Contacts of the helix formed by residues 324 - 337 (chain B) in PDB entry 2OHI
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 PRO 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ARG* 3.4 28.7 - - - +
328A ASP* 3.4 36.7 - - - +
331A MET* 4.0 9.3 - - + +
332A TYR* 3.6 35.4 - - + +
318B ILE* 5.0 4.9 - - + -
322B PRO 3.1 7.4 - - - +
323B TYR* 1.3 98.0 - - + +
325B SER* 1.3 50.0 + - - -
327B GLY* 2.7 29.5 + - - -
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Residues in contact with SER 325 (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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298A ARG* 4.3 4.7 - - - +
328A ASP* 3.6 16.7 + - - -
264B ASP* 2.7 30.8 + - - +
293B LEU* 3.5 28.3 - - - +
323B TYR* 3.0 12.6 + - - -
324B PRO* 1.3 78.7 - - - +
326B VAL* 1.3 64.5 + - - +
328B ASP* 3.1 20.1 + - - +
329B LEU* 3.6 4.2 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET* 4.1 5.8 - - - -
264B ASP* 5.4 0.7 - - + +
293B LEU* 3.6 22.4 - - + -
313B LEU* 3.9 20.2 - - + -
314B GLY 4.5 1.8 - - - +
315B ALA* 3.9 23.6 - - + -
322B PRO* 3.7 25.1 - - + -
323B TYR 3.2 9.2 + - - +
325B SER* 1.3 82.6 + - - +
327B GLY* 1.3 56.1 + - - +
329B LEU* 3.5 3.6 + - - +
330B LEU* 3.1 49.3 + - + +
362B MET* 4.1 6.7 - - + -
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Residues in contact with GLY 327 (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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327A GLY* 3.5 19.6 - - - -
331A MET* 3.6 23.9 - - - -
324B PRO 2.7 20.1 + - - -
326B VAL* 1.3 72.6 - - - +
328B ASP* 1.3 60.8 + - - -
330B LEU* 4.4 3.0 - - - +
331B MET* 3.2 25.3 + - - +
365B LEU* 5.7 0.2 - - - -
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Residues in contact with ASP 328 (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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324A PRO* 3.4 20.0 - - - +
325A SER* 3.1 20.3 + - - -
328A ASP* 3.7 18.8 - - + +
298B ARG* 2.8 50.5 + - - +
325B SER* 3.1 12.5 + - - +
327B GLY* 1.3 75.8 - - - +
329B LEU* 1.3 66.3 + - - +
332B TYR* 3.1 17.2 + - - +
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Residues in contact with LEU 329 (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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262B ILE* 3.9 37.2 - - + -
293B LEU* 4.2 15.9 - - + -
298B ARG* 4.5 17.3 - - + -
301B ILE* 3.8 23.1 - - + -
302B VAL* 4.5 5.8 - - + -
305B ILE* 4.7 0.2 - - + -
311B ILE* 6.4 0.2 - - + -
313B LEU* 4.0 19.5 - - + -
325B SER 3.6 2.8 + - - +
326B VAL* 3.5 7.4 + - - +
328B ASP* 1.3 83.0 + - - +
330B LEU* 1.3 58.8 + - - +
332B TYR* 3.0 8.6 + - + +
333B LEU* 2.8 57.8 + - + +
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Residues in contact with LEU 330 (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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313B LEU* 3.9 17.7 - - + -
326B VAL* 3.1 38.4 + - + +
327B GLY* 4.4 2.7 - - - +
328B ASP 3.4 0.2 - - - -
329B LEU* 1.3 76.5 - - + +
331B MET* 1.3 58.3 + - - +
333B LEU* 3.8 12.2 - - + +
334B ARG* 3.0 27.4 + - - +
362B MET* 4.4 8.1 - - + -
365B LEU* 3.8 39.1 - - + +
366B LEU* 3.8 45.3 - - + +
369B ALA* 4.8 4.0 - - + +
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Residues in contact with MET 331 (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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321A GLU* 4.0 19.0 - - + +
322A PRO* 3.6 44.0 - - + +
323A TYR 4.2 3.4 - - - +
324A PRO* 4.1 6.7 - - + +
326A VAL* 4.5 1.3 - - - -
327A GLY* 3.6 30.1 - - - -
330A LEU* 5.0 1.6 - - + -
361A THR* 5.0 1.1 - - + -
365A LEU* 3.8 28.9 - - + -
327B GLY 3.2 18.9 + - - +
328B ASP 3.9 3.1 - - - +
330B LEU* 1.3 73.7 - - - +
332B TYR* 1.3 68.3 + - - +
334B ARG* 3.3 16.6 + - - +
335B GLY* 3.3 7.4 + - - -
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Residues in contact with TYR 332 (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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318A ILE* 5.1 14.4 - - + -
319A TYR* 6.2 0.2 - + - -
324A PRO* 3.9 28.2 - - + +
27B GLY 5.2 4.0 + - - -
28B TYR* 5.4 1.2 - - - +
201B ASN* 2.7 44.5 + - - +
298B ARG* 3.9 30.1 - - + -
299B SER* 5.1 0.5 - - - -
302B VAL* 3.7 23.6 - - + -
328B ASP 3.1 13.3 + - - +
329B LEU* 3.0 12.7 + - + +
331B MET* 1.3 76.8 - - - +
333B LEU* 1.3 57.2 + - - +
335B GLY* 2.9 19.9 + - - -
336B LEU* 3.1 38.7 + - + +
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Residues in contact with LEU 333 (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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302B VAL* 3.8 14.1 - - + -
305B ILE* 3.8 22.4 - - + -
311B ILE* 5.1 3.1 - - + -
313B LEU* 5.9 0.4 - - + -
329B LEU* 2.8 41.4 + - + +
330B LEU* 3.9 21.1 - - + +
332B TYR* 1.3 72.6 - - - +
334B ARG* 1.3 56.9 + - - +
336B LEU* 3.8 4.7 - - - -
337B LYS* 3.1 26.7 + - - -
338B PHE* 3.6 32.8 + - + -
366B LEU* 4.6 6.3 - - + -
369B ALA* 4.0 17.9 - - + +
371B PHE* 4.0 18.4 - - + -
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Residues in contact with ARG 334 (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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321A GLU* 3.3 35.4 + - - +
361A THR* 5.8 4.4 + - - +
330B LEU 3.0 18.7 + - - +
331B MET* 3.6 10.1 - - - +
332B TYR 3.2 0.6 - - - -
333B LEU* 1.3 77.2 - - - +
335B GLY* 1.3 60.3 + - - +
337B LYS* 3.4 26.6 + - - +
365B LEU* 5.6 6.1 - - - +
368B GLU* 2.6 56.9 + - + +
369B ALA* 4.1 11.1 - - + +
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Residues in contact with GLY 335 (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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318A ILE 4.8 0.9 - - - -
319A TYR* 3.5 31.9 - - - +
321A GLU* 3.7 17.4 - - - +
205B PRO* 3.7 6.8 - - - +
331B MET 3.3 6.0 + - - -
332B TYR 2.9 9.6 + - - -
334B ARG* 1.3 79.0 - - - +
336B LEU* 1.3 61.5 + - - +
337B LYS* 3.7 13.1 - - - -
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Residues in contact with LEU 336 (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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319A TYR* 4.0 18.8 - - + -
200B ALA 3.7 11.2 - - - +
201B ASN 3.7 20.6 - - - +
204B THR* 3.3 7.3 - - + +
205B PRO* 3.2 31.4 - - + +
302B VAL* 3.7 26.5 - - + -
332B TYR* 3.1 53.2 + - + +
333B LEU* 3.4 3.3 + - - +
335B GLY* 1.3 74.3 - - - +
337B LYS* 1.3 75.2 + - - +
338B PHE* 4.0 16.8 - - + -
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Residues in contact with LYS 337 (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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319A TYR 4.5 9.4 + - - -
320A ASP* 5.2 11.6 + - - +
321A GLU* 5.0 5.1 + - - -
204B THR* 4.3 1.7 - - - +
205B PRO* 4.8 2.5 - - + -
333B LEU 3.1 13.4 + - - -
334B ARG* 3.4 26.0 + - - +
335B GLY 3.7 11.7 - - - +
336B LEU* 1.3 80.5 - - - +
338B PHE* 1.3 65.9 + - - +
339B ASN* 3.1 18.5 + - - +
340B ARG* 3.2 63.1 + - + +
368B GLU 5.9 3.2 + - - +
369B ALA 4.1 3.8 - - - +
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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