Contacts of the helix formed by residues 323 - 337 (chain B) in PDB entry 1OVM
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 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B GLN* 6.0 4.7 - - + +
188B ALA 3.3 25.8 - - - +
189B HIS 4.3 0.4 - - - -
190B ALA* 3.3 24.0 - - + +
309B PRO 3.6 7.0 - - - +
310B HIS* 4.7 4.5 - - - +
321B GLY 3.8 2.9 - - - +
322B ILE* 1.3 84.9 - - + +
324B MET* 1.3 66.9 + - - +
325B ASN* 3.3 18.2 - - - +
326B GLN* 2.9 27.9 + - - +
327B ALA* 3.1 9.9 + - - +
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 4.1 23.8 - - + +
220B VAL* 4.6 2.5 - - - +
223B HIS* 4.2 16.6 - - + -
225B LEU* 3.6 24.7 - - + -
283B VAL* 4.5 2.5 - - + -
284B GLY* 3.4 39.0 - - - +
307B VAL* 3.6 17.7 - - + +
308B GLN* 3.6 22.4 - - - +
309B PRO* 2.9 24.2 + - + +
322B ILE 3.4 1.2 + - - -
323B PRO* 1.3 70.4 - - - +
325B ASN* 1.3 62.3 + - - +
327B ALA* 3.2 8.7 + - - +
328B ILE* 3.0 35.5 + - + +
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLN* 4.8 10.4 - - - +
225B LEU* 3.8 32.3 - - + +
323B PRO* 3.3 20.4 - - - +
324B MET* 1.3 78.4 - - - +
326B GLN* 1.3 76.8 + - - +
328B ILE* 3.4 4.7 + - - +
329B GLU* 3.0 27.0 + - - +
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B HIS* 3.4 30.1 - - + +
190B ALA* 2.8 38.8 + - - +
195B LEU* 3.8 27.7 - - + +
322B ILE* 4.6 2.9 - - + -
323B PRO* 2.9 17.7 + - + +
325B ASN* 1.3 91.4 - - - +
327B ALA* 1.3 61.6 + - - +
329B GLU* 3.2 8.7 + - + +
330B THR* 2.9 32.8 + - - -
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Residues in contact with ALA 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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195B LEU* 4.9 0.2 - - - -
198B PHE* 3.8 20.6 - - + -
307B VAL* 4.1 21.1 - - + -
308B GLN 6.0 0.4 - - - +
312B ALA* 4.4 5.6 - - + -
322B ILE* 3.9 17.4 - - + +
323B PRO 3.1 11.4 + - - +
324B MET* 3.2 9.6 + - - +
326B GLN* 1.3 75.6 - - - +
328B ILE* 1.3 62.5 + - - +
330B THR* 3.3 3.9 + - - -
331B LEU* 3.0 28.7 + - - +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 5.4 0.7 - - + -
225B LEU* 3.9 26.5 - - + -
228B ALA* 4.9 11.4 - - + +
229B LEU* 3.7 27.1 - - + -
232B TRP* 3.8 26.2 - - + -
283B VAL* 3.7 25.8 - - + -
307B VAL* 4.4 6.3 - - + -
324B MET* 3.0 23.0 + - + +
325B ASN* 3.7 4.5 - - - +
327B ALA* 1.3 74.8 - - - +
329B GLU* 1.3 67.1 + - - +
331B LEU* 3.2 9.3 + - - +
332B VAL* 2.9 27.2 + - + +
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Residues in contact with GLU 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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325B ASN 3.0 13.9 + - - +
326B GLN* 3.3 14.8 - - + +
328B ILE* 1.3 77.1 - - - +
330B THR* 1.3 63.4 + - - +
332B VAL* 3.2 11.4 + - - +
333B GLU* 3.2 44.2 + - - +
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Residues in contact with THR 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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195B LEU* 3.5 21.8 - - - +
198B PHE* 4.2 13.7 - - + -
199B ARG* 3.6 54.0 + - + +
326B GLN 2.9 16.2 + - - -
327B ALA 3.5 8.3 - - - -
329B GLU* 1.3 77.8 - - - +
331B LEU* 1.3 62.3 + - + +
333B GLU* 3.3 6.9 + - - +
334B LEU* 3.1 27.9 + - + +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 3.9 22.2 - - + -
202B ALA* 4.0 20.0 - - + -
206B LEU* 4.6 11.4 - - + -
232B TRP* 3.8 23.1 - - + -
281B LEU* 4.2 22.2 - - + -
283B VAL* 5.3 1.6 - - + -
305B ILE* 4.5 8.3 - - + -
307B VAL* 3.8 27.1 - - + -
327B ALA 3.0 16.4 + - - +
328B ILE* 3.2 9.4 + - - +
330B THR* 1.3 77.8 - - - +
332B VAL* 1.3 57.8 - - - +
334B LEU* 3.4 4.4 + - + +
335B CYS* 2.9 35.9 + - - -
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Residues in contact with VAL 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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228B ALA 5.2 1.6 - - - +
232B TRP* 3.5 54.1 - - + +
235B GLU* 5.0 2.2 - - - +
236B VAL* 5.1 0.9 - - + -
328B ILE* 2.9 25.9 + - + +
329B GLU* 3.2 15.7 + - - +
331B LEU* 1.3 77.2 - - - +
333B GLU* 1.3 63.6 + - - +
335B CYS* 3.3 10.0 + - - +
336B LYS* 3.3 40.9 + - + +
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 3.3 34.4 + - - +
329B GLU* 3.2 37.6 + - - +
330B THR* 3.6 7.8 - - - +
332B VAL* 1.3 80.7 - - + +
334B LEU* 1.3 61.9 + - - +
336B LYS* 3.5 21.4 + - - +
337B GLN* 3.7 19.4 + - - +
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Residues in contact with LEU 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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199B ARG* 3.5 44.6 - - + +
202B ALA* 3.6 15.0 - - + -
203B GLU* 3.4 57.0 - - + +
206B LEU* 4.0 13.0 - - + -
330B THR* 3.1 20.4 + - + +
331B LEU* 3.8 5.6 - - + +
333B GLU* 1.3 77.7 - - - +
335B CYS* 1.3 62.4 + - - +
337B GLN* 3.1 12.9 + - - +
338B HIS* 3.0 28.9 + - + +
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Residues in contact with CYS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 4.4 16.2 - - - -
212B THR* 5.2 4.3 - - - -
232B TRP* 3.8 28.9 - - - +
236B VAL* 4.0 23.6 - - + +
238B MET* 4.2 6.7 - - - -
281B LEU* 4.2 13.2 - - - -
331B LEU 2.9 24.6 + - - +
332B VAL 3.3 5.8 + - - +
334B LEU* 1.3 78.1 - - - +
336B LYS* 1.3 57.1 + - - +
338B HIS* 3.0 32.0 + - - +
339B VAL* 4.8 0.9 - - - +
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Residues in contact with LYS 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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235B GLU* 3.1 31.1 + - + -
236B VAL* 3.6 20.4 - - + -
332B VAL* 3.3 36.4 + - + +
333B GLU* 3.8 13.9 - - + +
334B LEU 3.3 0.2 - - - -
335B CYS* 1.3 75.8 - - - +
337B GLN* 1.3 60.1 + - + +
338B HIS 3.2 1.8 + - - -
339B VAL* 3.8 19.1 - - - +
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Residues in contact with GLN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 4.0 20.6 - - - +
203B GLU* 3.2 21.8 + - - +
333B GLU* 3.7 17.5 + - - +
334B LEU* 3.1 17.3 + - - +
335B CYS 3.0 1.0 - - - -
336B LYS* 1.3 80.0 - - + +
338B HIS* 1.3 72.2 + - + +
339B VAL* 3.9 2.8 + - - +
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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