Contacts of the helix formed by residues 673 - 683 (chain C) in PDB entry 3T6A
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 TYR 673 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621C GLU 4.4 1.0 + - - -
624C ALA* 3.9 4.5 - - + -
625C ALA* 3.1 44.3 - - - +
628C SER* 3.5 33.4 - - - +
669C LEU* 3.0 31.1 + - + +
672C GLN* 1.3 112.8 + - + +
674C THR* 1.3 63.4 + - - +
675C GLN 3.3 2.2 - - - -
676C THR* 3.1 8.1 + - - +
677C ALA* 3.0 17.8 + - - +
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Residues in contact with THR 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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669C LEU 3.7 0.2 + - - -
670C ARG 2.6 27.5 + - - +
671C HIS* 4.0 9.5 + - - -
672C GLN 3.7 1.8 + - - -
673C TYR* 1.3 73.5 - - - +
675C GLN* 1.3 63.2 + - - +
677C ALA* 3.2 4.3 + - + +
678C ILE* 2.9 44.0 + - + +
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Residues in contact with GLN 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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673C TYR 3.3 0.8 - - - -
674C THR* 1.3 77.9 - - - +
676C THR* 1.3 64.1 + - - +
678C ILE* 3.3 20.2 + - - +
679C LEU* 2.9 39.3 + - + +
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Residues in contact with THR 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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628C SER* 3.7 28.9 + - - +
631C ILE* 3.4 40.7 - - + +
632C GLN* 4.2 16.4 + - + +
669C LEU* 4.6 2.0 - - + -
673C TYR* 3.1 12.3 + - - +
675C GLN* 1.3 79.7 - - - +
677C ALA* 1.3 58.1 + - - +
679C LEU* 3.3 9.1 + - + +
680C TYR* 2.9 28.1 + - - +
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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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669C LEU* 4.0 22.2 - - + +
670C ARG* 3.9 32.8 - - + -
673C TYR 3.0 11.5 + - - +
674C THR* 3.5 7.4 - - - +
676C THR* 1.3 78.4 - - - +
678C ILE* 1.3 62.9 + - + +
680C TYR* 3.4 6.1 + - - +
681C GLU* 3.0 24.7 + - - +
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Residues in contact with ILE 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 THR* 2.9 40.1 + - + +
675C GLN* 3.9 21.3 - - - +
677C ALA* 1.3 74.1 - - + +
679C LEU* 1.3 58.3 + - - +
681C GLU* 4.6 4.0 - - - -
682C LYS* 2.7 73.2 + - + +
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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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631C ILE* 4.3 8.1 - - + -
635C VAL* 2.9 41.5 - - + -
675C GLN* 2.9 30.8 + - + +
676C THR* 3.5 7.2 - - + +
678C ILE* 1.3 76.6 - - - +
680C TYR* 1.3 58.3 + - - +
683C GLN* 2.8 49.4 + - + +
684C LEU* 3.0 18.2 + - + -
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Residues in contact with TYR 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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631C ILE* 3.8 17.9 - - + -
651C MET* 3.5 30.3 - - + +
654C LEU* 3.5 52.2 + - + +
655C GLU* 4.1 10.7 - - - +
666C TRP* 3.6 30.5 - + - -
676C THR 2.9 17.3 + - - +
677C ALA* 3.6 6.1 - - - +
679C LEU* 1.3 76.5 - - - +
681C GLU* 1.3 68.0 + - + +
684C LEU* 3.3 15.2 - - + +
685C LYS* 3.0 61.4 + - + +
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Residues in contact with GLU 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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670C ARG* 6.0 0.2 + - - -
677C ALA 3.0 15.6 + - - +
678C ILE* 4.0 4.3 - - - +
680C TYR* 1.3 87.1 - - + +
682C LYS* 1.3 70.0 + - + +
685C LYS* 3.2 38.0 + - - +
686C PRO* 3.6 14.4 - - - +
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Residues in contact with LYS 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 ILE* 2.7 51.3 + - + +
681C GLU* 1.3 85.0 - - + +
683C GLN* 1.3 72.2 + - + +
686C PRO* 3.3 18.0 - - - +
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Residues in contact with GLN 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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638C LYS* 5.9 4.0 - - - +
679C LEU* 2.8 38.1 + - + +
682C LYS* 1.3 94.3 + - + +
684C LEU* 1.3 77.3 + - + +
685C LYS 3.5 0.4 - - - -
686C PRO* 3.3 3.3 - - - +
687C PHE* 3.1 25.6 + - - +
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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