Contacts of the helix formed by residues 251 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B MSE 5.3 7.9 + - - -
248B CYS* 5.4 4.4 + - - +
250B VAL* 5.8 3.8 - - - +
251B ARG* 4.5 14.2 - - - +
254B ASP* 4.9 10.1 + - - -
87D PHE* 6.2 1.4 - - - -
94D TYR* 3.7 28.8 + - + +
249D VAL* 4.5 0.2 - - - +
250D VAL* 1.3 86.0 + - + +
252D PHE* 1.3 67.0 + - - +
253D GLU* 3.4 43.6 + - - +
254D ASP* 2.9 46.4 + - - +
255D PHE 3.7 2.8 + - - -
274D TRP* 3.4 21.1 - - - +
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Residues in contact with PHE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ARG* 1.3 73.6 - - - +
253D GLU* 1.3 66.1 + - - +
255D PHE* 3.2 22.3 + - + +
256D ALA* 4.3 3.3 + - - +
274D TRP* 3.3 29.2 - + - -
279D ALA* 3.3 39.0 - - + -
282D ALA* 3.9 7.9 - - + -
283D LEU* 3.8 15.3 - - + -
286D HIS* 3.7 42.0 - + - -
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Residues in contact with GLU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B VAL* 4.0 27.2 - - + +
228B GLY* 4.9 11.9 - - - -
229B ILE* 5.1 5.9 + - - +
230B GLU* 5.6 0.7 + - - +
94D TYR* 4.2 7.5 + - - -
251D ARG* 3.0 55.3 + - - +
252D PHE* 1.3 78.6 + - - +
254D ASP* 1.3 58.0 + - - +
255D PHE 3.4 0.2 - - - -
256D ALA* 5.3 0.4 - - - +
257D PRO* 3.3 22.9 - - - +
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Residues in contact with ASP 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ARG* 4.3 12.1 + - - -
254B ASP* 5.5 0.5 - - - +
229D ILE* 3.9 8.4 - - + +
248D CYS 3.7 20.2 - - - +
249D VAL* 3.7 10.6 - - - -
250D VAL* 3.0 29.1 + - - +
251D ARG* 2.9 42.3 + - - +
253D GLU* 1.3 79.7 - - - +
255D PHE* 1.3 57.2 + - - +
257D PRO* 3.4 5.9 - - - +
258D ALA* 3.0 31.5 + - - +
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Residues in contact with PHE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D VAL* 4.4 6.7 - - + +
251D ARG 3.7 2.5 + - - +
252D PHE* 3.2 20.7 + + + +
254D ASP* 1.3 76.9 - - - +
256D ALA* 1.3 70.4 + - - +
258D ALA* 3.2 5.4 + - - +
259D MSE 2.9 57.8 + - + +
267D ILE* 3.6 32.3 - - + -
274D TRP* 5.5 1.3 - + + -
283D LEU* 4.4 13.0 - - + -
286D HIS* 3.6 48.2 - + + -
287D CYS 4.9 0.4 - - - -
290D PHE* 3.6 26.0 - + - -
292D LEU* 4.0 7.2 - - + -
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU* 3.4 35.4 - - + +
252D PHE 4.3 3.5 + - - +
253D GLU 5.3 0.2 - - - +
255D PHE* 1.3 81.0 - - - +
257D PRO* 1.3 74.0 - - + +
259D MSE 3.1 6.9 + - - +
260D ARG* 3.0 28.6 + - - +
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Residues in contact with PRO 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ILE* 4.0 32.1 - - + -
230B GLU* 4.3 7.8 - - + +
257B PRO* 5.0 4.7 - - + -
261B LEU* 3.7 23.8 - - + -
229D ILE* 4.3 12.1 - - + -
253D GLU 3.3 23.6 - - - +
254D ASP* 3.4 8.7 - - - +
256D ALA* 1.3 96.5 - - + +
258D ALA* 1.3 62.2 + - - +
260D ARG* 3.4 0.7 + - - +
261D LEU* 3.0 31.6 + - - +
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ILE* 4.0 17.9 - - + +
249D VAL* 3.4 26.5 - - + -
254D ASP 3.0 20.0 + - - +
255D PHE* 3.5 4.3 - - - +
257D PRO* 1.3 77.2 - - - +
259D MSE 1.3 69.8 + - + +
261D LEU 3.5 0.3 + - - -
262D ASN 3.0 21.0 + - - -
263D ALA* 3.0 21.8 + - + -
264D VAL* 5.0 1.3 - - + -
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Residues in contact with MSE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D PHE* 2.9 44.1 + - + +
256D ALA* 3.6 8.1 - - - +
258D ALA* 1.3 86.7 - - + +
260D ARG* 1.3 67.3 + - + +
262D ASN* 2.9 26.1 + - - +
264D VAL* 3.9 22.4 - - + +
267D ILE* 4.5 1.6 - - + -
290D PHE* 3.7 48.0 - - + +
292D LEU* 3.6 31.9 - - + -
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Residues in contact with ARG 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU* 2.7 41.3 + - - -
234B GLN* 3.7 14.7 - - - +
261B LEU* 3.9 27.5 - - + +
256D ALA* 3.0 18.0 + - - +
257D PRO 4.0 1.3 - - - +
259D MSE 1.3 78.1 - - + +
261D LEU* 1.3 62.0 + - - +
262D ASN* 3.3 8.7 + - - +
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B PRO* 3.7 32.3 - - + +
260B ARG* 3.9 30.1 - - + +
261B LEU* 3.7 25.1 - - + -
229D ILE* 3.6 31.9 - - + -
230D GLU* 5.3 3.1 - - - +
233D ALA* 3.3 17.5 - - + +
257D PRO 3.0 19.5 + - - +
258D ALA 4.2 0.2 - - - +
260D ARG* 1.3 77.9 - - - +
262D ASN* 1.3 73.7 + - - +
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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