Contacts of the helix formed by residues 684 - 699 (chain B) in PDB entry 6RKU
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 GLY 684 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680B GLU 2.9 16.5 + - - -
681B PHE* 3.4 5.9 + - - -
682B ILE 3.3 2.6 - - - -
683B THR* 1.3 75.2 - - - +
685B GLY* 1.3 60.9 + - - -
686B GLU* 3.2 4.5 - - - -
687B TYR* 3.2 6.8 + - - +
688B ARG* 2.9 28.1 + - - +
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Residues in contact with GLY 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B THR 3.4 2.6 + - - -
684B GLY* 1.3 72.5 - - - -
686B GLU* 1.3 55.7 + - - +
688B ARG* 3.4 15.2 - - - +
689B ARG* 2.9 39.8 + - - +
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Residues in contact with GLU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B MET* 4.3 18.7 - - - +
596B ARG* 6.0 0.2 + - - -
597B MET* 3.4 46.1 - - + +
600B ARG* 5.9 2.3 - - - -
684B GLY* 3.2 1.5 - - - -
685B GLY* 1.3 76.2 - - - +
687B TYR* 1.3 58.0 + - - +
689B ARG* 3.3 6.4 + - - +
690B ILE* 2.9 34.7 + - + +
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Residues in contact with TYR 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B LEU* 4.3 24.7 - - + +
614B THR 5.2 0.2 - - - -
615B LEU* 3.2 42.2 + - + +
629B TRP* 4.8 4.6 - + - -
677B LEU* 6.4 0.4 - - + -
681B PHE* 3.5 47.6 - + + +
682B ILE* 3.2 41.1 - - + -
684B GLY* 3.2 6.0 + - - +
686B GLU* 1.3 76.9 - - - +
688B ARG* 1.3 58.6 + - + +
690B ILE* 3.3 16.9 + - + +
691B CYS* 2.9 53.5 + - - -
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Residues in contact with ARG 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682B ILE 4.4 6.2 + - - +
683B THR* 3.4 30.7 + - - +
684B GLY 2.9 15.4 + - - +
685B GLY* 3.4 14.8 - - - +
686B GLU 3.2 0.2 - - - -
687B TYR* 1.3 78.2 - - + +
689B ARG* 1.3 57.1 + - + +
691B CYS* 3.3 6.4 + - - +
692B THR* 2.9 38.1 + - + +
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Residues in contact with ARG 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B THR* 5.6 4.4 + - + +
593B MET* 3.6 37.5 - - + -
596B ARG* 5.7 1.4 - - - +
685B GLY* 2.9 24.1 + - - +
686B GLU* 3.6 5.4 - - - +
688B ARG* 1.3 76.1 - - + +
690B ILE* 1.3 63.0 + - - +
692B THR* 2.5 23.8 + - - +
693B LEU* 2.9 13.7 + - - +
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Residues in contact with ILE 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B THR* 5.1 4.9 - - + -
593B MET* 4.7 9.9 - - + -
594B ILE* 4.8 17.0 - - + -
597B MET* 4.4 21.8 - - + -
606B LEU* 4.6 22.0 - - + +
609B LEU* 4.4 32.3 - - + +
610B ILE* 5.3 5.1 - - + +
681B PHE* 6.5 0.4 - - + -
686B GLU 2.9 26.1 + - - +
687B TYR* 3.5 18.2 - - + +
688B ARG 3.2 0.2 - - - -
689B ARG* 1.3 77.1 - - - +
691B CYS* 1.3 58.9 + - - +
693B LEU* 3.4 4.9 + - - +
694B GLY* 2.9 26.7 + - - -
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Residues in contact with CYS 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B LEU 6.0 0.9 - - - -
614B THR* 5.0 15.5 - - - +
615B LEU 5.2 5.8 - - - -
687B TYR* 2.9 64.7 + - - +
688B ARG* 3.7 6.1 - - - +
690B ILE* 1.3 75.6 - - - +
692B THR* 1.3 61.5 + - + +
694B GLY* 3.3 2.2 + - - +
695B GLU* 2.9 39.5 + - + +
698B ARG* 4.5 2.4 + - - +
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Residues in contact with THR 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586B GLU* 5.6 1.6 + - - -
688B ARG* 2.9 20.2 + - + +
689B ARG* 2.5 29.0 + - - +
691B CYS* 1.3 78.1 - - + +
693B LEU* 1.3 55.5 + - - -
695B GLU* 3.3 11.8 + - - +
696B LYS* 2.9 29.2 + - - +
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Residues in contact with LEU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B LEU* 5.1 4.7 - - + -
586B GLU* 4.7 26.0 - - + +
587B TYR* 4.2 21.8 - - + +
590B THR* 3.6 38.1 - - + +
591B GLN* 5.6 1.1 - - - +
610B ILE* 5.9 5.2 - - + -
689B ARG 2.9 12.6 + - - +
690B ILE* 3.8 5.2 - - - +
692B THR* 1.3 81.9 + - - +
694B GLY* 1.3 59.2 + - - +
696B LYS* 3.3 13.3 + - + +
697B LEU* 2.9 63.7 + - + +
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Residues in contact with GLY 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B LEU 4.9 1.1 - - - -
610B ILE* 3.6 24.0 - - - +
690B ILE 2.9 17.1 + - - -
691B CYS* 3.3 2.9 + - - -
693B LEU* 1.3 77.6 - - - +
695B GLU* 1.3 56.3 + - - +
697B LEU* 3.3 5.3 + - - +
698B ARG* 2.9 45.6 + - - +
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Residues in contact with GLU 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B THR* 3.5 22.5 + - - +
691B CYS* 2.9 25.2 + - - +
692B THR* 3.7 9.9 - - - +
694B GLY* 1.3 75.3 - - - +
696B LYS* 1.3 62.4 + - - +
698B ARG* 3.3 24.0 + - - +
699B GLY* 2.9 21.3 + - - -
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Residues in contact with LYS 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B LYS* 5.6 6.7 + - - +
583B LEU* 3.6 33.7 - - + +
586B GLU* 3.0 30.7 + - - +
692B THR 2.9 17.2 + - - +
693B LEU* 3.3 13.2 + - + +
695B GLU* 1.3 76.4 - - - +
697B LEU* 1.3 60.7 + - - +
699B GLY* 3.5 7.0 + - - -
700B LEU* 3.3 20.9 + - + +
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Residues in contact with LEU 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B LEU* 4.4 16.8 - - + -
587B TYR* 4.4 15.7 - - + -
610B ILE* 3.8 30.3 - - + +
611B TYR* 6.0 6.0 - - + -
693B LEU* 2.9 49.5 + - + +
694B GLY* 3.9 3.8 - - - +
696B LYS* 1.3 75.6 - - - +
698B ARG* 1.3 64.8 + - + +
700B LEU* 3.2 38.4 - - + +
701B LEU 4.4 1.9 + - - -
702B GLU* 4.5 16.4 - - - +
719B PHE* 5.1 11.4 - - + -
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Residues in contact with ARG 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B LEU 4.2 2.8 + - - -
610B ILE 3.4 22.7 + - - +
611B TYR* 3.7 24.0 - - + +
612B GLN 2.5 29.5 + - - -
613B PRO* 4.1 7.7 + - - +
614B THR* 3.6 21.4 - - - +
691B CYS* 4.5 3.2 + - - +
694B GLY* 2.9 26.7 + - - +
695B GLU* 3.4 35.6 - - - +
697B LEU* 1.3 72.6 - - + +
699B GLY* 1.3 58.9 + - - +
700B LEU 3.0 9.2 + - - -
701B LEU* 3.9 16.9 + - - +
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Residues in contact with GLY 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B GLU 2.9 15.3 + - - -
696B LYS* 3.5 4.4 + - - -
697B LEU 3.2 1.0 - - - -
698B ARG* 1.3 75.0 - - - +
700B LEU* 1.3 62.0 + - - +
701B LEU* 3.8 2.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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