Contacts of the helix formed by residues 559 - 563 (chain B) in PDB entry 3V9G
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 TYR 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ILE* 3.8 37.0 - - + +
157A GLN* 4.5 2.6 + - - -
338A ARG* 3.3 41.1 + - - -
342A GLU* 2.6 35.4 + - - -
387A PHE* 4.3 4.7 - + - -
509A LYS* 5.2 2.3 - - - -
557B TRP 3.7 4.5 - - - -
558B SER* 1.3 82.1 + - - +
560B ALA* 1.3 66.8 + - - +
561B TYR* 3.5 24.9 - + + -
562B MET* 3.0 33.7 + - - +
563B GLN* 3.8 2.6 + - - +
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Residues in contact with ALA 560 (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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39A ALA* 5.6 2.7 - - + +
41A THR* 4.4 18.1 - - + +
559B TYR* 1.3 72.8 - - - +
561B TYR* 1.3 58.9 + - - +
563B GLN* 2.8 31.0 + - - +
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Residues in contact with TYR 561 (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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39A ALA 3.3 18.1 + - - +
40A PHE* 3.3 28.0 - - + +
41A THR* 4.5 5.1 - - - +
47A ARG* 3.3 21.2 + - - +
154A THR* 3.6 29.1 + - - -
155A VAL* 3.4 36.3 - - + -
156A ILE* 3.7 26.3 + - + +
384A PHE* 3.5 29.2 - + + +
386A THR 3.9 4.9 + - - -
387A PHE 5.2 0.3 + - - -
559B TYR* 3.5 27.6 - + + -
560B ALA* 1.3 77.3 - - - +
562B MET* 1.3 74.8 + - + +
563B GLN 3.3 6.0 + - - +
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Residues in contact with MET 562 (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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156A ILE* 5.8 0.2 - - - -
384A PHE 3.3 22.4 - - - +
385A GLY* 3.8 32.2 + - - +
386A THR 4.2 4.3 - - - +
387A PHE* 3.8 32.3 - - + +
557B TRP* 4.5 5.4 - - + -
558B SER* 3.8 19.3 - - - +
559B TYR* 3.0 40.7 + - - +
560B ALA 2.9 1.4 + - - -
561B TYR* 1.3 96.3 - - + +
563B GLN* 1.3 65.3 + - - +
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Residues in contact with GLN 563 (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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42A GLN* 5.4 7.8 + - - +
47A ARG* 5.2 4.3 + - - -
558B SER* 5.4 0.4 + - - -
559B TYR 3.8 2.7 + - - +
560B ALA* 2.8 18.4 + - - +
561B TYR 3.9 6.4 - - - +
562B MET* 1.3 82.6 - - - +
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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