +
693F ARG* 3.2 44.6 + - - +
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Residues in contact with THR 690 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F LEU* 5.3 0.2 - - + -
648F GLY 3.8 7.8 + - - +
649F GLY* 5.5 0.2 - - - -
680F CYS* 2.9 36.3 + - + +
681F PHE* 3.7 26.7 - - + -
686F LEU* 2.8 13.0 + - - +
687F CYS 3.7 4.5 - - - -
689F GLN* 1.3 73.5 - - - +
691F LEU* 1.3 67.2 + - - +
692F GLN 3.2 0.7 + - - -
693F ARG* 3.4 19.2 + - - +
694F PHE* 3.2 49.1 + - + -
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Residues in contact with LEU 691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F LEU* 4.5 7.0 - - + -
252F VAL* 5.3 1.1 - - + -
255F GLY 4.0 28.3 - - - +
256F VAL* 4.2 13.2 - - + +
259F PHE* 4.3 19.7 - - + -
283F ILE* 4.3 19.7 - - + +
285F PHE* 4.1 24.2 - - + -
681F PHE* 4.2 14.6 - - + -
687F CYS* 3.1 27.5 + - - +
688F PHE* 3.9 5.2 - - - +
690F THR* 1.3 76.5 - - - +
692F GLN* 1.3 62.0 + - - +
694F PHE* 3.6 6.0 + - - +
695F THR* 3.1 26.9 + - - -
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Residues in contact with GLN 692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLU* 5.2 5.7 + - - +
141F SER 5.0 1.2 + - - +
142F ASP* 3.2 21.6 - - - +
143F ILE* 3.1 38.7 + - + +
259F PHE* 3.5 25.2 - - + -
262F ARG* 4.8 3.6 + - - +
688F PHE* 3.1 30.1 + - - +
689F GLN* 3.0 33.5 + - - +
690F THR 3.1 0.4 - - - -
691F LEU* 1.3 77.7 - - - +
693F ARG* 1.3 59.3 + - - +
695F THR* 3.2 3.3 + - - -
696F ALA* 2.8 28.2 + - + +
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Residues in contact with ARG 693 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ALA* 3.8 11.7 - - - +
140F GLU* 3.0 43.9 + - - +
141F SER 5.6 0.7 - - - -
648F GLY 2.7 29.8 + - - -
649F GLY* 3.1 23.1 + - - -
650F GLY* 3.7 8.1 - - - -
652F THR* 3.5 29.4 - - + -
653F HIS* 3.8 15.0 - - + +
689F GLN* 3.2 28.0 + - - +
690F THR* 3.4 29.3 + - - +
692F GLN* 1.3 76.7 - - - +
694F PHE* 1.3 64.6 + - + +
696F ALA* 4.4 3.4 - - - +
697F ALA* 2.9 35.5 + - - +
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Residues in contact with PHE 694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F VAL* 4.0 20.8 - - + +
172F LEU* 4.0 37.7 - - + -
283F ILE* 6.6 0.2 - - + -
645F VAL 4.2 7.2 - - - -
646F GLY* 5.8 0.9 - - - -
648F GLY* 4.5 12.8 - - - -
652F THR* 3.5 27.1 - - + -
656F ILE* 3.8 20.6 - - + -
668F ILE* 6.4 0.2 - - + -
670F VAL* 4.1 20.6 - - + -
672F VAL* 5.7 4.7 - - + -
681F PHE* 6.2 0.2 - + - -
690F THR* 3.2 42.9 + - + +
691F LEU* 3.9 4.7 - - - +
693F ARG* 1.3 82.3 - - + +
695F THR* 1.3 60.9 + - - +
697F ALA* 4.4 0.2 - - - +
698F THR* 2.8 32.1 + - - -
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Residues in contact with THR 695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ILE* 4.3 8.5 - - + -
165F LEU* 4.3 11.7 - - + -
168F GLN* 3.0 35.2 + - - +
170F VAL* 4.8 4.3 - - - +
259F PHE* 3.3 27.4 - - + -
263F VAL* 5.2 0.4 - - + -
282F LEU* 4.0 19.0 + - + +
283F ILE* 4.1 14.2 - - - +
691F LEU 3.1 16.7 + - - -
692F GLN 3.6 4.0 - - - -
694F PHE* 1.3 79.5 - - - +
696F ALA* 1.3 62.1 + - - +
699F LEU* 3.1 12.3 + - - +
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Residues in contact with ALA 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F SER 4.5 4.7 - - - +
143F ILE* 4.1 23.8 - - + +
146F THR* 3.6 26.5 - - - +
653F HIS* 4.3 13.5 - - + -
692F GLN 2.8 20.8 + - - +
693F ARG* 4.1 1.8 - - - +
695F THR* 1.3 70.7 - - - +
697F ALA* 1.3 66.0 + - - +
699F LEU* 3.3 3.4 + - - +
700F GLU* 3.0 26.0 + - - +
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Residues in contact with ALA 697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653F HIS* 3.5 43.0 + - + +
656F ILE* 3.8 19.6 - - + +
657F LEU* 3.8 10.4 - - + +
693F ARG 2.9 22.8 + - - +
696F ALA* 1.3 73.4 - - - +
698F THR* 1.3 64.0 + - - +
700F GLU* 4.8 0.2 - - - -
701F HIS* 3.1 25.6 + - - +
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Residues in contact with THR 698 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F GLN* 3.9 22.6 - - + +
170F VAL* 3.6 11.8 - - + +
656F ILE* 4.0 18.8 - - - +
664F ILE* 3.7 28.6 - - + +
666F GLY* 4.5 10.5 + - - -
668F ILE* 3.9 17.9 - - + +
694F PHE 2.8 22.7 + - - -
697F ALA* 1.3 79.1 - - - +
699F LEU* 1.3 64.7 + - - +
701F HIS* 3.6 8.4 + - - +
702F GLY* 3.7 8.3 + - - -
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Residues in contact with LEU 699 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ILE* 4.6 8.3 - - + -
146F THR* 5.0 6.3 - - + -
147F LEU* 3.6 31.0 - - + -
150F LEU* 5.6 2.0 - - + -
161F VAL* 4.3 4.9 - - + +
164F ALA* 3.7 18.6 - - + -
165F LEU* 4.0 29.2 - - + +
168F GLN* 3.1 24.8 + - - +
695F THR 3.1 15.4 + - - +
696F ALA 3.3 3.6 + - - +
698F THR* 1.3 78.8 - - - +
700F GLU* 1.3 63.5 + - - +
702F GLY* 3.4 8.5 + - - -
703F MET* 3.6 38.9 + - + +
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Residues in contact with GLU 700 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU* 4.9 0.2 - - - +
146F THR* 4.0 13.0 + - + +
149F ARG* 2.7 38.4 + - - -
150F LEU* 4.2 17.2 - - + +
653F HIS* 4.7 5.5 + - - -
657F LEU* 3.9 25.9 - - + +
696F ALA 3.0 16.4 + - - +
697F ALA 4.0 2.7 - - - +
699F LEU* 1.3 74.6 - - - +
701F HIS* 1.3 63.3 + - - +
703F MET* 3.0 3.5 + - - +
704F HIS* 2.7 61.9 + - + +
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Residues in contact with HIS 701 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656F ILE 3.5 22.9 - - - +
657F LEU* 3.6 22.6 - - - +
659F GLN* 3.0 23.7 + - - +
660F PRO 3.1 16.9 + - - -
661F PRO* 4.2 1.6 - - + -
662F ASP* 3.9 16.8 + - - -
663F THR* 4.1 2.0 - - - -
664F ILE* 3.7 33.2 - - + +
665F ASN 5.2 0.6 + - - -
697F ALA 3.1 17.6 + - - +
698F THR 4.0 4.7 - - - +
699F LEU 3.4 0.2 - - - -
700F GLU* 1.3 78.4 - - - +
702F GLY* 1.3 66.1 + - - +
703F MET 3.3 0.7 + - - -
704F HIS 3.3 13.3 + - - -
705F PRO* 3.5 13.7 - - - +
706F PRO* 3.9 9.9 - - + +
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Residues in contact with GLY 702 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662F ASP* 5.0 7.1 - - - +
664F ILE* 6.4 0.2 - - - -
665F ASN* 5.1 19.5 - - - +
666F GLY 5.8 0.9 - - - -
698F THR 3.7 5.6 + - - -
699F LEU 3.4 7.3 + - - -
700F GLU 3.1 1.6 + - - -
701F HIS* 1.3 84.9 + - - +
703F MET* 1.3 62.9 + - - +
705F PRO* 5.1 2.1 - - - +
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Residues in contact with MET 703 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F LEU* 3.6 33.9 - - + -
154F VAL* 3.5 16.5 - - - +
156F LYS* 3.7 42.2 - - - +
160F GLU* 4.8 4.7 - - - +
161F VAL* 4.4 17.9 - - + -
164F ALA* 3.9 17.5 - - + -
699F LEU* 3.6 42.3 + - + +
700F GLU 3.0 2.4 + - - +
702F GLY* 1.3 80.0 - - - +
704F HIS* 1.3 60.9 + - - +
705F PRO* 3.9 6.2 - - - +
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Residues in contact with HIS 704 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F ARG* 4.6 8.0 - - - -
150F LEU* 5.0 1.6 - - + -
154F VAL* 3.9 29.6 - - + +
657F LEU* 5.4 2.9 - - - +
700F GLU* 2.7 46.1 + - + +
701F HIS* 3.3 9.2 + - - +
703F MET* 1.3 81.8 - - + +
705F PRO* 1.3 79.3 + - + +
706F PRO* 3.9 0.5 - - - +
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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) + - + + + + + -
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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