Contacts of the helix formed by residues 666 - 677 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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665F LEU* 1.3 98.6 - - + +
667F LYS* 1.3 60.3 + - - +
668F PRO* 3.8 11.9 - - + -
669F VAL* 3.3 24.8 + - + +
670F GLN* 3.1 26.9 + - - +
803F VAL* 4.1 13.0 - - + -
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Residues in contact with LYS 667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665F LEU 5.4 1.1 - - - +
666F PRO* 1.3 72.5 - - - +
668F PRO* 1.3 69.1 - - + +
670F GLN* 3.5 13.5 + - - +
671F ASP* 3.1 33.1 + - - +
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Residues in contact with PRO 668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666F PRO* 3.5 11.7 - - + -
667F LYS* 1.3 96.6 - - + +
669F VAL* 1.3 56.0 + - - +
671F ASP* 3.4 10.6 + - + +
672F LEU 3.0 21.7 + - - -
803F VAL* 4.5 13.2 - - + -
835F ASP* 3.3 29.8 - - - +
837F PHE* 3.4 22.9 - - + -
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Residues in contact with VAL 669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665F LEU* 4.4 14.1 - - + -
666F PRO* 3.3 25.7 + - + +
667F LYS 3.3 0.8 - - - -
668F PRO* 1.3 73.4 - - - +
670F GLN* 1.3 65.3 + - - +
672F LEU* 3.3 6.0 + - + +
673F ILE* 3.3 23.3 + - + +
794F TYR* 3.9 33.2 - - + -
801F ILE* 4.6 19.7 - - + +
802F LYS* 5.4 0.2 - - - -
803F VAL* 3.6 27.1 - - + -
837F PHE* 3.9 14.1 - - + -
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Residues in contact with GLN 670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F SER* 3.4 28.7 + - - +
665F LEU* 3.0 33.3 + - + +
666F PRO 3.1 15.3 + - - +
667F LYS* 3.7 14.3 - - - +
669F VAL* 1.3 77.1 - - - +
671F ASP* 1.3 59.5 + - - +
673F ILE* 3.4 4.2 + - - +
674F LYS* 2.9 33.7 + - - +
790F ILE* 4.0 38.6 - - + +
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Residues in contact with ASP 671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667F LYS* 3.1 18.8 + - - +
668F PRO* 3.5 11.7 - - + +
669F VAL 3.3 0.2 - - - -
670F GLN* 1.3 77.2 - - - +
672F LEU* 1.3 59.1 + - - +
674F LYS* 3.4 16.7 - - - +
675F MET* 2.8 38.7 + - + +
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Residues in contact with LEU 672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668F PRO 3.0 13.6 + - - +
669F VAL* 3.4 11.4 - - - +
670F GLN 3.2 0.4 - - - -
671F ASP* 1.3 73.2 - - - +
673F ILE* 1.3 61.0 + - + +
675F MET* 3.3 5.9 + - + +
676F ILE* 3.0 45.8 + - + +
797F LEU* 6.2 0.2 - - + -
801F ILE* 3.7 40.4 - - + -
837F PHE* 4.3 25.4 - - + -
839F ILE* 5.9 2.0 - - + -
873F LEU* 6.3 2.2 - - + -
918F LEU* 3.9 37.2 - - + -
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Residues in contact with ILE 673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665F LEU* 4.8 2.2 - - + -
669F VAL 3.3 10.5 + - - +
670F GLN 3.8 6.1 - - - +
672F LEU* 1.3 75.0 - - + +
674F LYS* 1.3 61.9 + - - +
676F ILE* 4.0 6.1 - - - -
677F PHE* 2.9 49.7 + - + +
790F ILE* 3.4 43.1 - - + +
793F ASN* 4.0 17.5 - - + +
794F TYR* 3.5 33.4 - - + -
797F LEU* 4.2 18.4 - - + -
801F ILE* 6.2 0.9 - - + -
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Residues in contact with LYS 674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670F GLN* 2.9 22.1 + - - +
671F ASP* 3.4 20.0 - - - +
672F LEU 3.3 0.2 - - - -
673F ILE* 1.3 77.7 - - - +
675F MET* 1.3 58.8 + - - +
677F PHE* 5.6 0.4 - - - -
678F ASP* 3.5 23.9 + - - +
790F ILE* 4.4 19.5 - - + +
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Residues in contact with MET 675 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671F ASP* 2.8 22.3 + - + +
672F LEU* 3.6 8.1 - - + +
673F ILE 3.1 0.4 - - - -
674F LYS* 1.3 79.6 - - - +
676F ILE* 1.3 62.4 + - + +
677F PHE 3.7 0.7 + - - -
678F ASP* 4.1 10.8 + - - +
681F SER* 5.7 2.4 - - - -
682F MET* 5.5 0.9 - - - +
866F THR* 3.9 22.6 + - + +
916F ILE* 3.7 51.6 - - + -
917F GLY* 5.5 0.7 - - - -
918F LEU* 4.5 23.8 - - - -
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Residues in contact with ILE 676 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672F LEU* 3.0 35.2 + - + +
673F ILE* 3.9 2.0 - - - +
675F MET* 1.3 78.2 - - + +
677F PHE* 1.3 72.0 + - + +
678F ASP 3.7 0.7 - - - -
682F MET* 3.1 22.8 - - - +
797F LEU* 4.0 33.9 - - + -
801F ILE* 6.1 0.2 - - + -
866F THR* 4.2 13.2 - - - +
869F PHE* 4.0 19.5 - - + +
870F ALA* 3.4 18.2 - - - +
873F LEU* 5.2 5.6 - - + -
918F LEU* 3.6 30.7 - - + -
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Residues in contact with PHE 677 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673F ILE* 2.9 31.6 + - + +
674F LYS 4.5 0.4 - - - -
676F ILE* 1.3 90.9 - - + +
678F ASP* 1.3 60.1 + - - +
679F VAL* 3.2 21.4 + - + +
682F MET* 4.6 2.2 - - - -
774F ALA* 3.8 28.3 - - + -
777F LEU* 4.1 21.5 - - + -
778F LEU* 4.2 27.1 - - + +
793F ASN* 3.9 26.9 - - + +
796F LYS* 5.2 2.9 - - + -
797F LEU* 3.6 37.0 - - + -
870F ALA* 4.8 9.0 - - + -
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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
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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