Contacts of the helix formed by residues 671 - 681 (chain C) in PDB entry 3F7F
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 671 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413C SER* 5.3 1.6 - - - -
667C LEU 3.1 10.4 + - - +
669C ARG 3.4 0.8 - - - -
670C GLN* 1.3 86.1 - - + +
672C LYS* 1.3 63.4 + - - +
673C CYS* 3.4 9.0 + - - +
674C LEU* 3.0 40.5 + - + +
675C LEU* 3.0 18.4 + - - +
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Residues in contact with LYS 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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13C GLN* 3.4 40.6 - - + +
14C TYR* 3.9 15.7 - - + -
413C SER* 3.2 34.8 + - - +
414C ARG* 4.2 9.6 - - - +
613C ILE* 5.1 0.7 - - + -
616C LEU* 3.6 8.7 - - + +
617C GLU* 3.9 5.6 - - - +
668C TYR* 3.3 59.3 + - + +
669C ARG* 4.4 2.6 - - - +
671C ASP* 1.3 70.8 + - - +
673C CYS* 1.3 63.9 + - - +
675C LEU* 3.2 5.9 + - - +
676C ALA* 2.9 24.8 + - - +
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Residues in contact with CYS 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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14C TYR* 3.6 48.9 - - + +
15C TYR* 6.0 3.1 - - - -
671C ASP* 3.2 7.2 + - - +
672C LYS* 1.3 78.4 - - - +
674C LEU* 1.3 68.1 + - - +
676C ALA* 3.1 3.2 + - - +
677C GLU* 2.9 27.2 + - - +
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Residues in contact with LEU 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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671C ASP* 3.0 36.9 + - + +
673C CYS* 1.3 78.9 - - - +
675C LEU* 1.3 64.5 + - - +
677C GLU* 3.1 27.0 + - - +
678C VAL* 3.0 36.2 + - + +
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Residues in contact with LEU 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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616C LEU* 3.7 25.8 - - + -
664C LEU* 4.0 31.6 - - + -
667C LEU* 4.2 25.4 - - + +
668C TYR* 3.6 34.3 - - + +
671C ASP 3.0 12.5 + - - +
672C LYS* 3.5 9.4 - - - +
673C CYS 3.1 0.2 - - - -
674C LEU* 1.3 77.6 - - - +
676C ALA* 1.3 65.5 + - - +
678C VAL* 3.2 16.1 - - + +
679C LEU* 2.7 35.9 + - + +
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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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14C TYR* 3.6 32.3 - - + +
612C SER* 4.2 9.2 - - - +
616C LEU* 4.1 10.9 - - + +
672C LYS 2.9 11.2 + - - +
673C CYS* 3.5 7.4 - - - +
675C LEU* 1.3 76.7 - - - +
677C GLU* 1.3 54.2 + - - +
679C LEU* 4.3 2.9 - - - -
680C LEU* 2.7 51.9 + - + +
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Residues in contact with GLU 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 CYS* 2.9 18.8 + - - +
674C LEU* 3.3 28.9 - - - +
675C LEU 3.1 0.2 - - - -
676C ALA* 1.3 74.2 - - - +
678C VAL* 1.3 63.6 + - - +
680C LEU* 3.4 2.7 + - - +
681C LYS* 2.9 44.1 + - + +
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Residues in contact with VAL 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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667C LEU* 5.8 4.0 - - + -
674C LEU* 3.0 39.2 + - + +
675C LEU* 3.2 24.9 - - + +
677C GLU* 1.3 76.4 - - - +
679C LEU* 1.3 68.4 + - + +
681C LYS* 3.9 5.4 - - - -
682C ASP* 3.4 22.9 + - - +
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Residues in contact with LEU 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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616C LEU* 4.5 7.2 - - + -
619C LEU* 3.5 31.6 - - + -
664C LEU* 4.4 7.2 - - + -
675C LEU* 2.7 41.2 + - + +
676C ALA* 3.7 4.7 - - - +
678C VAL* 1.3 84.3 - - + +
680C LEU* 1.3 63.9 + - + +
682C ASP* 3.5 25.3 - - - +
683C SER* 4.3 3.1 + - - -
705C LEU* 4.4 22.8 - - + +
708C ASN* 4.8 10.2 + - + -
709C VAL* 4.5 15.7 - - + -
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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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607C PHE* 4.5 13.5 - - + -
612C SER* 4.2 27.4 - - - +
615C SER* 6.0 2.7 - - - -
616C LEU* 6.3 2.5 - - + +
676C ALA* 2.7 40.6 + - + +
677C GLU* 4.4 2.5 - - - +
679C LEU* 1.3 80.1 - - + +
681C LYS* 1.3 57.6 + - - +
682C ASP 3.1 6.5 + - - -
683C SER* 3.5 14.1 + - - +
686C PHE 3.5 20.2 - - - +
687C SER* 3.6 10.7 - - - +
688C PHE 4.7 1.8 - - - +
689C GLY* 4.2 24.5 - - - +
701C TYR* 4.0 19.7 - - - +
705C LEU* 5.1 8.5 - - + -
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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 GLU* 2.9 30.2 + - + +
678C VAL* 3.9 6.3 - - - +
679C LEU 3.4 0.2 - - - -
680C LEU* 1.3 77.1 - - - +
682C ASP* 1.3 60.2 - - - +
683C SER 3.6 4.3 - - - +
687C SER* 5.1 9.2 - - - +
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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