Contacts of the helix formed by residues 299 - 309 (chain A) in PDB entry 2XAR
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 GLY 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A VAL 3.3 4.7 + - - -
296A TYR 3.2 11.9 + - - -
297A GLY 3.2 5.0 - - - -
298A SER* 1.3 78.9 + - - +
300A VAL* 1.3 61.8 + - - +
301A LEU* 3.2 5.0 + - - -
302A ASP* 3.5 33.0 + - - +
303A ARG* 4.2 8.7 + - - +
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Residues in contact with VAL 300 (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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101A HIS* 3.7 32.8 - - + +
295A VAL* 4.2 3.0 + - - +
298A SER* 3.0 19.6 + - - +
299A GLY* 1.3 76.0 - - - +
301A LEU* 1.3 78.9 + - + +
302A ASP 3.4 0.2 - - - -
303A ARG* 3.7 17.5 + - + +
304A LEU* 3.6 12.3 + - - +
371A ILE* 4.6 5.4 - - + -
373A ILE* 6.3 0.2 - - + -
403A VAL* 3.8 27.8 - - + -
405A PHE* 3.7 30.8 - - + -
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Residues in contact with LEU 301 (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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217A LEU* 3.3 42.0 - - + +
218A PHE* 3.7 26.8 - - + -
225A VAL* 5.7 0.2 - - + -
295A VAL* 3.6 32.5 + - + +
299A GLY* 3.2 1.7 - - - -
300A VAL* 1.3 87.1 - - + +
302A ASP* 1.3 64.6 + - - +
304A LEU* 3.1 7.6 + - + +
305A LEU* 2.8 30.8 + - - +
371A ILE* 3.4 33.2 - - + -
405A PHE* 5.9 0.2 - - + -
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Residues in contact with ASP 302 (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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218A PHE 4.8 9.7 - - - +
220A GLY* 5.1 9.5 - - - -
299A GLY* 3.6 24.6 - - - +
300A VAL 3.4 0.2 - - - -
301A LEU* 1.3 81.3 - - - +
303A ARG* 1.3 61.5 + - + +
305A LEU* 3.5 10.7 + - - +
306A GLU* 3.2 30.2 + - - +
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Residues in contact with ARG 303 (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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96A LEU 5.1 5.3 - - - +
97A LEU* 3.6 35.6 + - + +
98A GLY* 4.9 4.2 - - - -
100A LYS* 5.4 5.3 - - - +
101A HIS* 4.0 26.4 + - - -
298A SER 5.6 4.0 + - - -
299A GLY 4.2 10.6 + - - +
300A VAL* 4.1 17.6 - - + +
301A LEU 3.2 0.6 - - - -
302A ASP* 1.3 73.6 - - + +
304A LEU* 1.3 65.1 + - - +
306A GLU* 3.3 19.7 + - - +
307A ILE* 3.3 21.5 + - - +
405A PHE* 5.6 0.4 - - + -
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Residues in contact with LEU 304 (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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97A LEU* 4.5 12.7 - - + +
169A PRO* 4.1 19.1 - - + -
218A PHE* 4.2 7.2 - - + -
300A VAL 3.6 5.1 + - - +
301A LEU* 3.1 9.7 + - + +
303A ARG* 1.3 75.5 - - - +
305A LEU* 1.3 67.0 + - - +
306A GLU 3.0 1.3 - - - -
307A ILE* 2.8 21.3 + - + +
308A GLN* 2.9 21.4 + - - +
366A ALA* 3.7 29.6 - - + +
369A CYS* 3.6 33.2 - - - -
371A ILE* 4.9 5.4 - - + -
405A PHE* 3.8 29.4 - - + -
408A LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 305 (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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172A GLY 3.6 30.3 - - - +
173A PHE* 4.0 17.7 - - + -
218A PHE* 3.8 34.9 - - + +
301A LEU 2.8 20.4 + - - +
302A ASP* 3.7 10.8 - - - +
304A LEU* 1.3 72.2 - - - +
306A GLU* 1.3 56.7 + - - +
308A GLN* 3.3 15.0 + - - +
309A LYS* 2.8 54.1 + - + +
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Residues in contact with GLU 306 (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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302A ASP* 3.2 21.8 + - - +
303A ARG* 3.3 15.0 - - - +
304A LEU 3.0 1.0 - - - -
305A LEU* 1.3 74.7 - - - +
307A ILE* 1.3 66.8 + - + +
309A LYS* 3.3 19.2 + - + +
310A LEU* 3.3 16.7 + - - +
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Residues in contact with ILE 307 (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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93A ILE* 5.5 3.8 - - + -
96A LEU* 3.5 52.7 - - + +
97A LEU* 4.1 18.4 - - + -
303A ARG 3.3 17.3 - - - +
304A LEU* 2.8 12.8 + - + +
306A GLU* 1.3 77.0 - - + +
308A GLN* 1.3 64.6 + - - +
310A LEU* 3.0 30.1 + - + +
362A ILE* 3.8 28.0 - - + +
363A ALA* 3.5 5.9 - - - +
366A ALA* 3.7 18.6 - - + -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PRO* 5.0 0.6 - - - +
170A LYS 3.2 19.5 + - - +
171A CYS* 3.3 6.2 - - - -
172A GLY 3.2 25.3 + - - -
173A PHE* 3.5 17.2 - - + -
218A PHE* 4.0 14.5 - - - -
304A LEU* 2.9 22.9 + - - +
305A LEU* 3.4 16.7 - - - +
307A ILE* 1.3 77.8 - - - +
309A LYS* 1.3 56.5 + - - +
310A LEU 2.9 5.4 + - - -
311A ASP* 3.1 14.9 + - - +
363A ALA* 3.3 14.6 - - - +
366A ALA* 3.1 32.2 + - + -
367A LYS* 3.5 18.4 - - + +
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Residues in contact with LYS 309 (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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173A PHE* 3.5 50.1 - - + +
305A LEU* 2.8 45.3 + - + +
306A GLU* 3.8 11.9 - - + +
307A ILE 3.3 0.8 - - - -
308A GLN* 1.3 68.6 - - - +
310A LEU* 1.3 59.0 + - - +
311A ASP 3.0 14.0 + - - +
312A LYS* 3.9 9.9 + - - +
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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