Contacts of the helix formed by residues 656 - 661 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D ALA* 3.4 41.1 - - + +
607D ILE* 4.2 0.9 - - - +
610D ALA* 3.8 21.5 - - + -
652D LYS* 3.2 20.9 + - + +
653D ALA* 3.2 15.1 + - - +
655D GLU* 1.3 79.3 - - - +
657D PRO* 1.3 68.9 - - + +
658D GLN* 4.0 6.1 - - - +
659D ILE* 2.9 9.7 + - + -
660D THR* 2.9 26.2 + - - +
724D PHE* 3.5 39.9 - - + -
725D GLU* 4.0 9.4 - - - +
808D LEU* 4.3 4.9 - - - -
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Residues in contact with PRO 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D GLU 3.5 3.8 - - - +
656D MET* 1.3 83.5 - - - +
658D GLN* 1.3 79.1 + - - +
659D ILE 3.1 1.0 + - - -
660D THR* 3.3 20.3 + - - +
661D ARG* 3.5 17.1 + - - +
725D GLU* 2.9 24.0 - - - +
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Residues in contact with GLN 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D LEU* 3.8 20.1 - - + +
656D MET* 4.0 9.0 - - + +
657D PRO* 1.3 85.7 - - - +
659D ILE* 1.3 59.0 + - + +
661D ARG* 3.9 5.6 - - - +
662D LEU* 3.7 8.7 - - - +
725D GLU* 2.7 21.1 + - - +
805D ASN* 2.8 31.9 - - - +
808D LEU* 3.5 11.0 - - + +
809D THR* 3.1 44.7 + - + +
812D SER* 2.7 28.6 + - - -
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Residues in contact with ILE 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ALA* 4.1 11.7 - - + +
613D ILE* 3.7 37.9 - - + -
614D LEU* 3.7 33.0 - - + -
627D LEU* 5.0 2.9 - - + -
653D ALA 3.4 24.0 - - - +
654D LEU* 4.0 13.9 - - - +
656D MET* 2.9 14.6 + - + +
658D GLN* 1.3 79.6 - - + +
660D THR* 1.3 63.7 + - - +
661D ARG 3.2 2.0 - - - -
662D LEU* 3.2 18.2 + - + +
666D TRP* 2.9 24.9 + - + +
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Residues in contact with THR 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654D LEU 3.5 15.7 - - - +
655D GLU* 3.5 17.3 - - - +
656D MET 2.9 17.5 + - - +
657D PRO* 3.3 15.2 + - - +
659D ILE* 1.3 76.9 - - - +
661D ARG* 1.3 62.5 + - - +
662D LEU 3.1 1.3 + - - -
663D GLU* 4.4 7.4 + - - +
666D TRP* 3.6 20.1 - - + +
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Residues in contact with ARG 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657D PRO 3.5 16.1 + - - +
658D GLN* 3.9 3.6 - - - +
660D THR* 1.3 77.8 + - - +
662D LEU* 1.3 50.5 - - - +
663D GLU* 2.6 25.4 + - - +
809D THR* 5.3 1.8 + - - +
812D SER* 3.3 36.3 + - - +
813D ARG* 3.4 36.0 - - - +
816D GLU* 2.8 33.8 + - - +
817D PRO 5.1 0.2 - - - -
818D PRO* 4.1 17.0 - - - +
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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