Contacts of the helix formed by residues 302 - 315 (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 LEU 302 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.2 45.8 - - + -
16D PRO 5.3 1.6 - - - +
17D LEU* 4.1 16.6 - - + -
31D GLU* 3.4 27.1 - - + +
33D ARG* 4.4 7.6 - - + -
49D GLU* 2.8 22.2 + - - +
300D GLY 4.1 1.3 - - - +
301D GLU* 1.3 77.5 - - - +
303D GLY* 1.3 68.4 + - - +
304D ILE 3.5 0.2 + - - -
305D ALA 3.5 0.2 + - - -
306D THR* 2.7 27.6 + - - -
326D MSE 5.7 1.3 - - - +
327D TYR* 3.8 7.2 - - + -
330D HIS* 4.2 20.0 - - + +
332D ASP 5.6 1.3 - - - +
333D ASP* 3.5 12.8 - - - +
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Residues in contact with GLY 303 (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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302D LEU* 1.3 71.9 - - - +
304D ILE* 1.3 62.8 + - - +
307D ALA* 3.0 23.6 + - - +
327D TYR* 3.5 16.3 - - - -
333D ASP* 2.6 25.5 + - - -
335D ILE* 3.5 19.9 - - - +
338D LEU* 3.8 8.2 - - - +
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Residues in contact with ILE 304 (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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35D VAL* 4.8 3.4 - - + -
47D TRP* 4.1 15.9 - - + +
48D GLY* 3.8 14.4 - - - +
49D GLU* 3.3 36.1 + - + +
102D VAL* 5.1 1.6 - - + -
303D GLY* 1.3 73.6 - - - +
305D ALA* 1.3 64.6 + - - +
307D ALA* 3.2 15.3 + - - +
308D ALA* 3.3 11.8 + - - +
333D ASP* 5.1 0.4 + - - -
334D ILE* 3.7 31.2 - - + -
335D ILE* 3.6 22.3 - - + +
353D LEU* 4.2 11.3 - - + +
355D VAL* 4.6 7.0 - - + -
357D VAL* 3.8 19.1 - - + -
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Residues in contact with ALA 305 (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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33D ARG* 3.8 1.6 - - - +
49D GLU* 3.0 34.6 + - - +
102D VAL* 6.0 0.2 - - - -
272D TYR* 2.7 37.7 + - + +
301D GLU* 3.4 30.1 - - + -
304D ILE* 1.3 77.3 - - - +
306D THR* 1.3 62.4 + - - +
308D ALA 3.3 0.9 + - - -
309D HIS* 3.2 14.4 + - - +
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Residues in contact with THR 306 (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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301D GLU* 3.4 20.8 + - - +
302D LEU 2.7 23.6 + - - -
303D GLY 3.8 2.7 - - - -
305D ALA* 1.3 73.1 - - - +
307D ALA* 1.3 55.4 + - - +
309D HIS* 3.1 10.1 + - + +
310D LEU* 2.7 37.8 + - + +
325D SER* 4.7 5.2 + - - +
327D TYR* 3.8 12.9 - - + +
338D LEU* 3.8 18.8 - - + -
345D LEU* 3.9 24.5 - - + -
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Residues in contact with ALA 307 (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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303D GLY 3.0 13.6 + - - +
304D ILE* 3.2 11.0 + - - +
306D THR* 1.3 76.6 - - - +
308D ALA* 1.3 61.2 + - - +
310D LEU* 3.2 14.5 + - - +
311D ALA* 3.0 21.7 + - - +
338D LEU* 4.2 3.1 - - + +
348D PRO* 4.4 9.0 - - + +
353D LEU* 4.0 22.4 - - + +
355D VAL* 3.9 25.1 - - + -
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 3.9 29.8 - - + -
271D VAL* 5.5 2.5 - - + -
272D TYR* 3.3 24.2 - - + +
277D ILE* 4.8 9.4 - - + +
304D ILE 3.3 5.2 + - - +
305D ALA 3.4 0.7 - - - +
306D THR 3.1 0.4 - - - -
307D ALA* 1.3 78.9 - - - +
309D HIS* 1.3 63.5 + - - +
311D ALA* 3.1 15.7 + - - +
312D VAL* 3.2 16.1 + - - +
353D LEU* 3.8 12.0 - - + +
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Residues in contact with HIS 309 (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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270D ASP* 3.5 20.1 + - - -
271D VAL* 3.0 49.4 - - + +
272D TYR* 3.7 15.2 - + - -
296D LEU* 3.5 27.5 - - + +
297D HIS 3.9 12.4 + - - -
298D SER* 5.8 0.2 - - - -
301D GLU* 4.1 19.0 - - + -
305D ALA 3.2 6.2 + - - +
306D THR* 3.1 13.3 + - + +
308D ALA* 1.3 79.0 - - - +
310D LEU* 1.3 62.6 + - + +
312D VAL* 3.3 6.0 + - - +
313D VAL* 3.0 29.1 + - + +
323D ILE* 5.4 8.1 - - + -
324D ASP 6.2 0.4 - - - -
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Residues in contact with LEU 310 (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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128D VAL* 3.7 36.8 - - + -
306D THR* 2.7 25.3 + - + +
307D ALA* 3.5 7.6 - - - +
308D ALA 3.1 0.2 - - - -
309D HIS* 1.3 76.5 - - + +
311D ALA* 1.3 55.6 + - - +
313D VAL* 3.9 2.3 - - - +
314D SER* 2.9 31.7 + - - -
323D ILE* 5.1 4.5 - - + -
338D LEU* 4.1 22.2 - - + -
345D LEU* 3.8 26.2 - - + +
346D ARG 3.7 11.0 - - - +
347D VAL* 4.0 8.3 - - + +
348D PRO* 3.6 30.5 - - + -
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Residues in contact with ALA 311 (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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116D VAL* 4.0 28.9 - - + -
117D THR* 3.4 28.6 + - - +
120D LEU* 4.2 4.9 - - + +
277D ILE* 5.9 0.2 - - + -
307D ALA 3.0 11.0 + - - +
308D ALA* 3.1 11.2 + - - +
310D LEU* 1.3 77.2 - - - +
312D VAL* 1.3 63.5 + - - +
314D SER 3.6 0.2 + - - -
315D SER* 3.1 24.1 + - - -
347D VAL* 4.7 2.0 - - - +
348D PRO* 5.6 0.2 - - - +
353D LEU* 5.2 2.7 - - + -
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Residues in contact with VAL 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU* 4.4 4.5 - - + -
271D VAL* 4.4 18.2 - - + -
277D ILE* 3.9 29.6 - - + +
280D THR* 3.9 21.8 - - + +
281D LYS* 4.4 8.1 - - + -
296D LEU* 5.0 4.0 - - + -
308D ALA 3.2 12.2 + - - +
309D HIS* 3.6 8.3 - - - +
311D ALA* 1.3 74.0 - - - +
313D VAL* 1.3 65.2 + - - +
315D SER* 3.2 6.9 + - - -
316D THR* 2.6 36.2 + - + +
319D LEU* 3.8 19.1 - - + -
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Residues in contact with VAL 313 (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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125D ARG* 2.8 32.5 + - - -
128D VAL* 3.6 35.9 - - + -
129D PRO* 6.3 0.2 - - + -
296D LEU* 3.5 23.6 - - + -
309D HIS 3.0 18.1 + - - +
310D LEU* 4.0 0.9 - - - +
312D VAL* 1.3 74.1 - - - +
314D SER* 1.3 62.4 + - - +
315D SER 3.1 1.0 + - - -
316D THR 3.2 6.1 + - - +
319D LEU* 3.6 36.1 - - + +
321D ARG 5.7 0.9 - - - +
323D ILE* 4.1 16.6 - - + -
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Residues in contact with SER 314 (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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117D THR* 3.7 7.8 - - - +
123D ALA* 3.4 14.9 - - - +
124D VAL* 2.8 38.5 + - - +
125D ARG* 2.7 29.8 + - - -
128D VAL* 4.7 0.6 - - - +
310D LEU 2.9 18.8 + - - -
311D ALA 3.8 4.5 - - - -
312D VAL 3.3 0.2 - - - -
313D VAL* 1.3 77.4 - - - +
315D SER* 1.3 54.3 + - - +
347D VAL* 3.5 28.7 - - - +
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Residues in contact with SER 315 (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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117D THR* 4.0 13.0 - - - -
120D LEU* 3.6 21.9 - - - +
121D GLY* 5.2 1.7 - - - -
122D GLY 3.2 24.7 - - - +
124D VAL* 4.3 4.6 - - - +
281D LYS* 3.0 23.6 + - - -
311D ALA 3.1 16.4 + - - -
312D VAL* 3.2 4.9 + - - -
313D VAL 3.1 0.4 - - - -
314D SER* 1.3 77.5 - - - +
316D THR* 1.3 58.4 + - - +
317D PRO* 3.6 9.8 - - - +
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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