Contacts of the helix formed by residues 251 - 261 (chain C) in PDB entry 2OQH
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 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A MSE 5.3 8.5 + - - -
248A CYS* 5.4 4.9 + - - +
250A VAL* 6.1 2.6 - - - +
251A ARG* 5.9 3.0 - - - +
254A ASP* 4.9 14.1 + - - -
87C PHE* 5.8 5.3 - - - -
94C TYR* 3.6 30.1 + - + +
249C VAL* 4.5 0.5 - - - +
250C VAL* 1.3 82.2 - - + +
252C PHE* 1.3 63.4 + - - +
253C GLU* 3.2 41.3 + - - +
254C ASP* 3.0 46.9 + - - +
255C PHE 3.7 2.3 + - - -
274C TRP* 3.4 21.6 - - - +
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Residues in contact with PHE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 1.3 73.7 - - - +
253C GLU* 1.3 65.9 + - - +
255C PHE* 3.0 24.9 + - + +
256C ALA* 4.2 2.9 + - - +
274C TRP* 3.3 28.9 - + - -
279C ALA* 3.4 37.2 - - + -
282C ALA* 3.8 8.5 - - + -
283C LEU* 3.7 15.3 - - + -
286C HIS* 3.7 43.1 - + - -
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A VAL* 5.3 9.8 - - + +
228A GLY* 4.9 21.3 - - - +
229A ILE* 5.0 6.6 + - - +
230A GLU* 5.5 0.7 + - - +
83C HIS* 4.8 11.3 + - - -
94C TYR* 4.3 5.9 + - - -
251C ARG* 3.1 52.9 + - - +
252C PHE* 1.3 77.0 + - - +
254C ASP* 1.3 58.4 + - - +
255C PHE 3.4 0.2 - - - -
256C ALA* 5.4 0.2 - - - +
257C PRO* 3.4 21.9 - - - +
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Residues in contact with ASP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 5.1 10.8 + - - -
254A ASP* 5.3 2.8 - - - +
229C ILE* 4.0 8.9 - - + +
248C CYS 3.8 12.2 - - - +
249C VAL* 3.8 17.1 - - - -
250C VAL* 3.2 28.1 + - - +
251C ARG* 3.0 42.8 + - - +
253C GLU* 1.3 79.4 - - - +
255C PHE* 1.3 62.8 + - - +
256C ALA 3.6 0.4 - - - -
257C PRO* 3.4 6.0 - - - +
258C ALA* 3.0 25.4 + - - +
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Residues in contact with PHE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C VAL* 4.4 8.2 - - + +
251C ARG 3.7 2.3 + - - +
252C PHE* 3.0 27.3 + + + +
254C ASP* 1.3 75.1 - - - +
256C ALA* 1.3 68.3 + - - +
258C ALA* 3.3 5.6 + - - +
259C MSE 2.9 55.7 + - + +
267C ILE* 3.5 32.8 - - + -
274C TRP* 5.3 0.4 - + - -
283C LEU* 4.4 12.6 - - + -
286C HIS* 3.7 43.7 - + + -
287C CYS 4.8 0.2 - - - -
290C PHE* 3.5 28.9 - + - -
292C LEU* 3.9 9.4 - - + -
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.5 36.3 - - + +
252C PHE 4.2 3.1 + - - +
253C GLU 5.4 0.4 - - - +
255C PHE* 1.3 80.3 - - - +
257C PRO* 1.3 72.9 - - + +
259C MSE 3.1 5.9 + - - +
260C ARG* 3.0 29.5 + - - +
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Residues in contact with PRO 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.9 34.5 - - + -
230A GLU* 4.3 6.7 - - + +
257A PRO* 4.9 4.7 - - + -
261A LEU* 3.7 23.6 - - + -
229C ILE* 4.4 12.1 - - + -
253C GLU 3.4 24.0 - - - +
254C ASP* 3.4 8.1 - - - +
256C ALA* 1.3 94.1 - - + +
258C ALA* 1.3 62.6 + - - +
260C ARG* 3.3 0.9 + - - +
261C LEU* 2.9 31.9 + - - +
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Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C ILE* 4.1 16.0 - - + +
249C VAL* 3.5 27.4 - - + -
254C ASP 3.0 19.7 + - - +
255C PHE 3.6 4.3 - - - +
256C ALA 3.2 0.2 - - - -
257C PRO* 1.3 77.2 - - - +
259C MSE 1.3 69.3 + - + +
261C LEU 3.6 0.2 + - - -
262C ASN* 3.1 6.9 + - - -
263C ALA* 2.9 36.3 + - + +
264C VAL* 5.3 0.7 - - + -
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Residues in contact with MSE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C PHE* 2.9 43.7 + - + +
256C ALA* 3.1 7.8 + - - +
258C ALA* 1.3 85.2 - - + +
260C ARG* 1.3 66.9 + - + +
262C ASN* 3.1 22.8 + - - +
264C VAL* 4.1 21.8 - - + +
267C ILE* 4.5 2.5 - - + -
290C PHE* 3.7 43.7 - - + -
292C LEU* 3.6 37.2 - - + -
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 2.7 41.0 + - - -
234A GLN* 4.0 12.8 - - - +
261A LEU* 3.9 28.4 - - + +
256C ALA* 3.0 17.9 + - + +
257C PRO 3.9 1.6 - - - +
259C MSE 1.3 77.2 - - + +
261C LEU* 1.3 62.9 + - - +
262C ASN* 3.2 7.3 + - - +
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PRO* 3.6 39.9 - - + +
260A ARG* 3.8 31.2 - - + +
261A LEU* 3.8 25.1 - - + -
229C ILE* 3.7 23.3 - - + -
230C GLU* 5.2 3.4 - - - +
233C ALA* 3.3 17.0 - - + +
257C PRO 2.9 19.7 + - - +
258C ALA 4.3 0.2 - - - +
260C ARG* 1.3 77.4 - - - +
262C ASN* 1.3 71.5 + - - +
263C ALA 3.3 1.2 + - - -
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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