Contacts of the helix formed by residues 323 - 337 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187D GLN* 6.0 5.4 - - + +
188D ALA 3.4 25.4 - - - +
189D HIS 4.3 0.2 - - - -
190D ALA* 3.3 25.1 - - + +
309D PRO 3.7 6.5 - - - +
310D HIS* 4.8 4.7 - - - +
321D GLY 3.8 2.7 - - - +
322D ILE* 1.3 86.0 - - + +
324D MET* 1.3 67.4 + - - +
325D ASN* 3.3 19.5 - - - +
326D GLN* 3.0 25.1 + - - +
327D ALA* 3.0 10.4 + - - +
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Residues in contact with MET 324 (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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219D LEU* 4.1 23.8 - - + +
220D VAL* 4.5 2.5 - - - -
223D HIS* 4.4 15.7 - - + -
225D LEU* 3.6 23.8 - - + -
283D VAL* 4.6 2.0 - - + -
284D GLY* 3.4 37.9 - - - +
307D VAL* 3.7 17.7 - - + +
308D GLN* 3.7 20.0 - - - +
309D PRO* 3.0 24.8 + - + +
322D ILE 3.4 0.8 + - - -
323D PRO* 1.3 70.2 - - - +
325D ASN* 1.3 61.3 + - - +
327D ALA* 3.1 8.2 + - - +
328D ILE* 3.0 35.5 + - + +
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Residues in contact with ASN 325 (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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187D GLN* 4.9 10.4 - - - +
225D LEU* 3.7 34.9 - - + +
323D PRO* 3.3 19.6 - - - +
324D MET* 1.3 80.2 - - - +
326D GLN* 1.3 71.8 + - - +
328D ILE* 3.6 3.5 + - - +
329D GLU* 3.1 26.7 + - - +
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Residues in contact with GLN 326 (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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189D HIS* 3.3 29.2 - - + +
190D ALA* 2.8 35.1 + - - +
195D LEU* 3.7 27.8 - - + +
322D ILE* 4.6 4.3 - - + -
323D PRO* 3.0 21.7 + - + +
325D ASN* 1.3 91.0 - - - +
327D ALA* 1.3 60.9 + - - +
329D GLU* 3.3 8.6 + - + +
330D THR* 3.0 31.6 + - - -
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Residues in contact with ALA 327 (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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195D LEU* 4.9 0.2 - - - -
198D PHE* 3.8 23.6 - - + -
307D VAL* 4.2 21.3 - - + -
308D GLN 6.0 0.2 - - - +
312D ALA* 4.3 4.9 - - + -
322D ILE* 3.9 14.5 - - + +
323D PRO 3.0 10.6 + - - +
324D MET* 3.1 9.4 + - - +
326D GLN* 1.3 73.3 - - - +
328D ILE* 1.3 65.1 + - - +
330D THR* 3.3 4.7 + - - -
331D LEU* 3.0 28.8 + - - +
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Residues in contact with ILE 328 (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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220D VAL* 5.4 0.4 - - + -
225D LEU* 3.7 32.3 - - + -
228D ALA* 4.8 12.3 - - + +
229D LEU* 3.8 17.9 - - + -
232D TRP* 3.9 25.8 - - + -
283D VAL* 3.7 31.9 - - + -
307D VAL* 4.3 6.5 - - + -
324D MET* 3.0 20.6 + - + +
325D ASN* 3.8 4.9 - - - +
327D ALA* 1.3 76.0 - - - +
329D GLU* 1.3 63.7 + - - +
331D LEU* 3.2 9.5 + - - +
332D VAL* 3.0 33.1 + - + +
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Residues in contact with GLU 329 (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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325D ASN 3.1 15.7 + - - +
326D GLN* 3.4 13.2 - - + +
327D ALA 3.3 0.2 - - - -
328D ILE* 1.3 77.7 - - - +
330D THR* 1.3 62.8 + - - +
332D VAL* 3.3 11.5 + - - +
333D GLU* 3.2 42.9 + - - +
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Residues in contact with THR 330 (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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195D LEU* 3.5 20.8 - - + +
198D PHE* 4.3 13.2 - - + -
199D ARG* 3.6 55.5 + - + +
326D GLN 3.0 15.1 + - - -
327D ALA 3.5 8.7 - - - -
329D GLU* 1.3 77.2 - - - +
331D LEU* 1.3 63.5 + - + +
333D GLU* 3.3 7.5 + - - +
334D LEU* 3.1 27.3 + - + +
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Residues in contact with LEU 331 (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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198D PHE* 4.0 15.3 - - + -
202D ALA* 4.0 27.8 - - + -
206D LEU* 4.7 8.3 - - + -
232D TRP* 3.7 22.9 - - + -
281D LEU* 4.3 17.5 - - + -
283D VAL* 5.3 1.1 - - + -
305D ILE* 4.2 14.1 - - + -
307D VAL* 3.8 27.1 - - + -
327D ALA 3.0 16.0 + - - +
328D ILE* 3.2 10.3 + - - +
330D THR* 1.3 78.1 - - + +
332D VAL* 1.3 57.3 + - - +
334D LEU* 3.5 6.5 + - + +
335D CYS* 2.9 36.5 + - - -
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Residues in contact with VAL 332 (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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228D ALA 5.3 1.6 - - - +
232D TRP* 3.5 54.1 - - + +
235D GLU* 5.0 2.5 - - - +
236D VAL* 4.7 0.8 - - + +
328D ILE* 3.0 20.6 + - + +
329D GLU* 3.6 15.3 - - - +
330D THR 3.2 0.4 - - - -
331D LEU* 1.3 74.3 - - - +
333D GLU* 1.3 64.7 + - + +
335D CYS* 3.3 2.4 + - - +
336D LYS* 3.2 49.5 + - + +
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Residues in contact with GLU 333 (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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199D ARG* 3.2 36.0 + - - +
329D GLU* 3.2 39.2 + - - +
330D THR* 3.6 7.5 - - - +
331D LEU 3.3 0.2 - - - -
332D VAL* 1.3 80.9 - - + +
334D LEU* 1.3 61.9 + - - +
336D LYS* 3.3 20.9 + - - +
337D GLN* 3.4 12.9 + - - +
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Residues in contact with LEU 334 (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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199D ARG* 3.6 43.7 - - + +
202D ALA* 3.7 14.4 - - + -
203D GLU* 3.6 56.3 - - + +
206D LEU* 4.1 12.2 - - + +
330D THR* 3.1 22.0 + - + +
331D LEU* 3.9 6.5 - - + +
333D GLU* 1.3 77.3 - - - +
335D CYS* 1.3 58.1 + - - +
337D GLN* 2.9 29.5 + - - +
338D HIS* 3.2 15.4 + - - +
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Residues in contact with CYS 335 (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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206D LEU* 4.1 15.7 - - - -
212D THR* 5.0 6.1 - - - -
232D TRP* 3.7 31.6 - - - +
236D VAL* 4.0 19.6 - - + +
238D MET* 4.2 7.0 - - - -
281D LEU* 4.0 14.1 - - - -
331D LEU 2.9 24.4 + - - +
332D VAL 3.7 4.7 - - - +
333D GLU 3.3 0.2 - - - -
334D LEU* 1.3 76.7 - - - +
336D LYS* 1.3 61.2 + - - +
337D GLN 3.4 0.2 + - - -
338D HIS* 3.5 20.0 + - - +
339D VAL* 3.9 5.9 + - - +
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Residues in contact with LYS 336 (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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235D GLU* 2.8 36.4 + - - +
236D VAL* 3.6 15.5 - - + -
332D VAL* 3.2 33.7 + - - +
333D GLU* 3.6 12.9 - - - +
334D LEU 3.2 0.4 - - - -
335D CYS* 1.3 77.2 - - - +
337D GLN* 1.3 60.3 + - - +
338D HIS 3.3 0.2 - - - -
339D VAL* 3.4 21.8 - - - +
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Residues in contact with GLN 337 (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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199D ARG* 4.9 7.3 - - - +
203D GLU* 2.5 29.8 + - - +
333D GLU 3.4 9.2 + - - +
334D LEU* 2.9 22.1 + - - +
336D LYS* 1.3 80.6 - - - +
338D HIS* 1.3 80.8 + - - +
339D VAL* 3.9 0.9 - - - -
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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