Contacts of the helix formed by residues 684 - 699 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680D GLU 2.9 16.9 + - - -
681D PHE* 3.4 6.3 + - - -
682D ILE 3.3 2.4 - - - -
683D THR* 1.3 76.2 - - - +
685D GLY* 1.3 61.1 + - - -
686D GLU* 3.2 3.4 - - - -
687D TYR* 3.2 7.4 + - - +
688D ARG* 2.9 27.5 + - - +
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Residues in contact with GLY 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683D THR 3.4 2.2 + - - -
684D GLY* 1.3 72.1 - - - -
686D GLU* 1.3 56.0 + - - +
688D ARG* 3.4 15.3 - - - +
689D ARG* 2.9 39.8 + - - +
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Residues in contact with GLU 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593D MET* 4.3 19.1 - - - +
596D ARG* 6.0 0.2 + - - -
597D MET* 3.4 47.7 - - + +
600D ARG* 5.9 2.3 - - - -
684D GLY* 3.2 1.5 - - - -
685D GLY* 1.3 76.6 - - - +
687D TYR* 1.3 58.4 + - - +
689D ARG* 3.3 7.0 + - - +
690D ILE* 2.9 34.2 + - + +
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Residues in contact with TYR 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D LEU* 4.3 25.7 - - + +
614D THR 5.2 0.2 - - - -
615D LEU* 3.2 42.3 - - + +
629D TRP* 4.8 4.6 - + - -
677D LEU* 6.4 0.9 - - + -
681D PHE* 3.5 47.1 - + + +
682D ILE* 3.2 40.8 - - + -
684D GLY* 3.2 5.8 + - - +
686D GLU* 1.3 79.0 - - - +
688D ARG* 1.3 59.6 + - + +
690D ILE* 3.3 16.6 + - + +
691D CYS* 2.9 53.2 + - - -
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Residues in contact with ARG 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682D ILE 4.4 6.5 + - - +
683D THR* 3.4 30.3 + - - +
684D GLY 2.9 14.5 + - - +
685D GLY* 3.4 14.6 - - - +
686D GLU 3.2 0.2 - - - -
687D TYR* 1.3 79.3 - - + +
689D ARG* 1.3 58.2 + - + +
691D CYS* 3.3 6.6 + - - +
692D THR* 2.9 37.5 + - + +
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Residues in contact with ARG 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590D THR* 5.4 4.3 + - + +
593D MET* 3.6 39.0 - - + -
596D ARG* 5.7 1.0 - - - +
685D GLY 2.9 22.6 + - - +
686D GLU* 3.3 6.4 + - - +
688D ARG* 1.3 74.8 - - + +
690D ILE* 1.3 62.2 + - - +
692D THR* 2.5 23.7 + - - +
693D LEU* 2.9 13.5 + - - +
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Residues in contact with ILE 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590D THR* 5.1 5.4 - - + -
593D MET* 4.7 9.9 - - + -
594D ILE* 4.8 16.6 - - + -
597D MET* 4.4 22.7 - - + -
606D LEU* 4.6 21.1 - - + +
609D LEU* 4.4 33.6 - - + +
610D ILE* 5.3 4.3 - - + +
681D PHE* 6.5 0.7 - - + -
686D GLU* 2.9 25.2 + - + +
687D TYR* 3.5 17.5 - - + +
689D ARG* 1.3 76.6 - - - +
691D CYS* 1.3 58.7 + - - +
693D LEU* 3.4 5.7 + - - +
694D GLY* 2.9 26.3 + - - -
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Residues in contact with CYS 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D LEU 6.0 0.9 - - - -
614D THR* 5.0 16.4 - - - +
615D LEU 5.2 5.8 - - - +
687D TYR* 2.9 64.5 + - - +
688D ARG* 3.7 5.8 - - - +
690D ILE* 1.3 75.5 - - - +
692D THR* 1.3 60.1 + - + +
694D GLY* 3.7 1.3 - - - +
695D GLU* 2.9 39.1 + - - +
698D ARG* 4.5 2.0 + - - +
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Residues in contact with THR 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586D GLU* 5.6 1.4 + - - -
688D ARG* 2.9 19.5 + - + +
689D ARG* 2.5 28.7 + - - +
691D CYS* 1.3 78.1 - - + +
693D LEU* 1.3 57.0 + - - +
695D GLU* 3.3 11.0 + - - +
696D LYS* 2.9 28.6 + - - +
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Residues in contact with LEU 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D LEU* 5.1 5.4 - - + -
586D GLU* 4.7 25.4 - - + +
587D TYR* 4.2 21.8 - - + -
590D THR* 3.6 37.0 - - + +
591D GLN* 5.6 0.9 - - - +
610D ILE* 5.9 4.9 - - + -
689D ARG 2.9 13.2 + - - +
690D ILE* 3.8 4.7 - - - +
692D THR* 1.3 80.8 + - - +
694D GLY* 1.3 58.6 + - - +
696D LYS* 3.3 12.4 + - + +
697D LEU* 2.9 62.6 + - + +
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Residues in contact with GLY 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D LEU 4.9 1.6 - - - -
610D ILE* 3.6 24.0 - - - -
690D ILE 2.9 17.1 + - - -
691D CYS* 3.3 2.4 + - - -
693D LEU* 1.3 76.4 - - - +
695D GLU* 1.3 56.3 + - - +
697D LEU* 3.3 4.2 + - - +
698D ARG* 2.9 46.7 + - - +
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Residues in contact with GLU 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D THR* 3.5 21.4 + - - +
691D CYS* 2.9 24.8 + - + +
692D THR* 3.7 8.8 - - - +
694D GLY* 1.3 76.0 - - - +
696D LYS* 1.3 63.4 + - - +
698D ARG* 3.3 23.6 + - - +
699D GLY* 2.9 22.0 + - - -
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Residues in contact with LYS 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LYS* 5.6 6.7 + - - +
583D LEU* 3.6 33.5 - - + +
586D GLU* 3.0 30.6 + - - +
692D THR 2.9 17.8 + - - +
693D LEU* 3.6 13.2 - - + +
695D GLU* 1.3 77.3 - - - +
697D LEU* 1.3 60.7 + - - +
699D GLY* 3.5 6.3 + - - -
700D LEU* 3.3 20.3 + - + +
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Residues in contact with LEU 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D LEU* 4.4 16.8 - - + -
587D TYR* 4.4 15.5 - - + -
610D ILE* 3.8 30.1 - - + +
611D TYR* 6.0 5.7 - - + -
693D LEU* 2.9 48.7 + - + +
694D GLY* 3.9 4.0 - - - +
696D LYS* 1.3 77.0 - - - +
698D ARG* 1.3 63.8 + - + +
700D LEU* 3.2 38.8 - - + +
701D LEU 4.4 1.4 + - - -
702D GLU* 4.5 18.1 - - - +
719D PHE* 5.1 11.4 - - + -
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Residues in contact with ARG 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D LEU 4.2 3.2 + - - -
610D ILE 3.4 22.9 + - - +
611D TYR* 3.7 25.8 - - + +
612D GLN 2.5 29.6 + - - -
613D PRO* 4.1 8.1 - - - +
614D THR* 3.6 21.8 - - - +
691D CYS* 4.5 3.8 + - - +
694D GLY* 2.9 26.5 + - - +
695D GLU* 3.3 35.6 + - - +
697D LEU* 1.3 71.3 - - + +
699D GLY* 1.3 57.0 + - - +
700D LEU 3.0 9.5 + - - -
701D LEU* 3.9 16.2 + - - +
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Residues in contact with GLY 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695D GLU 2.9 15.9 + - - -
696D LYS* 3.5 3.3 + - - -
697D LEU 3.2 0.8 - - - -
698D ARG* 1.3 75.2 - - - +
700D LEU* 1.3 64.0 + - - +
701D LEU* 5.2 2.6 - - - +
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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