Contacts of the helix formed by residues 662 - 673 (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 LEU 662 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613C ILE* 4.2 21.3 - - + -
614C LEU* 3.7 24.9 - - + -
623C ARG* 4.6 5.8 - - - +
658C GLN 3.7 7.2 - - - +
659C ILE* 3.0 22.0 + - + +
660C THR 3.2 0.6 - - - -
661C ARG* 1.3 74.0 - - + +
663C GLU* 1.3 64.3 + - - +
664C LYS 3.3 2.7 - - - -
665C THR* 2.9 30.3 + - + +
666C TRP* 3.0 19.2 + - + +
812C SER* 3.4 33.0 - - - +
815C LEU* 4.6 5.2 - - + -
816C GLU* 3.5 22.7 - - + -
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Residues in contact with GLU 663 (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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660C THR 4.8 6.2 - - - +
661C ARG 2.8 14.7 + - - +
662C LEU* 1.3 70.0 - - - +
664C LYS* 1.3 65.5 + - + +
666C TRP* 3.2 5.4 + - - +
667C THR* 2.9 44.8 + - - +
670C ARG* 3.6 17.8 + - - -
816C GLU* 3.5 2.3 + - - +
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Residues in contact with LYS 664 (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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620C LEU* 3.9 20.4 - - + +
623C ARG* 5.9 0.2 - - - +
663C GLU* 1.3 77.5 - - + +
665C THR* 1.3 58.1 + - - +
667C THR* 3.5 5.2 + - - -
668C ALA* 2.9 29.1 + - - +
815C LEU 5.9 0.6 + - - -
816C GLU* 3.0 36.6 + - + +
817C PRO* 5.6 8.7 + - - +
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Residues in contact with THR 665 (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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613C ILE* 5.2 2.5 - - + -
620C LEU* 3.8 7.4 - - + -
623C ARG* 2.9 34.7 + - + +
624C ALA* 4.1 22.6 - - - +
627C LEU* 4.1 19.5 - - + -
662C LEU* 2.9 22.5 + - + +
664C LYS* 1.3 76.8 - - - +
666C TRP* 1.3 57.4 + - + +
668C ALA* 3.2 5.1 + - - +
669C LEU* 2.9 25.6 + - - +
816C GLU* 2.8 20.4 + - - -
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Residues in contact with TRP 666 (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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627C LEU* 3.9 24.6 - - + +
631C ILE* 4.6 2.5 - - + -
654C LEU* 3.8 23.8 - - + -
659C ILE* 3.1 33.7 + - + +
660C THR* 3.9 15.1 - - - +
662C LEU* 3.0 30.6 + - + +
663C GLU* 3.9 8.1 - - - +
665C THR* 1.3 73.2 - - - +
667C THR* 1.3 60.0 + - - +
669C LEU* 3.1 37.5 + - + +
670C ARG* 2.8 63.0 + - + +
680C TYR* 3.6 40.4 - + - -
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Residues in contact with THR 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C GLU* 2.9 38.6 + - - +
664C LYS* 3.8 5.8 - - - -
666C TRP* 1.3 73.7 - - - +
668C ALA* 1.3 65.3 + - - +
670C ARG* 3.3 11.4 + - - +
671C HIS* 2.7 61.0 + - + +
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Residues in contact with ALA 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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620C LEU* 4.3 20.2 - - + -
624C ALA* 3.7 17.7 - - + -
664C LYS 2.9 14.9 + - - +
665C THR 3.3 9.9 - - - +
667C THR* 1.3 77.4 - - - +
669C LEU* 1.3 56.2 + - - +
671C HIS* 3.3 4.5 + - - -
672C GLN* 3.0 47.3 + - - +
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Residues in contact with LEU 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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624C ALA* 4.0 13.0 - - + +
627C LEU* 3.9 8.7 - - + -
628C SER* 3.9 35.0 - - - +
631C ILE* 3.9 14.8 - - + -
665C THR 2.9 13.3 + - - +
666C TRP* 3.1 42.6 + - + +
668C ALA* 1.3 77.0 - - - +
670C ARG* 1.3 58.5 + - + +
673C TYR* 3.0 49.1 + - + +
676C THR* 4.6 4.5 - - + -
677C ALA* 4.0 19.5 - - + -
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Residues in contact with ARG 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 GLU* 3.6 23.2 + - - -
666C TRP* 2.8 44.8 + - + +
667C THR* 3.3 34.1 + - - +
669C LEU* 1.3 73.6 - - + +
671C HIS* 1.3 68.0 + - + +
674C THR* 2.6 32.8 + - - +
677C ALA* 3.9 20.0 - - + -
681C GLU* 6.0 0.2 + - - -
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Residues in contact with HIS 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 THR* 2.7 46.8 + - + +
668C ALA* 4.0 4.4 - - - +
669C LEU 3.1 0.8 - - - -
670C ARG* 1.3 92.1 - - + +
672C GLN* 1.3 62.1 + - + +
673C TYR 3.7 0.2 - - - -
674C THR* 4.0 6.5 + - - -
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Residues in contact with GLN 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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620C LEU* 5.9 0.8 - - - +
621C GLU* 3.5 38.3 + - - +
624C ALA* 4.7 2.5 - - - -
668C ALA* 3.0 32.8 + - - +
671C HIS* 1.3 80.7 - - + +
673C TYR* 1.3 99.9 + - + +
674C THR 3.7 2.1 + - - -
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Residues in contact with TYR 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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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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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