Contacts of the helix formed by residues 295 - 303 (chain B) in PDB entry 2OT7
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 ARG 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 3.0 33.7 + - - -
40B HIS* 3.4 26.1 - - - +
195B TYR* 3.4 7.0 + - - +
271B PHE* 3.9 7.1 - - - +
272B PRO* 3.9 13.7 + - - +
293B THR* 3.2 5.1 - - - +
294B ARG* 1.3 75.9 - - - +
296B TRP* 1.3 63.0 + - - +
297B ILE 3.3 0.9 + - - -
298B GLU* 3.8 9.4 + - - +
299B TYR* 3.2 48.6 + - + -
342B ASP 5.5 1.1 + - - -
343B HIS* 4.4 3.6 + - - +
345B LEU* 3.1 28.3 + - - -
346B PRO 3.6 3.1 - - - +
347B THR* 3.1 30.6 + - - +
348B PRO* 4.4 4.6 - - + +
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Residues in contact with TRP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ILE* 5.3 0.2 - - + -
157B LEU* 4.8 0.9 - - + -
192B MET* 2.8 31.5 + - + -
193B ASP 3.3 21.2 + - - -
194B LEU* 3.5 35.0 - - + +
195B TYR* 4.1 10.5 - - + -
272B PRO* 4.4 4.2 - - + +
292B ALA* 3.6 17.0 - - + -
293B THR* 3.1 22.8 + - - +
295B ARG* 1.3 77.8 - - - +
297B ILE* 1.3 74.9 + - + +
299B TYR* 2.8 23.5 + - + -
300B GLY* 2.9 13.2 + - - +
315B ILE* 4.6 8.7 - - + -
317B MET* 3.4 39.5 - - + -
320B PHE* 3.8 33.9 - + - -
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ILE* 4.2 11.9 - - + -
294B ARG* 3.7 15.9 - - + +
295B ARG 3.3 1.8 - - - -
296B TRP* 1.3 85.4 - - + +
298B GLU* 1.3 59.4 + - - +
300B GLY 3.1 1.9 + - - -
301B LYS* 2.9 36.9 + - + +
317B MET* 3.5 12.8 - - + +
320B PHE* 4.0 30.5 - - + -
321B VAL* 4.5 1.3 - - + -
324B PHE* 3.4 46.4 - - + -
325B GLN* 3.8 24.9 - - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG 4.7 0.4 + - - -
295B ARG 3.8 8.3 + - - +
296B TRP 3.2 0.8 - - - -
297B ILE* 1.3 78.8 - - - +
299B TYR* 1.3 61.8 + - + +
301B LYS* 2.8 39.5 + - - +
302B GLN* 3.2 49.5 + - - +
325B GLN* 3.4 12.6 + - - +
328B ARG* 5.4 1.0 + - - -
337B ASP* 4.5 2.3 - - - +
339B THR* 3.7 28.1 + - + +
341B ILE* 3.6 26.6 - - + +
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Residues in contact with TYR 299 (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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192B MET 4.2 2.2 - - - +
193B ASP* 4.2 11.4 - - + +
213B PRO* 5.0 0.9 - - - +
272B PRO* 3.6 32.7 + - + -
273B TYR* 3.8 13.2 - + + -
295B ARG* 3.2 54.2 + - + -
296B TRP* 2.8 24.5 + - + +
298B GLU* 1.3 73.8 - - + +
300B GLY* 1.3 51.2 + - - +
302B GLN* 3.3 1.7 + - - -
303B ALA* 2.8 36.0 + - - +
341B ILE* 3.5 31.7 - - + +
342B ASP 4.7 0.2 + - - -
343B HIS* 2.7 49.3 + + - +
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B MET* 3.3 34.7 - - - +
296B TRP* 2.9 29.6 + - - +
297B ILE 3.5 3.4 - - - -
299B TYR* 1.3 74.6 - - - +
301B LYS* 1.3 63.6 + - - +
302B GLN 3.4 0.3 + - - -
303B ALA* 3.6 5.6 + - - +
317B MET* 3.7 11.2 - - - +
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 2.9 27.7 + - + +
298B GLU* 2.8 38.6 + - - +
299B TYR 3.4 0.2 - - - -
300B GLY* 1.3 75.7 - - - +
302B GLN* 1.3 61.6 + - + +
303B ALA 3.6 0.9 - - - +
317B MET* 4.0 10.3 - - + +
321B VAL* 4.1 13.4 - - + +
325B GLN* 2.7 29.0 + - - +
328B ARG* 4.5 0.8 - - - +
332B TRP* 3.4 43.1 + - + +
337B ASP* 3.0 24.7 + - - -
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Residues in contact with GLN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 5.3 0.2 - - - -
298B GLU* 3.2 33.9 + - - +
299B TYR 3.5 2.5 - - - +
300B GLY 3.2 0.4 - - - -
301B LYS* 1.3 81.2 - - + +
303B ALA* 1.3 65.4 + - - +
304B VAL* 3.2 12.3 + - - +
339B THR 2.8 28.7 + - - +
340B VAL* 5.3 0.2 - - - -
341B ILE* 3.6 33.5 + - + +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B MET* 4.0 20.0 - - + -
193B ASP* 3.8 17.7 - - - +
239B ARG* 4.1 2.0 - - - +
299B TYR 2.8 19.8 + - - +
300B GLY 3.6 10.1 + - - +
301B LYS 3.6 3.4 - - - +
302B GLN* 1.3 73.1 - - - +
304B VAL* 1.3 62.7 + - - +
305B LEU* 3.6 28.1 + - + +
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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