Contacts of the helix formed by residues 660 - 670 (chain B) in PDB entry 1UWH
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 ASN 660 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B ILE* 3.4 8.6 + - + +
659B ASN* 1.3 84.2 + - - +
661B ARG* 1.3 64.1 + - - +
662B ASP* 3.0 18.6 + - - +
663B GLN* 2.9 40.1 + - + +
664B ILE* 3.0 26.1 + - - +
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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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612B LEU 5.0 8.3 + - - -
613B SER* 5.8 0.4 - - - +
614B GLY* 3.3 16.2 + - - +
616B ILE* 2.8 41.2 - - + +
659B ASN 4.2 0.4 - - - -
660B ASN* 1.3 71.9 + - - +
662B ASP* 1.3 65.5 + - - +
664B ILE* 3.1 12.3 + - + +
665B ILE* 2.8 55.6 + - + +
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Residues in contact with ASP 662 (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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660B ASN* 3.0 12.8 + - - +
661B ARG* 1.3 80.8 + - - +
663B GLN* 1.3 60.6 + - + +
665B ILE* 3.6 14.3 - - - +
666B PHE* 2.9 30.7 + - - +
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Residues in contact with GLN 663 (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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658B ILE* 4.7 8.3 - - + -
660B ASN* 2.9 36.3 + - + +
662B ASP* 1.3 75.9 - - - +
664B ILE* 1.3 66.8 + - - +
666B PHE* 3.3 13.7 + - - +
667B MET* 2.8 53.8 + - - +
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Residues in contact with ILE 664 (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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616B ILE* 4.3 15.3 - - + -
617B LEU* 4.7 9.4 - - + -
655B TYR* 3.5 48.2 - - + +
658B ILE* 3.6 33.6 - - + +
660B ASN 3.0 16.4 + - - +
661B ARG* 3.6 11.2 - - + +
663B GLN* 1.3 75.5 - - - +
665B ILE* 1.3 64.8 - - - +
667B MET* 4.7 0.4 - - - -
668B VAL* 2.8 35.3 + - + +
673B LEU* 4.1 9.6 - - + -
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Residues in contact with ILE 665 (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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616B ILE* 4.0 21.8 - - + -
624B ILE* 3.2 41.8 - - + +
661B ARG* 2.8 59.8 + - - +
662B ASP* 3.6 13.7 - - - +
664B ILE* 1.3 75.1 - - - +
666B PHE* 1.3 65.0 + - - +
668B VAL 4.0 0.2 - - - -
669B GLY* 3.1 15.1 + - - -
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Residues in contact with PHE 666 (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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662B ASP 2.9 18.8 + - - +
663B GLN* 3.7 15.5 - - - +
665B ILE* 1.3 77.1 - - - +
667B MET* 1.3 74.6 + - + +
669B GLY* 3.1 3.6 + - - -
670B ARG* 3.1 70.1 + - + +
672B TYR* 4.0 24.2 - + - -
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Residues in contact with MET 667 (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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658B ILE* 5.1 8.3 - - + -
663B GLN* 2.8 43.9 + - - +
664B ILE 4.0 0.9 - - - +
666B PHE* 1.3 84.0 - - + +
668B VAL* 1.3 63.2 + - - +
670B ARG 3.2 1.9 + - - -
671B GLY 3.1 3.5 + - - -
672B TYR* 3.0 62.4 + - + +
673B LEU* 3.7 24.9 - - + -
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Residues in contact with VAL 668 (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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619B MET 4.4 7.2 - - - +
621B PRO* 3.7 28.2 - - + +
624B ILE* 3.5 24.2 - - + -
639B TYR* 4.6 5.6 - - - +
655B TYR* 3.7 28.9 - - + +
664B ILE* 2.8 30.5 + - + +
667B MET* 1.3 73.7 - - - +
669B GLY* 1.3 61.2 + - - +
671B GLY* 3.3 10.4 + - - -
673B LEU* 3.9 32.0 - - + +
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Residues in contact with GLY 669 (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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621B PRO* 4.3 8.6 - - - +
624B ILE* 3.8 14.8 - - - +
625B ARG* 3.1 39.0 + - - -
665B ILE 3.1 14.6 + - - -
666B PHE 3.1 4.0 + - - -
668B VAL* 1.3 80.1 - - - +
670B ARG* 1.3 62.2 + - - +
671B GLY 3.7 0.2 + - - -
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Residues in contact with ARG 670 (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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625B ARG* 5.4 8.6 - - - +
666B PHE* 3.1 54.1 + - + +
667B MET 3.2 2.0 + - - +
669B GLY* 1.3 81.5 - - - +
671B GLY* 1.3 58.9 + - - +
672B TYR* 3.2 41.5 + - + -
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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