Contacts of the helix formed by residues 323 - 338 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C GLN* 6.0 4.3 - - + +
188C ALA 3.4 26.5 - - - +
189C HIS 4.3 0.7 - - - +
190C ALA* 3.3 23.3 - - + +
309C PRO 3.7 7.0 - - - +
310C HIS* 4.8 3.8 - - - +
321C GLY 3.7 4.5 - - - +
322C ILE* 1.3 85.3 - - + +
324C MET* 1.3 67.8 + - - +
325C ASN* 3.3 18.6 - - - +
326C GLN* 2.9 26.8 + - - +
327C ALA* 3.1 9.5 + - - +
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Residues in contact with MET 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C LEU* 4.1 23.3 - - + +
220C VAL* 4.7 2.0 - - - +
223C HIS* 4.4 13.2 - - + -
225C LEU* 3.7 23.8 - - + -
283C VAL* 4.6 2.5 - - + -
284C GLY* 3.4 38.4 - - - +
307C VAL* 3.6 18.6 - - + +
308C GLN* 3.6 26.2 - - - +
309C PRO* 3.0 22.4 + - + +
322C ILE 3.5 0.6 + - - -
323C PRO* 1.3 70.6 - - - +
325C ASN* 1.3 62.7 + - - +
327C ALA* 3.2 7.5 + - - +
328C ILE* 3.0 36.0 + - + +
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Residues in contact with ASN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLN* 4.8 11.8 - - - +
225C LEU* 3.8 32.7 - - + +
323C PRO* 3.3 19.2 - - - +
324C MET* 1.3 79.4 - - - +
326C GLN* 1.3 70.8 + - - +
328C ILE* 3.6 4.9 + - - +
329C GLU* 3.1 25.6 + - - +
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C HIS* 3.3 29.8 - - + +
190C ALA* 2.8 35.2 + - - +
195C LEU* 3.7 30.4 - - + +
323C PRO* 2.9 21.6 + - + +
325C ASN* 1.3 91.9 - - - +
327C ALA* 1.3 61.3 + - - +
329C GLU* 3.3 8.4 + - + +
330C THR* 3.0 32.2 + - - -
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.9 23.2 - - + -
307C VAL* 4.2 21.5 - - + -
312C ALA* 4.4 4.5 - - + -
322C ILE* 4.0 14.5 - - + +
323C PRO 3.1 11.3 + - - +
324C MET* 3.2 10.1 + - - +
326C GLN* 1.3 74.4 - - - +
328C ILE* 1.3 66.2 + - - +
330C THR* 3.3 4.7 + - - -
331C LEU* 3.0 28.5 + - - +
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Residues in contact with ILE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C VAL* 5.5 0.7 - - + -
225C LEU* 3.7 29.2 - - + -
228C ALA* 4.7 13.2 - - + +
229C LEU* 3.9 17.9 - - + -
232C TRP* 4.1 23.1 - - + -
283C VAL* 3.9 30.5 - - + -
307C VAL* 4.4 7.0 - - + -
324C MET* 3.0 23.8 + - + +
325C ASN* 3.7 6.1 - - - +
327C ALA* 1.3 77.2 - - - +
329C GLU* 1.3 57.2 + - - +
331C LEU* 3.2 10.0 + - - +
332C VAL* 2.9 38.3 + - + +
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Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C ASN 3.1 16.1 + - - +
326C GLN* 3.5 10.3 - - + +
327C ALA 3.2 0.2 - - - -
328C ILE* 1.3 82.5 - - - +
330C THR* 1.3 60.4 + - - +
332C VAL* 3.4 12.6 + - - +
333C GLU* 3.2 42.7 + - - +
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Residues in contact with THR 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 3.7 18.9 - - - +
198C PHE* 4.3 14.1 - - + -
199C ARG* 3.5 50.9 + - + +
326C GLN 3.0 14.5 + - - -
327C ALA 3.5 8.7 - - - -
329C GLU* 1.3 75.9 - - - +
331C LEU* 1.3 63.1 + - - +
333C GLU* 3.3 11.3 + - - +
334C LEU* 3.1 27.7 + - + +
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Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.8 23.6 - - + -
202C ALA* 3.9 20.9 - - + -
206C LEU* 4.7 7.9 - - + -
232C TRP* 3.7 23.6 - - + -
281C LEU* 4.3 15.0 - - + -
283C VAL* 5.4 1.1 - - + -
305C ILE* 4.2 14.1 - - + -
307C VAL* 3.7 27.8 - - + -
327C ALA 3.0 17.3 + - - +
328C ILE* 3.5 9.2 - - - +
330C THR* 1.3 77.9 - - - +
332C VAL* 1.3 55.5 + - - +
334C LEU* 3.4 7.3 + - + +
335C CYS* 3.0 36.2 + - - -
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ALA 5.2 1.8 - - - +
232C TRP* 3.5 52.0 - - + +
235C GLU* 5.1 1.3 - - - +
236C VAL* 4.7 0.4 - - + +
328C ILE* 2.9 27.1 + - + +
329C GLU* 3.6 16.4 - - - +
330C THR 3.2 0.2 - - - -
331C LEU* 1.3 77.9 - - - +
333C GLU* 1.3 62.5 + - + +
335C CYS* 3.3 2.9 + - - +
336C LYS* 3.0 48.1 + - + +
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ARG* 3.3 36.4 + - - +
329C GLU* 3.2 39.4 + - - +
330C THR* 3.3 7.3 + - - +
332C VAL* 1.3 79.4 - - + +
334C LEU* 1.3 61.0 + - - +
336C LYS* 3.2 19.6 + - + +
337C GLN* 3.3 22.5 + - - +
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Residues in contact with LEU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ARG* 3.6 48.0 - - + +
202C ALA* 3.7 14.8 - - + -
203C GLU* 3.7 44.2 - - + +
206C LEU* 4.0 14.7 - - + +
330C THR* 3.1 27.9 + - + +
331C LEU* 3.8 5.8 - - + +
333C GLU* 1.3 75.8 - - - +
335C CYS* 1.3 62.7 + - - +
337C GLN* 3.2 10.0 + - - +
338C HIS* 2.8 31.7 + - + +
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Residues in contact with CYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.3 19.7 - - - -
212C THR* 5.3 4.5 - - - -
232C TRP* 3.9 30.7 - - - +
236C VAL* 4.0 19.1 - - + +
238C MET* 4.3 9.4 - - - -
281C LEU* 4.3 7.6 - - - -
331C LEU* 3.0 23.8 + - - +
332C VAL 3.6 5.2 - - - +
334C LEU* 1.3 73.4 - - - +
336C LYS* 1.3 61.1 + - - +
337C GLN 3.0 4.5 - - - -
338C HIS* 3.0 26.3 + - - +
339C VAL* 3.8 5.0 + - - +
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Residues in contact with LYS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LYS* 6.0 0.6 - - - +
235C GLU* 2.6 37.7 + - + +
236C VAL* 3.7 16.4 - - + -
332C VAL* 3.0 36.8 + - + +
333C GLU* 3.2 12.1 + - + +
335C CYS* 1.3 74.6 - - - +
337C GLN* 1.3 59.6 + - + +
338C HIS 3.4 0.2 - - - -
339C VAL* 4.0 15.5 - - - +
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Residues in contact with GLN 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ARG* 3.7 23.9 + - - +
203C GLU* 3.3 22.5 - - - +
333C GLU* 3.3 19.7 + - - +
334C LEU* 3.2 13.3 + - - +
335C CYS 3.0 0.8 - - - -
336C LYS* 1.3 82.2 - - + +
338C HIS* 1.3 73.9 + - + +
339C VAL* 3.8 4.3 + - - +
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Residues in contact with HIS 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLU* 3.9 29.8 + - + +
206C LEU* 4.4 18.5 - - + +
207C ALA* 3.9 30.9 - - + +
334C LEU* 2.8 26.4 + - + +
335C CYS* 3.0 14.4 + - - +
337C GLN* 1.3 98.4 + - + +
339C VAL* 1.3 63.2 + - - +
340C HIS* 3.6 20.4 + - + +
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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