Contacts of the helix formed by residues 264 - 277 (chain A) in PDB entry 4OWW
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 ILE 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ILE* 3.5 31.6 - - + -
229A ARG* 3.8 27.1 - - + +
233A VAL* 4.1 17.3 - - + -
261A VAL* 3.0 19.4 + - + +
262A ALA 4.4 0.2 - - - -
263A ARG* 1.3 76.7 - - - +
265A PRO* 1.3 58.7 - - + -
266A GLU* 3.3 20.9 - - - +
267A PHE* 2.8 19.5 + - + -
268A GLU 2.8 30.0 + - - -
80C SER* 3.8 16.8 - - - +
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Residues in contact with PRO 265 (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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263A ARG 3.4 7.8 - - - +
264A ILE* 1.3 85.2 - - + +
266A GLU* 1.3 73.5 + - - +
268A GLU* 3.2 16.9 + - + +
269A LEU* 3.0 22.3 + - - +
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Residues in contact with GLU 266 (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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230A GLN* 2.9 30.5 + - - +
233A VAL* 3.7 26.0 - - + +
234A ASP* 4.2 5.9 - - - +
237A ILE* 3.9 17.8 - - + +
241A ARG* 4.7 1.7 + - - -
264A ILE* 3.3 17.8 - - - +
265A PRO* 1.3 84.1 - - - +
267A PHE* 1.3 57.2 + - - +
269A LEU* 3.3 12.1 + - - +
270A LEU* 3.0 23.7 + - - +
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Residues in contact with PHE 267 (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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213A LEU* 3.4 33.4 - - + -
216A ILE* 4.2 8.1 - - + -
233A VAL* 3.9 28.5 - - + -
236A CYS* 4.2 8.7 - - + -
237A ILE* 3.5 26.9 - - + -
240A LEU* 4.1 6.1 - - + -
258A LEU* 3.9 16.8 - - + -
261A VAL* 3.3 47.3 - - + +
262A ALA* 4.0 4.0 - - - -
264A ILE* 2.8 21.7 + - + +
266A GLU* 1.3 70.8 - - - +
268A GLU* 1.3 58.9 + - - +
269A LEU 3.1 1.3 - - - -
270A LEU* 3.7 7.0 - - + +
271A TRP* 2.8 36.6 + + + -
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Residues in contact with GLU 268 (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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262A ALA 3.4 18.2 + - - +
263A ARG* 4.8 6.0 - - - +
264A ILE 2.8 13.5 + - - +
265A PRO* 3.2 18.3 + - + +
267A PHE* 1.3 71.6 - - - +
269A LEU* 1.3 60.7 + - - +
271A TRP* 3.4 7.3 + - - +
272A LYS* 3.3 40.5 + - + +
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Residues in contact with LEU 269 (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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241A ARG* 3.8 18.5 + - - +
265A PRO 3.0 11.9 + - - +
266A GLU* 3.4 12.6 - - - +
267A PHE 3.1 0.2 - - - -
268A GLU* 1.3 75.2 - - - +
270A LEU* 1.3 64.0 + - - +
272A LYS* 3.2 39.2 + - + +
273A ASP* 3.5 9.8 + - - +
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Residues in contact with LEU 270 (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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237A ILE* 4.1 13.5 - - + -
240A LEU* 3.7 35.9 - - + -
241A ARG* 3.6 35.8 - - + +
244A PHE* 5.5 2.2 - - + -
258A LEU* 4.4 8.5 - - + -
266A GLU 3.0 13.5 + - - +
267A PHE* 3.2 16.8 + - + +
269A LEU* 1.3 75.5 - - - +
271A TRP* 1.3 59.0 + - + +
273A ASP* 3.0 5.5 + - + +
274A ILE* 2.9 37.1 + - + +
281A LEU* 3.8 26.2 - - + -
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Residues in contact with TRP 271 (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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255A VAL* 3.9 26.7 - - + -
258A LEU* 2.9 45.8 + - + +
259A GLN* 3.7 14.8 - - + -
262A ALA* 3.7 18.5 - - + +
267A PHE* 2.8 27.5 + + + +
268A GLU* 3.6 7.6 - - - +
269A LEU 3.2 0.2 - - - -
270A LEU* 1.3 77.6 - - + +
272A LYS* 1.3 61.7 + - - +
274A ILE* 3.7 20.6 - - + +
275A ILE* 3.0 55.6 + - + +
288A ILE* 3.7 21.1 - - + -
98C LEU* 3.9 10.5 - - + -
99C PRO* 3.4 34.1 - - + -
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Residues in contact with LYS 272 (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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268A GLU* 3.6 31.7 + - + +
269A LEU* 3.2 28.0 + - + +
270A LEU 3.2 0.4 - - - -
271A TRP* 1.3 77.6 - - - +
273A ASP* 1.3 61.3 + - - +
275A ILE* 5.0 0.4 - - - -
276A HIS* 2.9 46.6 + - + +
277A ASN* 3.6 1.2 + - - +
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Residues in contact with ASP 273 (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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241A ARG* 2.8 35.8 + - - +
269A LEU* 3.5 9.6 + - - +
270A LEU* 3.0 8.8 + - - +
272A LYS* 1.3 78.8 - - - +
274A ILE* 1.3 67.8 + - - +
277A ASN* 2.8 55.0 + - - +
278A PRO* 2.9 2.0 - - - -
280A ALA* 4.6 8.0 - - - +
281A LEU* 4.2 14.8 - - + -
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Residues in contact with ILE 274 (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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244A PHE* 4.5 11.2 - - + -
258A LEU* 3.7 30.5 - - + -
270A LEU* 2.9 31.1 + - + +
271A TRP* 3.7 38.4 - - + +
273A ASP* 1.3 76.8 - - - +
275A ILE* 1.3 62.5 + - - +
278A PRO* 3.8 14.9 - - - +
281A LEU* 3.8 21.7 - - + +
285A PHE* 4.2 12.2 - - + -
287A GLY* 5.3 0.3 - - - -
288A ILE* 3.9 29.5 + - + +
291A LEU* 6.2 2.2 - - + -
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Residues in contact with ILE 275 (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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271A TRP* 3.0 46.5 + - + +
272A LYS* 4.4 1.3 - - - +
274A ILE* 1.3 80.7 - - + +
276A HIS* 1.3 88.2 + - + +
278A PRO* 4.5 4.3 - - - +
288A ILE* 5.3 5.6 - - + -
445A TYR* 3.3 38.5 + - + +
98C LEU* 4.9 1.3 - - + -
99C PRO* 3.3 33.9 - - + +
100C ARG 6.2 0.2 - - - -
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 2.9 28.9 + - + +
275A ILE* 1.3 95.9 + - + +
277A ASN* 1.3 62.1 + - + +
278A PRO* 3.6 6.2 - - - +
100C ARG 6.3 0.8 - - - -
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Residues in contact with ASN 277 (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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272A LYS 3.6 1.5 + - - +
273A ASP* 2.8 29.1 + - - +
276A HIS* 1.3 82.1 - - + +
278A PRO* 1.3 65.9 - - - +
279A GLN* 3.2 6.4 + - - +
280A ALA* 3.1 36.3 + - - +
281A LEU 4.3 0.2 + - - -
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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