Contacts of the helix formed by residues 323 - 337 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A GLN* 6.0 5.4 - - + +
188A ALA 3.4 25.4 - - - +
189A HIS 4.3 0.7 - - - +
190A ALA* 3.3 24.0 - - + +
309A PRO 3.7 7.4 - - - +
310A HIS* 4.7 3.8 - - - +
321A GLY 3.8 4.3 - - - +
322A ILE* 1.3 85.0 - - + +
324A MET* 1.3 67.5 + - - +
325A ASN* 3.3 18.6 - - - +
326A GLN* 3.0 26.1 + - - +
327A ALA* 3.1 9.9 + - - +
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Residues in contact with MET 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 4.0 23.1 - - + +
220A VAL* 4.5 2.0 - - - -
223A HIS* 4.3 15.0 - - + -
225A LEU* 3.6 25.4 - - + -
283A VAL* 4.5 1.6 - - + -
284A GLY* 3.4 39.5 - - - +
307A VAL* 3.6 18.6 - - + +
308A GLN* 3.6 27.4 - - - +
309A PRO* 3.1 19.5 + - + +
322A ILE 3.4 1.4 + - - -
323A PRO* 1.3 70.4 - - - +
325A ASN* 1.3 61.9 + - - +
327A ALA* 3.1 9.2 + - - +
328A ILE* 3.0 35.2 + - + +
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Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLN* 4.9 10.7 - - - +
225A LEU* 3.8 31.7 - - + +
323A PRO* 3.3 19.8 - - - +
324A MET* 1.3 79.9 - - - +
326A GLN* 1.3 72.3 + - - +
328A ILE* 3.6 4.3 + - - +
329A GLU* 3.1 25.5 + - - +
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A HIS* 3.4 29.3 - - + +
190A ALA* 2.8 35.8 + - - +
195A LEU* 3.6 26.9 - - + +
322A ILE* 4.7 4.7 - - + -
323A PRO* 3.0 21.9 + - + +
325A ASN* 1.3 91.0 - - - +
327A ALA* 1.3 61.0 + - - +
329A GLU* 3.3 7.8 + - + +
330A THR* 3.0 32.6 + - - -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 5.0 0.2 - - - -
198A PHE* 3.8 22.0 - - + -
307A VAL* 4.2 21.5 - - + -
311A ALA 6.2 0.2 - - - -
312A ALA* 4.4 5.6 - - + -
322A ILE* 4.0 16.5 - - + +
323A PRO 3.1 12.1 + - - +
324A MET* 3.6 9.6 - - - +
326A GLN* 1.3 76.8 - - - +
328A ILE* 1.3 63.8 + - - +
330A THR* 3.3 5.2 + - - -
331A LEU* 3.0 27.3 + - - +
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 5.5 0.4 - - + -
225A LEU* 3.5 35.9 - - + -
228A ALA* 4.7 13.5 - - + +
229A LEU* 3.8 24.7 - - + -
232A TRP* 4.0 23.8 - - + -
283A VAL* 4.0 20.4 - - + -
307A VAL* 4.5 4.5 - - + -
324A MET* 3.0 23.9 + - + +
325A ASN* 3.7 4.9 - - - +
327A ALA* 1.3 76.1 - - - +
329A GLU* 1.3 64.8 + - - +
331A LEU* 3.0 11.3 + - - +
332A VAL* 2.9 31.2 + - + +
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ASN 3.1 12.9 + - - +
326A GLN* 3.4 13.0 - - + +
328A ILE* 1.3 80.2 - - - +
330A THR* 1.3 62.8 + - - +
332A VAL* 3.2 13.4 + - - +
333A GLU* 3.2 44.3 + - - +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 3.5 21.0 - - - +
198A PHE* 4.2 14.1 - - + -
199A ARG* 3.5 54.1 + - + +
326A GLN 3.0 14.8 + - - -
327A ALA 3.5 7.9 - - - -
329A GLU* 1.3 76.5 - - - +
331A LEU* 1.3 63.1 + - - +
333A GLU* 3.4 7.4 + - - +
334A LEU* 3.2 27.4 + - + +
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.9 23.1 - - + -
202A ALA* 4.0 20.0 - - + -
206A LEU* 4.5 12.1 - - + -
232A TRP* 3.6 26.7 - - + -
281A LEU* 4.3 16.8 - - + -
283A VAL* 5.3 1.3 - - + -
305A ILE* 4.4 13.7 - - + +
307A VAL* 3.8 26.5 - - + -
327A ALA 3.0 16.1 + - - +
328A ILE* 3.4 9.4 - - - +
330A THR* 1.3 75.1 - - - +
332A VAL* 1.3 59.8 + - - +
334A LEU* 3.4 3.9 + - + +
335A CYS* 2.9 34.1 + - - -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA 5.3 1.6 - - - +
232A TRP* 3.5 52.5 - - + +
235A GLU* 5.1 2.0 - - + +
236A VAL* 5.3 0.2 - - + -
328A ILE* 2.9 26.4 + - + +
329A GLU* 3.2 15.9 + - - +
331A LEU* 1.3 73.6 - - - +
333A GLU* 1.3 66.3 + - + +
335A CYS* 3.2 2.9 + - - +
336A LYS* 3.2 50.1 + - + +
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ARG* 3.3 34.0 + - - +
329A GLU* 3.2 38.6 + - - +
330A THR* 3.7 8.3 + - - +
332A VAL* 1.3 82.6 - - + +
334A LEU* 1.3 61.7 + - - +
336A LYS* 3.4 19.3 + - + +
337A GLN* 3.5 19.1 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ARG* 3.6 46.0 - - + +
202A ALA* 3.8 13.2 - - + -
203A GLU* 3.5 55.4 - - + +
206A LEU* 3.9 14.1 - - + -
330A THR* 3.2 19.5 + - + +
331A LEU* 3.8 5.8 - - + +
333A GLU* 1.3 73.4 - - - +
335A CYS* 1.3 61.7 + - - +
337A GLN* 3.0 11.9 + - - +
338A HIS* 2.7 33.5 + - + -
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Residues in contact with CYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.7 12.8 - - - -
212A THR* 5.1 5.4 - - - -
232A TRP* 3.7 32.5 - - - +
236A VAL* 4.0 19.6 - - + +
238A MET* 4.0 10.8 - - - -
281A LEU* 4.1 10.8 - - - -
331A LEU* 2.9 25.0 + - - +
332A VAL 3.2 5.4 + - - +
334A LEU* 1.3 75.2 - - - +
336A LYS* 1.3 63.2 + - - +
338A HIS* 3.0 27.8 + - - +
339A VAL* 4.6 1.6 - - - +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 2.7 36.9 + - - +
236A VAL* 3.7 15.9 - - + -
332A VAL* 3.2 33.9 + - + +
333A GLU* 3.6 13.3 - - + +
334A LEU 3.2 0.4 - - - -
335A CYS* 1.3 76.4 - - - +
337A GLN* 1.3 59.0 + - + +
338A HIS 3.3 0.7 + - - -
339A VAL* 3.9 16.2 - - - +
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Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ARG* 3.8 23.2 - - - +
203A GLU* 2.9 25.0 + - - +
333A GLU* 3.7 16.9 + - - +
334A LEU* 3.0 16.9 + - - +
336A LYS* 1.3 79.7 - - + +
338A HIS* 1.3 72.4 + - + +
339A VAL 4.1 1.1 + - - -
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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