Contacts of the helix formed by residues 660 - 667 (chain N) in PDB entry 3HOU
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 LYS 660 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656N GLY 2.8 19.3 + - - +
657N HIS* 3.1 13.6 + - + +
658N ILE 2.8 0.2 - - - -
659N ALA* 1.3 77.5 - - - +
661N LEU* 1.3 58.4 - - - +
663N ALA* 3.3 19.6 - - + +
664N THR* 3.7 8.1 + - - -
678N GLU* 6.3 2.0 - - - -
679N TYR* 3.4 48.3 - - + +
687N GLU* 4.4 6.5 + - - -
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Residues in contact with LEU 661 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA* 4.6 6.7 - - + +
33N VAL* 4.5 22.0 - - + +
36N ALA* 3.9 13.2 - - + -
39N ARG* 5.5 2.4 + - - +
653N VAL* 6.1 0.2 - - + -
657N HIS 3.2 16.3 + - - +
658N ILE* 2.6 23.9 + - + +
660N LYS* 1.3 69.3 - - - +
662N MET* 1.3 53.8 + - + +
663N ALA 2.8 4.5 - - - -
664N THR* 2.7 28.4 + - - -
665N GLU* 3.1 17.9 + - + +
679N TYR* 3.0 37.2 - - + +
680N THR 3.4 16.4 - - - +
684N LEU* 3.6 29.4 - - + -
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Residues in contact with MET 662 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N ASP* 4.9 1.3 - - - +
32N ALA* 4.1 13.0 - - + -
655N LYS* 3.8 12.8 - - - +
658N ILE* 3.0 34.5 + - + +
659N ALA* 3.3 23.6 - - + +
661N LEU* 1.3 74.2 - - - +
663N ALA* 1.3 59.9 + - - +
665N GLU* 3.1 29.5 - - + +
666N TYR* 3.1 24.4 + - - +
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Residues in contact with ALA 663 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659N ALA 3.4 13.1 + - - +
660N LYS* 3.3 17.7 - - + +
662N MET* 1.3 79.5 - - - +
664N THR* 1.3 61.8 + - - +
666N TYR* 3.5 6.2 + - - +
667N GLN* 3.3 32.0 + - - +
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Residues in contact with THR 664 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N ARG* 5.4 6.7 - - - -
660N LYS 3.7 2.3 + - - -
661N LEU 2.7 16.2 + - - -
663N ALA* 1.3 71.4 - - - +
665N GLU* 1.3 63.7 + - - -
667N GLN* 3.4 20.2 + - + +
668N ASP* 3.1 20.1 - - - +
678N GLU* 2.8 29.7 + - - +
679N TYR* 3.1 36.8 + - - +
680N THR* 6.0 0.4 - - - -
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Residues in contact with GLU 665 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA* 4.0 15.1 - - - +
35N SER* 3.9 15.7 + - - -
39N ARG* 2.5 50.2 + - - +
661N LEU* 3.1 7.8 + - + +
662N MET* 3.1 42.3 + - + +
663N ALA 3.2 0.2 - - - -
664N THR* 1.3 74.2 - - - +
666N TYR* 1.3 66.1 + - - +
667N GLN 3.0 2.8 + - - -
668N ASP* 3.2 21.3 + - - +
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Residues in contact with TYR 666 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662N MET 3.1 13.9 + - - +
663N ALA* 3.7 7.2 - - - +
665N GLU* 1.3 79.8 - - - +
667N GLN* 1.3 61.6 + - + +
668N ASP 2.8 15.5 + - - +
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Residues in contact with GLN 667 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663N ALA* 3.3 22.4 + - - +
664N THR* 3.4 15.8 + - + +
665N GLU 3.0 1.8 + - - -
666N TYR* 1.3 80.5 - - + +
668N ASP* 1.3 70.7 + - - +
678N GLU* 4.1 22.8 + - - +
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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