Contacts of the helix formed by residues 683 - 704 (chain C) in PDB entry 3K23
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 GLN 683 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C LEU* 5.2 5.5 - - - +
675C VAL* 4.7 15.1 - - - +
679C GLY* 3.6 10.7 - - - -
680C LEU 2.5 49.5 + - - +
681C LYS* 3.2 22.0 - - + +
684C GLU* 1.3 67.3 + - - +
685C LEU 3.6 2.1 - - - +
686C PHE* 3.2 48.0 - - - +
687C ASP* 3.0 46.2 + - - +
772C LEU* 5.6 2.0 - - - +
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Residues in contact with GLU 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C LYS* 4.9 2.7 - - + +
683C GLN* 1.3 79.5 - - - +
685C LEU* 1.3 67.2 + - - +
687C ASP* 3.3 2.6 + - - +
688C GLU* 3.0 21.9 + - - +
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Residues in contact with LEU 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C GLY* 3.6 26.7 - - - +
586C ASN* 3.5 28.9 - - + +
587C LEU* 3.9 19.7 - - + -
683C GLN 4.7 0.8 - - - +
684C GLU* 1.3 79.3 - - - +
686C PHE* 1.3 53.5 + - - +
688C GLU* 3.3 10.9 - - + +
689C ILE* 2.6 49.9 + - + +
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Residues in contact with PHE 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C LEU* 4.5 19.7 - - + +
595C LEU* 4.1 15.7 - - + -
672C LEU* 3.2 55.4 - - + +
675C VAL* 3.5 16.8 - - + -
680C LEU 5.3 1.1 - - - +
683C GLN* 3.2 40.5 - - - +
684C GLU 3.2 0.4 - - - -
685C LEU* 1.3 78.5 - - - +
687C ASP* 1.3 66.7 + - - +
689C ILE* 3.6 4.8 - - - +
690C ARG* 2.7 46.0 + - - +
772C LEU* 3.5 24.0 - - + -
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Residues in contact with ASP 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C GLN* 3.0 36.9 + - - +
684C GLU* 4.0 2.5 - - - +
686C PHE* 1.3 96.2 - - - +
688C GLU* 1.3 63.1 + - - +
690C ARG* 4.1 9.7 + - - +
691C MET* 3.2 34.4 + - + +
772C LEU* 5.2 1.9 - - - +
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Residues in contact with GLU 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C GLU 3.0 14.2 + - - +
685C LEU* 3.3 18.2 - - + +
687C ASP* 1.3 75.5 - - - +
689C ILE* 1.3 58.8 + - + +
691C MET* 3.9 3.4 - - - +
692C THR* 2.7 30.6 + - - -
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Residues in contact with ILE 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ILE* 5.6 1.8 - - + -
582C PRO 3.4 24.0 - - - +
583C GLY* 3.7 9.6 - - - -
584C PHE* 3.6 20.6 - - + +
587C LEU* 5.0 7.2 - - + -
668C THR* 5.7 0.2 - - + -
672C LEU* 3.4 21.1 - - + -
685C LEU* 2.6 36.3 + - + +
686C PHE* 3.6 3.8 - - - +
688C GLU* 1.3 71.1 - - + +
690C ARG* 1.3 59.4 + - - +
692C THR* 2.7 38.1 + - - +
693C TYR* 3.2 25.6 + - + -
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Residues in contact with ARG 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C LEU* 3.8 11.9 + - + +
672C LEU* 3.2 47.4 + - + +
673C SER* 4.8 4.4 - - - +
686C PHE* 2.7 37.1 + - - +
687C ASP* 4.1 10.9 + - - +
689C ILE* 1.3 72.4 - - - +
691C MET* 1.3 61.9 + - + +
693C TYR* 3.4 2.2 + - - -
694C ILE* 3.1 44.2 + - + +
772C LEU* 3.8 34.2 + - - +
773C LEU 4.6 4.0 + - - -
774C PHE* 3.4 37.7 - - - -
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Residues in contact with MET 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687C ASP* 3.2 24.6 + - + +
688C GLU* 3.9 4.5 - - - +
689C ILE 3.1 1.0 - - - -
690C ARG* 1.3 82.5 - - + +
692C THR* 1.3 65.6 + - - +
694C ILE* 3.8 27.4 - - + +
695C LYS* 3.1 22.9 + - + +
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Residues in contact with THR 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU* 3.9 27.1 - - + -
688C GLU 2.7 22.2 + - - -
689C ILE* 2.7 24.6 + - - +
691C MET* 1.3 71.1 - - - +
693C TYR* 1.3 64.8 + - + +
695C LYS* 3.1 10.2 + - - +
696C GLU* 2.9 26.0 + - - +
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Residues in contact with TYR 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU* 4.0 22.8 - - + +
536C LEU* 3.9 31.7 - - + +
581C ILE* 3.1 28.2 - - + +
582C PRO* 3.5 20.4 + - - +
665C CYS* 4.4 7.3 - - - +
668C THR* 3.7 29.8 - - + -
669C LEU* 3.9 21.2 - - + +
672C LEU* 4.9 2.2 - - + -
689C ILE* 3.2 38.5 + - + -
690C ARG* 3.4 1.3 + - - +
692C THR* 1.3 80.6 - - + +
694C ILE* 1.3 57.8 + - - +
695C LYS 3.2 0.9 - - - -
696C GLU* 3.4 12.8 - - + +
697C LEU* 2.7 34.5 + - - +
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Residues in contact with ILE 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C LEU* 3.8 17.0 - - + +
690C ARG* 3.1 45.9 + - + +
691C MET* 3.8 30.3 - - + +
693C TYR* 1.3 76.7 - - - +
695C LYS* 1.3 59.3 + - - +
697C LEU* 3.6 7.5 + - - +
698C GLY* 3.3 16.5 + - - -
715C PHE* 3.6 33.0 - - + -
774C PHE* 4.1 20.9 - - + -
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Residues in contact with LYS 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C MET* 3.1 14.3 + - + +
692C THR* 3.1 10.1 + - - +
694C ILE* 1.3 76.1 - - - +
696C GLU* 1.3 60.5 + - - +
698C GLY* 3.4 2.9 + - - +
699C LYS* 3.0 32.7 + - + +
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Residues in contact with GLU 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C THR* 4.9 1.2 - - - -
532C LEU* 3.7 45.2 + - + +
533C VAL* 4.2 12.7 + - + +
536C LEU* 5.4 1.1 - - + -
665C CYS* 3.6 20.6 - - - -
692C THR* 2.9 16.3 + - - +
693C TYR* 3.0 19.5 + - + +
695C LYS* 1.3 75.9 - - - +
697C LEU* 1.3 64.4 + - - +
699C LYS* 3.0 43.2 + - - +
700C ALA* 3.1 17.0 + - - +
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Residues in contact with LEU 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C GLU* 4.0 13.0 - - + +
665C CYS* 3.8 20.5 - - + -
666C MET* 3.7 28.0 - - + -
669C LEU* 4.3 19.3 - - + -
693C TYR 2.7 19.1 + - - +
694C ILE* 3.6 6.1 - - - +
696C GLU* 1.3 69.8 - - - +
698C GLY* 1.3 57.6 + - - +
700C ALA* 2.7 26.0 + - - +
701C ILE* 3.0 21.7 + - + +
715C PHE* 4.1 20.6 - - + -
718C LEU* 4.1 21.1 - - + -
719C THR* 4.4 13.0 - - + -
722C LEU* 4.9 0.9 - - + -
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Residues in contact with GLY 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694C ILE 3.3 11.0 + - - -
695C LYS* 3.4 5.3 + - - -
697C LEU* 1.3 78.7 - - - +
699C LYS* 1.3 60.5 + - - +
701C ILE* 3.2 23.8 + - - +
702C VAL* 3.3 20.0 + - - +
715C PHE* 4.6 6.9 - - - -
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Residues in contact with LYS 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C THR* 4.7 16.9 - - - +
532C LEU 5.5 0.6 - - - +
695C LYS* 3.0 17.8 + - + +
696C GLU* 3.0 45.5 + - - +
697C LEU 3.0 0.4 + - - -
698C GLY* 1.3 76.2 - - - +
700C ALA* 1.3 61.6 + - - +
701C ILE 3.2 0.5 + - - -
702C VAL* 3.2 17.3 + - - +
703C LYS* 3.3 13.3 + - - +
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Residues in contact with ALA 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C VAL* 5.9 0.7 - - + -
659C SER* 4.8 2.6 + - - -
661C GLU* 4.1 20.1 - - + +
662C GLU* 3.8 37.9 - - + +
665C CYS* 4.6 1.6 - - - -
696C GLU 3.1 9.0 + - - +
697C LEU* 2.7 17.1 + - - +
699C LYS* 1.3 75.7 - - - +
701C ILE* 1.3 57.3 + - - -
703C LYS* 3.7 8.0 + - - +
704C ARG* 3.4 19.6 + - - +
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Residues in contact with ILE 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C GLU* 3.5 21.3 - - + +
697C LEU* 3.0 24.6 + - + +
698C GLY* 3.5 17.7 - - - +
699C LYS 3.1 0.4 - - - -
700C ALA* 1.3 75.9 - - - +
702C VAL* 1.3 65.8 + - + +
704C ARG* 3.5 13.2 - - - +
706C GLY 4.0 2.9 - - - +
711C ASN* 3.4 39.4 - - - +
714C ARG* 4.1 18.8 - - + -
715C PHE* 3.8 37.7 - - + +
718C LEU* 4.7 6.7 - - + -
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Residues in contact with VAL 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C GLY 3.4 16.2 - - - +
699C LYS* 3.2 9.1 + - - +
701C ILE* 1.3 79.1 - - + +
703C LYS* 1.3 63.7 + - - +
704C ARG 3.0 12.0 + - - +
706C GLY 4.4 2.8 - - - +
707C ASN* 4.5 7.4 - - + +
711C ASN* 4.3 23.1 - - - +
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Residues in contact with LYS 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661C GLU* 5.1 10.8 - - - +
699C LYS 3.3 12.0 + - - +
700C ALA* 4.1 8.1 - - - +
701C ILE 3.5 0.4 - - - -
702C VAL* 1.3 79.3 - - - +
704C ARG* 1.3 62.0 + - - +
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Residues in contact with ARG 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C ARG* 6.0 0.6 - - - +
656C LEU 4.6 0.2 + - - -
657C GLN* 2.6 37.5 + - - +
658C VAL 4.2 1.0 + - - -
659C SER* 3.9 20.9 - - - +
662C GLU* 3.7 14.1 + - - -
700C ALA 3.4 11.9 + - - +
701C ILE 3.5 15.9 - - - +
702C VAL 3.0 13.8 + - - +
703C LYS* 1.3 80.7 - - - +
705C GLU* 1.3 89.2 + - - +
706C GLY* 3.5 10.9 - - - +
707C ASN* 4.8 0.3 - - - +
714C ARG* 3.6 36.0 - - - +
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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