Contacts of the helix formed by residues 400 - 406 (chain A) in PDB entry 4RQE
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 ASP 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 5.6 1.2 - - - +
137A ASN* 4.5 4.9 - - - +
399A THR* 1.3 86.8 + - - +
401A TYR* 1.3 59.7 + - - +
402A GLN 3.4 1.8 - - - -
403A ALA* 3.6 3.6 - - - -
404A ARG* 2.4 70.9 + - - +
422A PHE* 3.7 16.9 - - + +
423A VAL 3.2 18.4 - - - +
424A HIS* 3.5 18.0 + - + -
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Residues in contact with TYR 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A VAL* 2.7 57.9 + - + +
3A LEU* 3.8 20.0 - - + -
132A LEU 4.5 1.4 + - - -
133A ARG 3.6 17.0 + - - -
135A ILE 2.8 30.3 + - - -
136A GLY 3.9 0.7 - - - -
137A ASN* 3.3 26.7 - - + +
371A HIS* 3.5 17.2 - - + +
372A ALA* 3.6 29.4 - - + +
398A CYS 3.2 15.7 + - - +
399A THR 3.2 0.6 - - - -
400A ASP* 1.3 84.2 + - - +
402A GLN* 1.3 67.8 + - + +
404A ARG* 4.5 0.7 - - - +
405A ARG* 3.5 13.7 + - + +
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLU 5.6 3.8 - - - +
237A VAL* 4.8 19.0 + - + +
273A GLU* 3.5 23.1 + - - +
277A ALA* 4.2 13.2 - - - +
327A PHE* 5.0 3.8 - - - -
372A ALA* 3.3 24.8 - - + +
398A CYS* 3.8 19.8 + - + +
399A THR 4.4 0.6 + - - +
400A ASP 3.4 0.2 - - - -
401A TYR* 1.3 88.6 - - + +
403A ALA* 1.3 56.7 + - - +
404A ARG 3.2 0.4 - - - -
405A ARG* 3.1 7.0 + - - +
406A LEU* 2.7 44.8 + - + +
425A MET* 3.5 22.6 - - + +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A THR 4.4 0.6 + - - -
400A ASP* 3.2 7.7 + - - +
402A GLN* 1.3 80.3 - - - +
404A ARG* 1.3 55.8 + - - +
406A LEU* 4.9 0.9 - - - -
407A ARG* 3.1 4.9 + - - -
408A ILE* 2.9 51.8 + - + +
422A PHE* 3.6 8.1 - - + -
423A VAL 3.2 27.6 - - - +
425A MET* 3.6 18.8 - - + +
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A VAL* 2.4 47.7 + - + +
3A LEU* 3.4 9.2 - - - +
4A ASP* 3.3 46.8 + - - +
7A LEU* 5.8 0.6 - - - +
400A ASP* 2.4 56.9 + - - +
401A TYR* 4.5 0.8 - - - +
403A ALA* 1.3 75.0 - - - +
405A ARG* 1.3 64.6 + - - +
407A ARG* 3.5 14.3 + - - +
422A PHE* 3.5 45.4 - - + -
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A VAL* 3.5 34.2 - - + +
129A PHE* 3.5 34.5 - - - -
133A ARG* 4.2 29.9 + - - +
235A GLN* 3.1 24.9 + - - +
236A GLU* 3.2 59.2 + - + +
401A TYR* 3.5 16.5 + - + +
402A GLN* 3.1 11.8 + - - +
404A ARG* 1.3 79.4 - - - +
406A LEU* 1.3 61.0 + - + +
407A ARG* 3.2 21.5 + - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 5.0 2.7 - - - +
236A GLU* 3.9 26.7 - - + +
237A VAL* 3.7 34.5 - - + -
277A ALA* 3.4 35.0 - - + +
278A ALA* 4.1 6.3 - - + +
281A ARG* 3.2 24.4 - - + +
282A ASP 2.9 27.2 + - - -
402A GLN* 2.7 22.4 + - + +
403A ALA* 4.9 0.2 - - - -
405A ARG* 1.3 73.6 - - + +
407A ARG* 1.3 65.2 + - - +
408A ILE* 3.4 13.2 - - + +
425A MET* 4.2 9.4 - - + -
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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