Contacts of the helix formed by residues 656 - 661 (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 MET 656 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C ALA* 3.8 39.3 - - + +
607C ILE* 4.1 1.6 - - - +
610C ALA* 3.5 25.1 - - + -
652C LYS* 3.2 13.1 + - + +
653C ALA* 3.0 20.4 + - - +
655C GLU* 1.3 77.5 - - - +
657C PRO* 1.3 59.4 - - + +
658C GLN* 4.1 6.5 - - + +
659C ILE* 2.8 12.3 + - + +
660C THR* 2.7 32.6 + - - -
724C PHE* 3.5 35.9 - - + -
725C GLU* 3.2 16.8 - - - +
808C LEU* 4.0 6.7 - - - -
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Residues in contact with PRO 657 (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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655C GLU 3.4 5.8 - - - +
656C MET* 1.3 83.3 - - - +
658C GLN* 1.3 71.6 + - + +
659C ILE 3.1 0.5 + - - -
660C THR* 3.5 13.5 - - + -
661C ARG* 3.2 29.7 + - - +
725C GLU* 3.5 18.4 - - - +
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Residues in contact with GLN 658 (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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614C LEU* 3.8 21.6 - - + +
656C MET* 3.1 4.6 - - + +
657C PRO* 1.3 83.3 - - - +
659C ILE* 1.3 61.7 + - + +
661C ARG* 4.1 2.6 - - - +
662C LEU* 3.7 6.9 - - - +
725C GLU* 2.4 25.2 + - - +
805C ASN* 2.8 48.9 + - - +
808C LEU* 3.5 11.9 - - + +
809C THR* 3.0 33.7 + - + +
812C SER* 2.5 30.2 + - - -
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Residues in contact with ILE 659 (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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610C ALA* 3.9 24.7 - - + +
613C ILE* 4.1 27.8 - - + -
614C LEU* 3.7 31.4 - - + -
627C LEU* 5.2 1.8 - - + -
653C ALA 3.4 24.9 - - - +
654C LEU* 4.1 13.7 - - + +
656C MET* 2.8 14.9 + - + +
658C GLN* 1.3 79.3 - - + +
660C THR* 1.3 65.5 + - - +
661C ARG 3.1 2.2 - - - -
662C LEU* 3.0 23.5 + - + +
666C TRP* 3.1 24.8 + - + +
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Residues in contact with THR 660 (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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654C LEU 4.5 9.5 + - - -
655C GLU* 4.4 8.1 + - - +
656C MET 2.7 15.5 + - - -
657C PRO* 3.5 22.0 - - + +
659C ILE* 1.3 74.5 - - - +
661C ARG* 1.3 67.4 + - + +
662C LEU 3.2 1.8 + - - -
663C GLU* 4.5 6.4 + - - +
666C TRP* 3.9 18.3 + - - +
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Residues in contact with ARG 661 (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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657C PRO 3.3 17.9 - - - +
658C GLN* 4.1 1.3 - - - +
659C ILE 3.1 1.0 - - - -
660C THR* 1.3 83.8 - - + +
662C LEU* 1.3 57.5 + - - +
663C GLU* 2.8 18.2 + - - +
812C SER* 2.8 46.8 + - - +
813C ARG* 2.8 33.9 - - - +
816C GLU* 2.9 23.4 + - - +
817C PRO* 4.4 7.5 - - - +
818C PRO* 4.6 9.9 - - - +
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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