Contacts of the helix formed by residues 666 - 677 (chain C) in PDB entry 4OQB
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 PRO 666 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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665C LEU* 1.3 97.9 - - + +
667C LYS* 1.3 59.6 + - - +
668C PRO* 3.4 13.0 - - + -
669C VAL* 3.3 25.4 + - + +
670C GLN* 3.1 27.3 + - - +
803C VAL* 4.1 12.8 - - + +
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Residues in contact with LYS 667 (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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665C LEU 5.4 0.9 - - - +
666C PRO* 1.3 73.2 - - - +
668C PRO* 1.3 69.9 - - + +
670C GLN* 3.5 14.8 + - - +
671C ASP* 3.1 33.4 + - - +
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Residues in contact with PRO 668 (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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666C PRO* 3.5 11.0 - - + -
667C LYS* 1.3 96.1 - - + +
669C VAL* 1.3 56.9 + - - +
671C ASP* 3.4 9.6 + - + +
672C LEU* 3.0 21.3 + - - -
803C VAL* 4.5 13.5 - - + -
835C ASP* 3.3 30.5 - - - +
837C PHE* 3.4 22.5 - - + -
1004C LYS* 4.0 3.0 + - - +
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Residues in contact with VAL 669 (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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665C LEU* 4.4 13.7 - - + -
666C PRO* 3.3 25.3 + - + +
667C LYS 3.3 0.4 - - - -
668C PRO* 1.3 74.0 - - - +
670C GLN* 1.3 63.8 + - - +
672C LEU* 3.3 5.9 + - + +
673C ILE* 3.3 23.4 + - + +
794C TYR* 3.9 31.9 - - + +
801C ILE* 4.6 20.2 - - + +
802C LYS* 5.4 0.2 - - - -
803C VAL* 3.6 26.7 - - + -
837C PHE* 3.9 14.4 - - + -
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Residues in contact with GLN 670 (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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663C SER* 3.4 28.2 + - - +
665C LEU* 3.0 33.3 + - + +
666C PRO 3.1 15.5 + - - +
667C LYS* 3.7 14.9 - - - +
668C PRO 3.3 0.2 - - - -
669C VAL* 1.3 77.4 - - - +
671C ASP* 1.3 59.7 + - - +
673C ILE* 3.4 4.2 + - - +
674C LYS* 2.9 32.8 + - - +
790C ILE* 4.0 38.6 - - + +
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Residues in contact with ASP 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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667C LYS* 3.1 17.9 + - - +
668C PRO* 3.5 11.8 - - + +
669C VAL 3.3 0.2 - - - -
670C GLN* 1.3 77.5 - - - +
672C LEU* 1.3 59.4 + - - +
674C LYS* 3.4 17.2 - - - +
675C MET* 2.8 33.8 + - + +
1004C LYS* 3.7 15.6 + - - +
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Residues in contact with LEU 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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668C PRO 3.0 13.8 + - - +
669C VAL* 3.4 11.7 - - + +
670C GLN 3.2 0.4 - - - -
671C ASP* 1.3 73.6 - - - +
673C ILE* 1.3 60.8 + - + +
675C MET* 3.3 4.0 + - + +
676C ILE* 3.0 45.9 + - + +
801C ILE* 3.7 40.2 - - + -
837C PHE* 4.3 17.0 - - + -
873C LEU* 6.3 0.2 - - + -
918C LEU* 3.9 37.7 - - + -
1002C LEU* 4.1 20.2 - - + -
1004C LYS* 4.4 10.5 - - - +
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Residues in contact with ILE 673 (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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665C LEU* 4.8 1.8 - - + -
669C VAL* 3.3 11.0 + - + +
670C GLN 3.8 6.5 - - - +
671C ASP 3.4 0.2 - - - -
672C LEU* 1.3 75.1 - - + +
674C LYS* 1.3 61.3 + - - +
676C ILE* 4.0 6.1 - - - -
677C PHE* 2.9 48.6 + - + +
790C ILE* 3.4 42.8 - - + +
793C ASN* 4.0 16.8 - - + +
794C TYR* 3.5 34.5 - - + +
797C LEU* 4.2 17.5 - - + -
801C ILE* 6.2 0.9 - - + -
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Residues in contact with LYS 674 (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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670C GLN* 2.9 22.2 + - - +
671C ASP* 3.4 20.2 - - - +
673C ILE* 1.3 78.2 - - - +
675C MET* 1.3 60.9 + - - +
677C PHE 4.5 0.2 - - - -
678C ASP* 3.5 23.8 + - - +
790C ILE* 4.4 19.9 - - + +
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Residues in contact with MET 675 (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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671C ASP* 2.8 15.8 + - + +
672C LEU* 3.6 6.3 - - - +
673C ILE 3.1 0.2 - - - -
674C LYS* 1.3 78.8 - - - +
676C ILE* 1.3 63.5 + - + +
677C PHE 3.4 0.6 + - - -
678C ASP* 4.1 10.7 + - - +
681C SER* 5.6 2.8 - - - -
682C MET* 5.5 0.7 - - - +
866C THR* 3.9 22.1 + - + +
916C ILE* 3.7 48.7 - - + -
917C GLY* 5.5 0.4 - - - -
918C LEU* 4.5 17.5 - - - -
1004C LYS* 4.1 32.5 - - + +
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Residues in contact with ILE 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 LEU* 3.0 33.9 + - + +
673C ILE* 3.9 2.2 - - - +
675C MET* 1.3 77.8 - - + +
677C PHE* 1.3 71.0 + - + +
678C ASP 3.7 0.4 - - - -
682C MET* 3.1 22.2 - - - +
797C LEU* 4.0 34.3 - - + -
866C THR* 4.2 13.9 - - - +
869C PHE* 4.0 19.5 - - + +
870C ALA* 3.4 17.9 - - - +
873C LEU* 5.2 5.8 - - + -
918C LEU* 3.6 30.7 - - + -
1002C LEU* 6.3 0.7 - - + -
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Residues in contact with PHE 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 ILE* 2.9 31.8 + - + +
674C LYS* 4.5 0.4 - - - -
676C ILE* 1.3 90.6 - - + +
678C ASP* 1.3 60.3 + - - +
679C VAL* 3.2 20.1 + - + +
682C MET* 4.6 2.0 - - - -
774C ALA* 3.9 26.5 - - + -
777C LEU* 4.1 21.5 - - + -
778C LEU* 4.2 27.3 - - + +
793C ASN* 3.9 26.7 - - + +
796C LYS* 5.2 2.7 - - + -
797C LEU* 3.6 38.1 - - + -
870C ALA* 4.8 10.5 - - + -
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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