Contacts of the helix formed by residues 675 - 687 (chain C) in PDB entry 7KHI
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 ASP 675 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674C ASP* 1.3 74.0 - - - +
676C ALA* 1.3 73.8 + - - +
677C ASN* 3.3 27.4 + - - +
678C ARG* 3.2 13.0 + - + +
679C ALA 3.0 18.0 + - - -
1107C MET* 3.3 46.3 + - + +
1108C ASN* 4.7 0.6 - - - +
744D ARG* 3.9 21.8 + - - +
763D PHE* 3.9 14.3 - - + -
772D TYR* 3.6 1.7 + - - -
775D SER* 4.1 4.7 + - - -
779D ALA* 5.1 2.6 - - - +
77M ALA* 5.0 6.1 - - - +
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Residues in contact with ALA 676 (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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561C ILE* 4.7 9.2 - - + +
674C ASP 3.6 1.2 + - - -
675C ASP* 1.3 77.8 + - - +
677C ASN* 1.3 63.6 + - - +
679C ALA* 3.2 3.7 + - - +
680C LEU* 2.9 24.2 + - - +
772D TYR* 3.7 18.3 + - + +
775D SER* 4.2 9.9 + - - +
776D THR* 4.1 25.8 - - + +
779D ALA* 3.8 21.8 - - + -
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Residues in contact with ASN 677 (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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675C ASP* 3.3 15.4 + - - +
676C ALA* 1.3 79.6 - - - +
678C ARG* 1.3 61.5 + - - +
680C LEU* 3.1 10.7 + - - +
681C MET* 3.0 31.4 + - - +
779D ALA* 3.4 32.9 + - - +
780D ARG* 5.3 0.2 - - - -
783D LEU* 3.2 35.7 - - - +
73M VAL* 4.1 22.6 - - + +
76M ALA* 5.2 4.6 + - - +
77M ALA* 4.8 17.1 - - + +
80M GLU* 5.9 1.6 - - - +
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Residues in contact with ARG 678 (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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674C ASP* 5.4 1.6 - - + -
675C ASP* 3.2 20.9 + - + +
677C ASN* 1.3 80.7 - - + +
679C ALA* 1.3 61.0 + - - +
681C MET* 3.4 20.1 + - - +
682C GLY* 2.8 26.5 + - - -
1070C HIS 3.6 23.1 - - - +
1071C GLY* 4.0 10.8 + - - -
1106C ARG* 3.2 47.2 - - - +
1107C MET 4.8 2.6 - - - +
1108C ASN* 3.9 26.9 - - + +
71M ASP* 4.0 6.5 + - - -
73M VAL* 3.4 31.6 + - - +
74M ASP* 3.7 26.7 + - - +
77M ALA* 6.1 0.2 - - - +
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Residues in contact with ALA 679 (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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561C ILE* 3.9 15.1 - - + +
668C ILE* 3.9 8.7 - - + +
671C LEU* 3.5 23.8 - - + -
674C ASP* 4.9 5.6 - - + +
675C ASP 3.0 6.8 + - - +
676C ALA 3.4 6.7 - - - +
678C ARG* 1.3 77.3 - - - +
680C LEU* 1.3 63.6 + - - +
682C GLY* 3.2 1.1 + - - +
683C ALA* 3.0 25.6 + - - +
1069C ARG 5.9 0.2 - - - -
1070C HIS* 5.8 1.1 - - - +
772D TYR* 3.4 25.6 - - - +
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Residues in contact with LEU 680 (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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560C PRO 5.8 0.2 - - - +
561C ILE* 3.2 31.6 + - - +
562C GLU* 4.8 0.7 - - - +
563C THR* 3.1 26.7 - - + +
565C GLU* 4.1 20.9 - - + +
569C ILE* 5.3 5.4 - - + -
676C ALA 2.9 13.3 + - - +
677C ASN* 3.1 13.4 + - - +
679C ALA* 1.3 77.1 - - - +
681C MET* 1.3 64.8 + - + +
683C ALA* 3.3 3.4 + - - +
684C ASN* 3.0 53.7 + - - +
780D ARG* 5.5 10.5 - - + +
783D LEU* 4.5 18.6 - - + -
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Residues in contact with MET 681 (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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565C GLU* 3.0 32.9 - - - +
677C ASN 3.0 15.8 + - - +
678C ARG* 3.4 33.7 - - - +
680C LEU* 1.3 76.6 - - + +
682C GLY* 1.3 67.4 + - - +
684C ASN* 3.8 7.1 - - - +
685C MET* 2.9 45.2 + - + +
1071C GLY* 4.0 14.8 - - - +
1073C LYS* 4.2 16.8 - - - +
71M ASP* 5.0 0.7 - - - +
73M VAL* 3.4 28.9 - - + -
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Residues in contact with GLY 682 (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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668C ILE* 4.3 1.1 - - - -
678C ARG 2.8 19.1 + - - -
679C ALA 3.2 1.8 + - - -
681C MET* 1.3 76.7 - - - +
683C ALA* 1.3 56.7 + - - +
685C MET* 3.4 5.6 - - - +
686C GLN* 2.8 34.6 + - - +
1069C ARG 3.6 23.4 - - - +
1071C GLY* 3.9 10.9 - - - -
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Residues in contact with ALA 683 (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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521C LEU* 5.8 0.3 - - - +
561C ILE* 6.3 0.2 - - + -
562C GLU* 3.4 24.0 - - + +
664C GLY* 4.3 3.9 - - - -
665C ALA* 4.2 19.5 - - + +
668C ILE* 3.8 13.5 - - + +
679C ALA 3.0 16.0 + - - +
680C LEU* 3.8 2.9 - - - +
682C GLY* 1.3 75.3 - - - +
684C ASN* 1.3 64.6 + - - +
686C GLN* 3.7 11.9 - - - +
687C ARG* 3.0 27.2 + - - +
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Residues in contact with ASN 684 (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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562C GLU* 3.9 16.7 - - - +
563C THR 2.8 34.1 + - - +
564C PRO* 4.1 6.0 - - - +
565C GLU* 4.0 19.0 + - - +
680C LEU* 3.0 33.4 + - - +
681C MET* 3.8 4.7 - - - +
683C ALA* 1.3 77.8 - - - +
685C MET* 1.3 59.0 + - - +
687C ARG* 2.8 38.6 + - - +
688C GLN* 3.7 14.2 + - - +
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Residues in contact with MET 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C GLU* 5.4 2.9 - - - +
681C MET* 2.9 47.9 + - + +
682C GLY* 3.4 5.4 - - - +
684C ASN* 1.3 73.4 - - - +
686C GLN* 1.3 61.7 + - - +
687C ARG 3.1 2.5 - - - -
688C GLN* 2.6 40.8 + - - +
1067C ALA* 3.7 26.5 - - + -
1068C GLY 4.0 8.3 - - - +
1071C GLY* 4.0 17.7 - - - -
1073C LYS* 3.4 31.9 - - + +
1233C LEU* 6.0 0.4 - - + -
1235C LEU* 3.3 26.1 - - + +
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Residues in contact with GLN 686 (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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519C ASN* 4.0 5.2 + - - -
521C LEU* 3.7 11.4 - - - +
664C GLY* 3.4 19.9 - - - +
667C LEU* 3.8 22.2 - - - +
668C ILE* 4.2 5.9 - - - +
682C GLY 2.8 19.1 + - - +
683C ALA* 3.7 10.6 - - - +
685C MET* 1.3 78.8 - - + +
687C ARG* 1.3 61.6 + - - +
688C GLN 3.1 1.2 + - - -
689C ALA* 3.3 16.3 + - - +
796C LEU* 3.2 33.1 - - + +
1068C GLY 5.4 0.2 - - - +
1069C ARG* 3.8 28.5 - - + +
1233C LEU* 3.6 22.4 - - + +
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Residues in contact with ARG 687 (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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516C ASP* 3.4 24.1 + - - -
518C ASN* 3.9 3.8 + - - +
519C ASN* 4.0 4.9 - - - +
521C LEU* 4.6 15.9 - - + -
522C SER* 3.5 32.3 - - - +
525C THR* 3.5 23.8 - - + +
526C HIS* 5.2 1.2 - - - +
529C ARG* 3.5 34.7 - - - +
562C GLU* 4.0 15.9 - - - -
564C PRO* 6.3 1.2 - - - +
683C ALA 3.0 14.3 + - - +
684C ASN* 2.8 42.6 + - - +
686C GLN* 1.3 77.7 + - - +
688C GLN* 1.3 69.2 + - + +
689C ALA 3.4 1.2 + - - -
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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