Contacts of the helix formed by residues 656 - 661 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B ALA* 3.4 36.1 - - + +
607B ILE 4.3 0.2 - - - +
610B ALA* 3.6 21.3 - - + -
652B LYS* 3.0 17.0 + - + +
653B ALA* 3.1 26.0 + - - +
655B GLU* 1.3 76.8 - - - +
657B PRO* 1.3 57.9 - - - -
658B GLN* 3.5 11.9 - - - +
659B ILE* 2.7 30.6 + - + -
660B THR 2.8 13.7 + - - -
724B PHE* 3.6 33.4 - - + -
725B GLU* 3.2 16.2 - - - +
727B THR* 6.5 0.2 - - + -
808B LEU* 4.1 6.5 - - - -
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Residues in contact with PRO 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B GLU 3.3 6.4 - - - +
656B MET* 1.3 84.3 - - + +
658B GLN* 1.3 71.7 + - - +
660B THR* 3.3 16.2 - - + +
661B ARG* 3.2 30.3 + - - +
725B GLU* 4.2 10.5 - - - +
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Residues in contact with GLN 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B LEU* 3.8 12.6 - - + +
656B MET* 3.5 18.4 - - + +
657B PRO* 1.3 82.8 - - - +
659B ILE* 1.3 60.2 + - + +
661B ARG* 4.1 3.0 - - - +
662B LEU* 3.5 11.1 - - - +
725B GLU* 2.7 29.6 + - - +
805B ASN* 3.3 12.8 - - - +
808B LEU* 3.7 30.5 - - + +
809B THR* 3.2 31.6 + - - +
812B SER* 2.8 30.2 + - - -
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Residues in contact with ILE 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ALA* 4.3 12.1 - - + +
613B ILE* 3.9 26.7 - - + -
614B LEU* 3.2 40.4 - - + -
627B LEU* 4.9 2.5 - - + -
653B ALA* 3.4 21.8 - - + +
654B LEU* 4.0 25.6 - - + +
656B MET* 2.7 20.4 + - + +
658B GLN* 1.3 72.8 - - + +
660B THR* 1.3 64.8 + - - +
661B ARG 3.2 2.0 - - - -
662B LEU* 3.1 20.5 + - + +
666B TRP* 3.0 27.2 + - + +
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Residues in contact with THR 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B LEU 4.6 8.6 + - - -
655B GLU* 4.4 8.8 - - - +
656B MET 2.8 9.5 + - - -
657B PRO* 3.3 26.5 - - + +
659B ILE* 1.3 79.2 - - - +
661B ARG* 1.3 65.7 + - + +
662B LEU 3.4 1.6 + - - -
663B GLU* 4.6 2.6 + - - +
666B TRP* 3.7 19.5 - - - +
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Residues in contact with ARG 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657B PRO 3.2 17.3 - - - +
658B GLN* 4.1 1.8 - - - +
660B THR* 1.3 82.0 - - + +
662B LEU* 1.3 52.7 + - - +
663B GLU* 2.6 26.7 + - - +
812B SER* 2.7 37.8 + - - +
813B ARG* 3.1 26.4 - - - +
816B GLU* 2.5 33.3 + - - +
817B PRO* 4.4 2.2 + - - +
818B PRO* 4.3 20.4 - - - +
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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