Contacts of the helix formed by residues 315 - 328 (chain D) in PDB entry 2OZL
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 GLN 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D HIS* 5.0 9.3 + - - -
310D ASP* 2.8 39.9 + - + +
311D ASN* 5.7 0.9 - - - +
313D ILE* 3.1 26.4 + - - +
314D PRO* 1.3 76.3 + - - +
316D VAL* 1.3 69.8 + - - +
317D LYS* 3.1 30.7 - - + +
318D ASP* 2.8 30.8 + - - +
319D ILE* 3.1 15.7 + - - +
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Residues in contact with VAL 316 (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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218D HIS* 4.0 28.6 - - + +
221D GLU* 3.4 28.7 - - + +
222D ALA* 3.9 26.2 - - + +
225D VAL* 5.1 4.5 - - + -
315D GLN* 1.3 74.8 + - - +
317D LYS* 1.3 58.7 + - - +
319D ILE* 3.0 12.6 + - - +
320D ILE* 2.9 38.7 + - + +
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Residues in contact with LYS 317 (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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311D ASN* 5.2 10.5 + - - -
315D GLN* 3.9 26.6 - - + +
316D VAL* 1.3 79.5 - - - +
318D ASP* 1.3 70.0 + - - +
320D ILE* 3.9 9.9 - - - +
321D PHE* 3.0 28.9 + - - +
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Residues in contact with ASP 318 (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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351A ALA* 3.5 28.5 - - + +
352A ASN* 3.6 17.3 + - - +
355A ILE* 3.4 19.8 - - - +
295D VAL* 4.1 10.2 - - + +
311D ASN* 6.2 0.5 - - - -
313D ILE 4.1 1.0 - - - +
314D PRO* 3.9 0.2 - - - +
315D GLN* 2.8 42.6 + - - +
317D LYS* 1.3 86.1 - - - +
319D ILE* 1.3 64.8 + - - +
321D PHE* 4.3 1.1 - - - -
322D ALA* 3.1 21.8 + - - +
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Residues in contact with ILE 319 (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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209D VAL* 4.8 2.7 - - + -
218D HIS* 3.8 39.5 - - + +
219D CYS* 4.1 8.1 - - - +
222D ALA* 3.8 17.7 - - + -
260D VAL* 5.2 1.1 - - + +
262D VAL* 3.8 42.0 - - + -
295D VAL* 4.3 15.0 - - + -
314D PRO* 5.0 2.7 - - + -
315D GLN 3.5 13.0 - - - +
316D VAL* 3.0 7.6 + - - +
318D ASP* 1.3 77.7 - - - +
320D ILE* 1.3 61.8 + - - +
322D ALA* 3.4 3.1 + - - +
323D ILE* 3.0 40.9 + - + +
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Residues in contact with ILE 320 (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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222D ALA* 3.9 18.6 - - + +
225D VAL* 3.8 33.2 - - + -
226D LEU* 4.2 12.3 - - + -
229D GLU* 5.9 0.7 - - - +
316D VAL* 2.9 35.4 + - + +
317D LYS* 3.9 8.5 - - - +
319D ILE* 1.3 77.5 - - - +
321D PHE* 1.3 57.1 + - - +
323D ILE* 3.3 8.0 + - - +
324D LYS* 2.9 54.0 + - + +
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Residues in contact with PHE 321 (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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352A ASN* 3.8 17.0 - - - +
354A TRP* 3.7 31.6 - + + -
355A ILE* 6.4 0.2 - - + -
317D LYS 3.0 20.7 + - - +
318D ASP* 3.7 5.8 - - - +
320D ILE* 1.3 78.1 - - - +
322D ALA* 1.3 57.9 + - - +
324D LYS* 3.3 7.6 + - - +
325D LYS* 3.0 57.1 + - + +
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Residues in contact with ALA 322 (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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352A ASN* 4.7 3.6 - - + -
354A TRP* 3.9 24.9 - - + -
260D VAL* 4.5 4.5 - - + -
293D VAL* 4.2 11.6 - - + +
294D ARG 5.7 0.2 - - - +
295D VAL* 3.7 22.4 - - + -
318D ASP 3.1 15.3 + - - +
319D ILE 3.8 2.2 - - - +
321D PHE* 1.3 79.0 - - - +
323D ILE* 1.3 61.7 + - - +
325D LYS* 3.3 2.8 + - - +
326D THR* 2.8 29.3 + - - -
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Residues in contact with ILE 323 (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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207D ILE* 4.1 15.3 - - + -
209D VAL* 4.0 20.4 - - + -
222D ALA* 4.9 2.9 - - + -
226D LEU* 3.5 36.6 - - + -
231D VAL* 4.8 0.2 - - + -
233D CYS* 4.1 4.7 - - - -
260D VAL* 4.3 18.4 - - + -
319D ILE* 3.0 39.9 + - + +
320D ILE* 3.3 4.9 + - - +
322D ALA* 1.3 76.4 - - - +
324D LYS* 1.3 58.0 + - - +
326D THR* 3.3 5.7 + - - -
327D LEU* 3.0 47.2 + - + +
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Residues in contact with LYS 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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226D LEU* 4.0 10.3 - - + -
229D GLU* 3.2 35.1 + - - -
320D ILE* 2.9 39.9 + - + +
321D PHE* 3.8 6.3 - - - +
323D ILE* 1.3 73.7 - - + +
325D LYS* 1.3 60.9 + - - +
328D ASN* 2.8 22.5 + - - -
329D ILE* 2.9 56.0 + - + +
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Residues in contact with LYS 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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354A TRP* 3.6 51.3 - - + +
321D PHE* 3.0 47.1 + - + +
322D ALA 3.5 9.2 - - - +
323D ILE 3.2 0.2 - - - -
324D LYS* 1.3 78.1 - - - +
326D THR* 1.3 61.4 + - - +
328D ASN* 3.2 14.7 + - - +
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Residues in contact with THR 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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207D ILE* 4.2 10.8 - - + -
258D HIS* 3.5 33.2 + - + -
259D LEU 4.5 7.6 - - - +
260D VAL* 3.6 2.4 - - - +
290D ALA* 3.4 28.3 - - + +
291D PRO 4.1 12.8 - - - +
293D VAL* 3.3 23.3 - - - +
322D ALA 2.8 21.3 + - - -
323D ILE 3.6 4.3 - - - -
324D LYS 3.3 0.2 - - - -
325D LYS* 1.3 77.6 - - - +
327D LEU* 1.3 59.3 + - - +
328D ASN* 3.6 1.4 + - - +
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Residues in contact with LEU 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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206D HIS* 3.6 26.0 - - + +
207D ILE* 4.3 7.9 - - + -
231D VAL* 3.8 30.1 - - + -
258D HIS* 3.6 34.5 + - + +
323D ILE* 3.0 29.6 + - + +
326D THR* 1.3 74.7 - - - +
328D ASN* 1.3 70.9 + - - +
329D ILE* 3.6 30.3 - - + +
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Residues in contact with ASN 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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324D LYS 2.8 10.7 + - - -
325D LYS* 3.2 12.1 + - - +
326D THR 3.2 2.0 - - - +
327D LEU* 1.3 83.0 - - - +
329D ILE* 1.3 60.7 + - - +
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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