Contacts of the helix formed by residues 670 - 682 (chain C) in PDB entry 5Y3R
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 LEU 670 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664C SER* 3.1 36.6 - - - +
665C GLY* 3.3 20.0 - - - +
667C TYR* 3.1 16.6 - - + +
668C LYS 3.4 4.0 + - - +
669C LEU* 1.3 74.8 - - - +
671C SER* 1.3 54.6 + - - +
672C ILE 3.0 1.6 - - - -
673C THR* 2.4 29.8 + - + +
674C VAL* 2.2 50.5 + - + -
707C PHE* 4.8 0.9 - - + -
739C ASN* 4.1 8.5 - - - +
740C ILE* 3.4 27.6 - - + -
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Residues in contact with SER 671 (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 LYS 4.0 10.5 + - - -
669C LEU* 3.9 17.4 - - - +
670C LEU* 1.3 75.5 - - - +
672C ILE* 1.3 64.1 + - - +
674C VAL* 4.2 3.3 - - - +
675C ARG* 2.9 52.6 + - - +
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Residues in contact with ILE 672 (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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638C GLN* 5.0 15.9 - - - +
669C LEU* 3.5 44.2 - - + +
671C SER* 1.3 79.9 - - - +
673C THR* 1.3 66.3 + - + +
675C ARG* 4.1 10.5 - - - +
676C ASN* 3.0 32.8 + - - +
700C LYS* 3.9 15.0 - - - +
704C PHE* 3.3 31.0 - - + -
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Residues in contact with THR 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C GLN* 6.5 0.9 - - + -
669C LEU 4.3 4.3 - - - +
670C LEU* 2.4 49.0 + - + +
672C ILE* 1.3 72.3 - - + +
674C VAL* 1.3 58.0 + - - -
677C ALA* 2.7 39.0 + - - +
704C PHE* 3.8 22.7 - - + -
707C PHE* 3.2 37.9 - - + -
740C ILE* 3.1 8.1 - - - +
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Residues in contact with VAL 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C LEU* 2.2 46.3 + - + +
671C SER* 4.2 2.7 - - - +
673C THR* 1.3 73.7 + - - +
675C ARG* 1.3 57.8 + - - +
678C LYS* 2.9 13.2 + - - +
739C ASN 5.4 0.7 - - - +
740C ILE* 2.9 29.6 - - - +
741C ILE 4.1 1.8 - - - -
742C GLU* 3.8 17.0 - - + +
743C LEU* 3.2 44.6 - - + +
744C ASP* 2.7 27.8 - - - +
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Residues in contact with ARG 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C LEU* 5.6 0.6 - - - +
671C SER* 2.9 61.9 + - - +
672C ILE* 3.7 18.0 - - - +
674C VAL* 1.3 78.1 - - - +
676C ASN* 1.3 75.8 + - - +
678C LYS* 2.9 8.1 + - + +
679C LYS* 2.8 32.9 + - + +
743C LEU* 3.6 17.3 - - + -
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Residues in contact with ASN 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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672C ILE* 3.0 39.0 + - - +
675C ARG* 1.3 98.4 + - - +
677C ALA* 1.3 57.2 + - - +
679C LYS* 2.6 48.6 + - + +
680C ILE* 3.0 11.6 + - - +
700C LYS* 4.1 12.7 - - - +
701C TYR* 4.4 10.8 - - + -
704C PHE* 4.1 14.1 - - + -
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Residues in contact with ALA 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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673C THR 2.7 22.1 + - - +
676C ASN* 1.3 76.1 - - - +
678C LYS* 1.3 48.6 + - - +
680C ILE* 4.3 4.7 - - - +
681C LYS* 2.7 36.8 + - - +
701C TYR 5.3 1.1 - - - -
704C PHE* 3.5 35.8 - - + +
705C ALA* 5.2 3.5 - - - +
707C PHE* 5.3 1.6 - - + -
708C VAL* 4.0 10.3 - - + +
744C ASP* 3.0 14.5 - - - +
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Residues in contact with LYS 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 VAL 2.9 12.9 + - - +
675C ARG* 2.9 13.0 + - + +
677C ALA* 1.3 75.3 - - - +
679C LYS* 1.3 54.8 + - + +
681C LYS* 2.9 6.2 + - + -
682C TYR* 2.2 71.8 + - + +
743C LEU* 3.7 35.2 - - + +
744C ASP* 3.1 19.2 + - - +
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Residues in contact with LYS 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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675C ARG* 2.8 24.8 + - + +
676C ASN* 2.6 41.3 + - + +
678C LYS* 1.3 71.9 - - + +
680C ILE* 1.3 61.3 + - + +
682C TYR* 3.1 23.9 - - - +
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Residues in contact with ILE 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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676C ASN 3.0 13.2 + - - +
677C ALA* 4.4 3.8 - - - +
679C LYS* 1.3 74.1 - - + +
681C LYS* 1.3 66.8 + - - +
682C TYR 3.0 8.2 + - - -
701C TYR* 3.7 41.7 - - + +
702C SER* 4.2 9.6 - - - +
705C ALA* 5.1 13.2 - - + -
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Residues in contact with LYS 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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677C ALA 2.7 20.2 + - - +
678C LYS* 2.9 8.9 + - + +
680C ILE* 1.3 76.8 - - - +
682C TYR* 1.3 59.6 + - - +
708C VAL* 5.1 11.1 - - + +
743C LEU 4.2 2.9 - - - +
744C ASP* 3.2 57.3 + - + +
745C VAL 4.0 1.1 - - - -
746C ARG* 2.6 74.4 + - - +
748C TYR* 5.1 1.6 + - - -
1323C SER 5.5 1.0 + - - -
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Residues in contact with TYR 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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678C LYS* 2.2 55.8 + - - +
679C LYS* 3.1 17.7 - - - +
680C ILE 3.0 7.5 - - - -
681C LYS* 1.3 77.6 - - - +
746C ARG* 4.2 5.7 + - - +
1323C SER 5.5 3.8 + - - -
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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