Contacts of the helix formed by residues 683 - 704 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLU* 4.7 9.1 + - + +
115E VAL* 5.7 1.3 - - + -
118E ALA* 3.4 22.4 - - + +
119E HIS* 4.2 6.1 + - - -
194E ARG* 3.7 31.9 - - + +
251E THR* 4.1 2.5 - - - -
678E GLU 4.6 0.6 + - - -
682E GLY* 1.3 77.9 - - - +
684E GLU* 1.3 70.2 + - - +
685E HIS* 2.8 47.6 + - - +
686E LEU* 3.0 31.4 + - + +
687E CYS* 2.8 22.7 + - - +
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Residues in contact with GLU 684 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E GLU 5.3 6.1 - - - +
251E THR* 3.8 18.0 + - - +
254E LYS* 6.4 0.9 - - - -
258E LYS* 4.0 25.1 + - + +
682E GLY 4.2 0.6 + - - -
683E GLU* 1.3 75.9 + - - +
685E HIS* 1.3 74.7 + - + +
687E CYS* 3.3 3.9 + - - +
688E PHE* 3.1 21.7 + - - +
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Residues in contact with HIS 685 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ALA* 4.0 24.9 - - + +
119E HIS* 3.9 22.6 - + - -
683E GLU* 2.8 35.9 + - - +
684E GLU* 1.3 82.6 - - + +
686E LEU* 1.3 55.8 + - - +
688E PHE* 3.2 9.7 + - - +
689E GLN* 3.0 35.9 + - - +
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Residues in contact with LEU 686 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E GLU* 4.1 36.3 - - + +
117E ILE* 3.5 35.4 - - + -
118E ALA* 4.1 15.0 - - - -
679E PHE* 3.5 27.6 - - + +
680E CYS* 3.3 5.2 - - - +
683E GLU* 3.0 21.5 + - + +
685E HIS* 1.3 74.0 - - - +
687E CYS* 1.3 60.5 + - - +
689E GLN* 3.4 16.3 + - + +
690E THR* 2.9 33.8 + - - +
693E ARG* 5.0 0.5 + - - -
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Residues in contact with CYS 687 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E THR* 3.6 35.9 - - - +
252E VAL* 4.2 5.4 - - - -
255E GLY* 4.4 6.7 - - - -
680E CYS 3.3 11.5 + - - +
681E PHE* 3.9 24.9 - - + -
683E GLU 2.8 12.2 + - - +
684E GLU* 3.5 9.0 - - - +
686E LEU* 1.3 74.1 - - - +
688E PHE* 1.3 64.7 + - - +
690E THR* 3.3 1.9 + - - -
691E LEU* 3.0 44.8 + - - +
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Residues in contact with PHE 688 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E GLY* 5.1 3.1 - - - -
258E LYS* 3.8 20.6 - - + -
259E PHE* 3.5 39.0 - + + -
262E ARG* 3.7 46.0 - - + -
684E GLU 3.1 13.1 + - - +
685E HIS* 3.3 12.1 - - - +
687E CYS* 1.3 78.7 - - - +
689E GLN* 1.3 67.8 + - + +
691E LEU* 3.3 7.1 + - - +
692E GLN* 3.0 47.0 + - - +
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Residues in contact with GLN 689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 4.8 10.0 + - - +
118E ALA 4.8 11.5 + - - -
137E ALA* 5.0 6.1 - - - +
140E GLU* 4.8 3.0 - - - +
685E HIS* 3.0 24.3 + - - +
686E LEU* 4.0 20.9 - - - +
688E PHE* 1.3 82.3 - - + +
690E THR* 1.3 61.4 + - - +
692E GLN* 3.6 18.7 + - - +
693E ARG* 3.1 49.7 + - - +
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Residues in contact with THR 690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E LEU* 5.1 0.4 - - + -
648E GLY 3.8 6.2 + - - +
649E GLY* 4.9 0.5 - - - -
680E CYS* 2.9 29.0 + - + +
681E PHE* 3.6 27.4 - - + -
686E LEU 2.9 22.7 + - - -
687E CYS 3.6 4.7 - - - -
689E GLN* 1.3 78.8 - - - +
691E LEU* 1.3 63.4 + - - +
692E GLN 3.2 0.7 + - - -
693E ARG* 3.4 18.1 + - - +
694E PHE* 3.3 47.3 + - + -
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Residues in contact with LEU 691 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E LEU* 4.4 8.5 - - + -
252E VAL* 5.4 0.7 - - + -
255E GLY 4.1 8.1 - - - +
256E VAL* 4.1 34.1 - - + +
259E PHE* 4.0 16.6 - - + -
283E ILE* 4.0 26.1 - - + +
285E PHE* 4.0 22.9 - - + -
681E PHE* 4.1 13.9 - - + -
687E CYS* 3.0 32.4 + - - +
688E PHE* 3.8 4.5 - - - +
690E THR* 1.3 76.2 - - - +
692E GLN* 1.3 61.6 + - - +
694E PHE* 3.7 5.3 + - - +
695E THR* 3.2 27.9 + - - +
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Residues in contact with GLN 692 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E GLU* 5.3 6.1 + - - +
141E SER 5.2 1.1 + - - +
142E ASP* 3.1 22.0 - - - +
143E ILE* 3.0 40.7 + - + +
259E PHE* 3.5 24.5 - - + -
262E ARG* 4.9 2.8 + - - +
688E PHE* 3.0 33.7 + - + +
689E GLN* 3.6 22.3 + - - +
690E THR 3.1 0.4 - - - -
691E LEU* 1.3 74.5 - - - +
693E ARG* 1.3 61.6 + - - +
695E THR* 3.0 4.2 + - - -
696E ALA* 2.9 30.3 + - + +
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Residues in contact with ARG 693 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ALA* 3.9 18.0 - - - +
140E GLU* 2.8 44.5 + - - +
141E SER 5.6 0.9 - - - -
648E GLY 2.9 27.8 + - - +
649E GLY* 3.4 11.3 - - - -
650E GLY* 3.6 25.2 - - - +
652E THR* 4.5 4.9 - - - -
653E HIS* 3.7 19.8 - - + +
656E ILE* 5.0 0.4 - - - +
686E LEU 5.0 0.2 + - - -
689E GLN* 3.1 31.1 + - - +
690E THR* 3.5 29.5 + - - +
692E GLN* 1.3 78.6 - - - +
694E PHE* 1.3 65.3 + - + +
696E ALA* 4.4 3.8 - - - -
697E ALA* 2.9 34.0 + - - +
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Residues in contact with PHE 694 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E VAL* 3.8 19.4 - - + +
172E LEU* 4.0 34.5 - - + -
645E VAL 4.0 7.4 - - - -
646E GLY* 5.8 0.4 - - - -
648E GLY* 4.5 13.7 - - - -
652E THR* 3.4 29.6 - - + -
656E ILE* 3.7 17.0 - - + +
668E ILE* 6.2 0.2 - - + -
670E VAL* 4.0 24.7 - - + -
672E VAL* 5.7 4.5 - - + -
681E PHE* 6.3 0.2 - + - -
690E THR* 3.3 40.3 + - + +
691E LEU* 4.0 5.4 - - - +
692E GLN 3.2 1.0 - - - -
693E ARG* 1.3 86.6 - - + +
695E THR* 1.3 60.8 + - + +
698E THR* 3.0 32.8 + - + +
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Residues in contact with THR 695 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ILE* 4.6 6.7 - - - +
165E LEU* 5.4 2.4 - - - +
168E GLN* 3.1 23.6 + - - +
170E VAL* 4.4 7.9 - - + -
259E PHE* 3.0 26.2 - - + -
282E LEU* 4.2 13.9 - - + -
283E ILE* 3.8 29.4 - - + -
691E LEU 3.2 10.3 + - - +
692E GLN 3.0 11.3 + - - -
694E PHE* 1.3 76.6 - - + +
696E ALA* 1.3 65.3 + - - +
699E LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 696 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E SER 4.6 3.4 - - - +
142E ASP 5.0 0.2 - - - -
143E ILE* 4.2 19.9 - - + +
146E THR* 3.6 30.7 - - + +
653E HIS* 4.3 14.1 - - + -
692E GLN* 2.9 17.9 + - + +
693E ARG* 4.1 2.9 - - - +
695E THR* 1.3 76.2 + - - +
697E ALA* 1.3 65.7 + - - +
699E LEU* 3.7 1.7 - - - +
700E GLU* 3.0 26.2 + - - +
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Residues in contact with ALA 697 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653E HIS* 3.6 41.0 + - + +
656E ILE* 3.7 20.6 - - + -
657E LEU* 3.4 14.2 - - + +
693E ARG 2.9 19.1 + - - +
696E ALA* 1.3 76.4 - - - +
698E THR* 1.3 58.5 + - - +
700E GLU* 4.8 0.2 - - - -
701E HIS* 3.0 28.2 + - - +
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Residues in contact with THR 698 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLN* 2.9 31.3 + - - +
170E VAL* 3.6 7.1 - - + +
656E ILE* 3.6 29.8 - - + -
664E ILE* 4.4 18.1 - - + +
666E GLY* 5.1 7.1 + - - -
668E ILE* 3.8 25.6 - - + -
694E PHE* 3.0 18.6 + - + +
696E ALA 3.3 0.2 - - - -
697E ALA* 1.3 72.9 - - - +
699E LEU* 1.3 66.6 + - - +
701E HIS* 3.7 3.5 + - - +
702E GLY* 3.6 14.0 + - - -
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Residues in contact with LEU 699 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ILE* 4.7 8.3 - - + -
146E THR* 4.8 3.4 - - + -
147E LEU* 3.6 31.4 - - + -
150E LEU* 4.0 9.4 - - + -
161E VAL* 4.4 2.9 - - + +
164E ALA* 3.6 19.7 - - + -
165E LEU* 3.9 30.1 - - + +
168E GLN* 3.2 20.4 - - - +
695E THR 3.0 19.7 + - - +
696E ALA 3.7 2.0 - - - +
698E THR* 1.3 80.0 + - - +
700E GLU* 1.3 64.1 + - - +
702E GLY* 3.4 7.6 + - - -
703E MET* 3.6 36.6 + - + +
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Residues in contact with GLU 700 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 4.6 0.7 - - - +
146E THR* 3.9 15.0 + - + +
149E ARG* 2.6 40.9 + - - -
150E LEU* 4.4 17.7 - - + -
653E HIS* 4.8 3.8 + - - -
657E LEU* 3.7 25.7 - - + +
696E ALA 3.0 16.4 + - - +
697E ALA 3.9 2.7 - - - +
699E LEU* 1.3 75.2 - - - +
701E HIS* 1.3 58.0 + - - +
703E MET* 2.9 4.5 + - - +
704E HIS* 2.8 65.7 + - + +
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Residues in contact with HIS 701 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656E ILE 3.3 22.9 - - - +
657E LEU* 3.6 22.8 - - + +
659E GLN* 2.9 24.4 + - - +
660E PRO 3.2 17.3 + - - -
661E PRO* 4.2 2.0 - - + -
662E ASP 4.0 14.5 + - - -
663E THR* 3.9 2.7 - - - -
664E ILE* 3.5 35.0 + - + +
665E ASN* 5.2 0.8 + - - -
697E ALA 3.0 17.8 + - - +
698E THR 4.0 5.4 - - - +
699E LEU 3.4 0.2 - - - -
700E GLU* 1.3 76.6 - - - +
702E GLY* 1.3 65.4 + - - +
703E MET 3.2 1.0 + - - -
704E HIS 3.3 14.7 + - - -
705E PRO* 3.5 13.9 - - - +
706E PRO* 4.0 8.2 - - + +
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Residues in contact with GLY 702 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662E ASP* 5.3 3.3 - - - +
664E ILE* 5.8 0.2 - - - +
665E ASN* 4.4 25.5 - - - +
666E GLY 5.7 0.7 - - - -
698E THR 3.6 6.0 + - - -
699E LEU 3.4 6.9 + - - -
700E GLU 3.2 1.4 - - - -
701E HIS* 1.3 82.9 + - - +
703E MET* 1.3 64.4 + - - +
705E PRO* 5.3 1.5 - - - +
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Residues in contact with MET 703 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LEU* 3.6 39.3 - - + -
154E VAL* 3.4 17.3 - - - +
156E LYS* 3.5 41.6 + - + +
160E GLU* 4.5 5.6 - - - +
161E VAL* 4.3 18.2 - - - -
164E ALA* 3.9 17.7 - - + -
699E LEU* 3.6 34.0 + - + +
700E GLU 2.9 2.8 + - - +
702E GLY* 1.3 80.2 - - - +
704E HIS* 1.3 61.8 + - - +
705E PRO* 3.9 5.4 - - - +
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Residues in contact with HIS 704 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ARG* 4.6 8.2 - - - -
150E LEU* 4.6 2.2 - - + -
154E VAL* 3.7 31.3 - - + +
657E LEU* 5.2 3.8 - - - +
700E GLU* 2.8 42.4 + - + +
701E HIS* 3.3 9.9 + - - +
703E MET* 1.3 81.6 - - - +
705E PRO* 1.3 77.3 + - + +
706E PRO* 4.5 0.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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