Contacts of the helix formed by residues 264 - 279 (chain A) in PDB entry 6YBO
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 ASP 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLN* 4.1 19.7 + - - +
248A GLY* 5.5 0.4 - - - -
249A GLN 3.7 8.2 + - - +
262A ALA 3.5 4.1 + - - +
263A GLY* 1.3 67.6 - - - -
265A LEU* 1.3 64.2 + - - +
266A ARG* 3.4 7.3 + - - +
267A ALA* 3.0 32.7 + - + +
268A ALA* 3.1 19.9 + - - +
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Residues in contact with LEU 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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261A GLY* 3.7 25.4 - - - +
263A GLY 3.2 8.2 + - - +
264A ASP* 1.3 73.8 + - - +
266A ARG* 1.3 64.6 + - + +
268A ALA* 3.1 5.6 + - - +
269A PHE* 3.0 19.8 + - - +
309A ASN* 6.4 0.9 - - + -
313A LEU* 4.3 26.2 - - + -
383A LEU* 4.6 17.0 - - + -
384A LEU* 5.9 5.8 - - + -
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Residues in contact with ARG 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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264A ASP* 3.4 6.7 + - - +
265A LEU* 1.3 78.9 - - + +
267A ALA* 1.3 63.0 + - - +
269A PHE* 3.2 8.7 + - - +
270A TRP* 3.0 46.7 + - + +
376A ASP* 2.7 53.0 + - - -
379A ALA* 4.3 6.1 - - - +
380A MET* 3.6 39.1 - - - +
383A LEU* 3.6 26.7 - - + -
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Residues in contact with ALA 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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218A VAL* 6.2 0.2 - - + -
222A GLN* 3.9 17.5 - - - +
228A PHE* 5.7 0.7 - - + +
229A PRO* 3.6 22.7 - - + +
264A ASP* 3.0 33.7 + - - +
266A ARG* 1.3 76.1 - - - +
268A ALA* 1.3 58.1 + - - +
270A TRP* 3.4 4.2 + - - +
271A LEU* 2.9 30.2 + - - +
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Residues in contact with ALA 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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218A VAL* 6.5 0.4 - - - -
260A PHE* 3.9 20.4 - - + -
261A GLY* 4.6 10.3 - - - +
262A ALA 5.8 0.7 - - - +
264A ASP 3.1 11.9 + - - +
265A LEU* 3.1 14.2 + - - +
267A ALA* 1.3 78.3 - - - +
269A PHE* 1.3 61.4 + - - +
271A LEU* 3.3 7.6 + - - +
272A VAL* 3.0 28.8 + - - +
313A LEU* 3.7 18.6 - - + -
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Residues in contact with PHE 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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265A LEU 3.0 11.6 + - - +
266A ARG* 3.2 11.9 + - - +
268A ALA* 1.3 75.9 - - - +
270A TRP* 1.3 107.0 + + - +
272A VAL* 3.3 3.1 + - - +
273A ASP* 3.0 24.3 + - + +
313A LEU* 4.0 18.0 - - + +
316A ARG* 3.9 9.4 - - + -
317A ALA* 3.7 39.2 - - + +
320A PHE* 4.3 19.7 - + + -
379A ALA* 4.4 15.0 - - + -
383A LEU* 3.8 39.5 - - + -
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Residues in contact with TRP 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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229A PRO* 4.0 21.0 - - + +
266A ARG* 3.0 48.0 + - + +
267A ALA* 4.0 2.2 - - - +
269A PHE* 1.3 97.3 - + - +
271A LEU* 1.3 62.3 + - - +
273A ASP* 3.5 16.4 + - - +
274A LEU* 3.1 23.7 + - - +
320A PHE* 4.0 22.2 - + - -
321A ARG* 4.0 12.3 - - - -
375A LEU* 6.3 1.1 - - + -
376A ASP* 4.1 12.5 + - - -
379A ALA* 3.7 31.4 - - + -
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Residues in contact with LEU 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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218A VAL* 4.0 8.1 - - + -
228A PHE* 3.7 33.9 - - + -
229A PRO* 3.8 12.9 - - + +
232A ILE* 3.9 20.2 - - + -
244A ILE* 4.2 2.0 - - + -
246A LEU* 3.6 30.7 - - + -
260A PHE* 4.2 12.8 - - + -
267A ALA 2.9 18.1 + - - +
268A ALA* 3.5 5.2 - - - +
269A PHE 3.2 0.2 - - - -
270A TRP* 1.3 74.7 - - - +
272A VAL* 1.3 61.5 + - + +
274A LEU* 3.2 4.8 + - + +
275A LEU* 2.9 46.9 + - + +
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Residues in contact with VAL 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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260A PHE* 3.9 17.3 - - + -
268A ALA 3.0 20.9 + - - +
269A PHE 3.9 3.1 - - - +
271A LEU* 1.3 76.2 - - + +
273A ASP* 1.3 63.5 + - - +
275A LEU* 3.3 5.6 + - - +
276A GLU* 2.9 33.8 + - + +
310A TYR* 3.8 31.0 - - + -
313A LEU* 4.0 16.4 - - + +
314A LYS* 3.6 38.6 - - + +
317A ALA* 4.9 1.1 - - + -
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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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269A PHE* 3.0 18.2 + - + +
270A TRP* 3.6 20.8 - - + +
272A VAL* 1.3 78.3 - - - +
274A LEU* 1.3 59.6 + - - +
276A GLU* 4.1 2.2 - - - +
277A SER* 2.8 39.4 + - - -
317A ALA* 3.8 22.7 - - + +
320A PHE* 4.7 2.5 - - - -
321A ARG* 2.7 56.6 + - - +
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Residues in contact with LEU 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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229A PRO* 3.4 33.0 - - + +
232A ILE* 3.8 15.3 - - + -
233A ALA* 3.7 25.4 - - + +
236A LEU* 4.0 16.8 - - + -
270A TRP 3.1 17.7 + - - +
271A LEU* 3.2 5.4 + - + +
273A ASP* 1.3 77.2 - - - +
275A LEU* 1.3 66.4 + - - +
277A SER* 4.5 4.7 - - - -
278A ALA* 2.9 33.0 + - + +
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Residues in contact with LEU 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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232A ILE* 4.1 15.0 - - + -
236A LEU* 5.1 2.2 - - + -
241A LEU* 3.9 28.3 - - + -
244A ILE* 4.2 17.0 - - + -
246A LEU* 4.7 4.3 - - + -
271A LEU* 2.9 38.4 + - + +
272A VAL* 3.9 3.1 - - - +
274A LEU* 1.3 76.0 - - - +
276A GLU* 1.3 62.0 + - - +
278A ALA* 3.9 1.7 - - - -
279A GLY 3.2 2.9 + - - -
280A TYR* 3.1 54.9 + - + +
284A ARG* 4.5 2.6 + - + +
310A TYR* 4.0 30.5 - - + +
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Residues in contact with GLU 276 (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 VAL* 2.9 33.2 + - + +
273A ASP* 4.2 2.9 - - - +
275A LEU* 1.3 75.0 - - - +
277A SER* 1.3 64.8 - - - +
279A GLY* 3.3 11.1 + - - -
284A ARG* 3.1 19.0 + - - +
310A TYR* 2.6 30.2 + - - +
314A LYS* 3.8 34.8 + - + +
317A ALA* 6.2 1.1 - - + -
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Residues in contact with SER 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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273A ASP* 2.8 36.6 + - - -
274A LEU* 3.9 6.5 - - - -
276A GLU* 1.3 77.0 - - - +
278A ALA* 1.3 60.7 + - - +
279A GLY* 3.4 1.0 + - - -
321A ARG* 4.6 11.3 + - - +
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Residues in contact with ALA 278 (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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236A LEU* 3.8 33.4 - - + +
274A LEU* 2.9 23.1 + - + +
275A LEU* 4.1 2.9 - - - +
277A SER* 1.3 76.5 - - - +
279A GLY* 1.3 61.6 + - - +
280A TYR 3.6 1.5 + - - +
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Residues in contact with GLY 279 (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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275A LEU 3.2 5.3 + - - -
276A GLU* 3.3 7.7 + - - -
277A SER 3.2 5.2 + - - -
278A ALA* 1.3 78.9 - - - +
280A TYR* 1.3 68.4 + - - +
281A SER* 3.1 9.9 + - - -
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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