Contacts of the helix formed by residues 261 - 272 (chain A) in PDB entry 1YA8
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 VAL 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A SER* 3.5 35.9 - - - +
181A GLY* 4.7 10.5 - - - +
257A LYS* 4.4 20.6 - - + +
258A LYS 5.6 0.7 - - - +
259A GLY 3.6 10.0 + - - +
260A ASP* 1.3 73.5 + - - +
262A LYS* 1.3 65.7 + - - +
263A PRO* 3.2 3.1 - - - -
264A LEU* 3.0 24.6 + - + +
265A ALA* 3.0 15.2 + - - +
319A LEU* 6.2 1.8 - - + -
322A VAL* 4.3 24.2 - - + -
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Residues in contact with LYS 262 (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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180A THR* 3.4 25.4 + - - +
182A ASP* 5.0 1.6 + - - -
260A ASP* 3.3 18.2 + - - +
261A VAL* 1.3 77.0 - - - +
263A PRO* 1.3 71.6 - - + +
265A ALA* 3.1 6.3 + - + +
266A GLU* 3.0 40.5 + - - +
279A SER* 2.9 21.9 + - - +
282A MET* 3.8 21.1 - - + -
1382C SIA 2.9 48.6 + - - +
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Residues in contact with PRO 263 (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 ASP* 2.9 39.9 - - + +
261A VAL 3.4 3.4 - - - -
262A LYS* 1.3 84.0 - - + +
264A LEU* 1.3 56.2 + - - +
266A GLU* 3.4 11.4 + - + +
267A GLN* 3.0 39.5 + - - +
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Residues in contact with LEU 264 (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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179A SER 6.3 0.4 - - - +
257A LYS* 5.2 3.8 - - + -
260A ASP 5.2 0.6 + - - +
261A VAL* 3.0 23.0 + - + +
263A PRO* 1.3 75.7 - - - +
265A ALA* 1.3 68.5 + - - +
267A GLN* 3.2 12.2 + - - +
268A ILE* 2.9 58.4 + - + +
301A MET* 4.4 2.7 - - + -
303A PHE* 5.2 0.7 - - + -
316A GLN* 3.7 27.8 - - - +
317A PRO* 3.7 26.0 - - + -
318A LEU 4.4 1.1 - - - +
319A LEU* 4.0 28.7 - - + +
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Residues in contact with ALA 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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178A PHE* 3.9 22.1 - - + -
179A SER 3.3 25.3 + - - +
180A THR* 4.1 11.0 - - + -
261A VAL 3.0 7.0 + - - +
262A LYS* 3.2 12.1 - - - +
264A LEU* 1.3 78.7 - - - +
266A GLU* 1.3 51.1 + - - +
268A ILE* 3.1 8.9 + - - +
269A ALA* 2.8 32.4 + - - +
282A MET* 4.2 10.1 - - + -
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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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262A LYS* 3.0 41.8 + - - +
263A PRO* 3.6 10.6 - - + +
265A ALA* 1.3 72.5 - - - +
267A GLN* 1.3 66.5 - - - +
268A ILE 3.0 1.8 - - - -
269A ALA* 3.0 1.2 + - - -
270A ILE* 2.8 35.1 + - + +
276A THR* 3.9 20.4 - - + -
282A MET* 3.5 27.5 - - + +
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Residues in contact with GLN 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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263A PRO* 3.0 26.9 + - - +
264A LEU* 3.2 17.9 + - + +
266A GLU* 1.3 75.3 - - - +
268A ILE* 1.3 59.7 + - - +
270A ILE* 4.0 7.3 - - - +
271A THR* 2.9 28.5 + - - -
301A MET* 4.5 6.2 - - + +
316A GLN* 3.2 26.3 + - - +
317A PRO* 4.3 10.9 - - - +
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Residues in contact with ILE 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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174A ILE* 4.1 24.5 - - + -
178A PHE* 4.4 24.5 - - + -
264A LEU* 2.9 38.2 + - + +
265A ALA* 3.3 7.2 - - - +
266A GLU 3.0 0.2 - - - -
267A GLN* 1.3 76.0 - - - +
269A ALA* 1.3 66.2 + - - +
271A THR* 3.3 3.6 + - - -
272A ALA* 3.1 21.1 + - - +
286A LEU* 4.8 8.1 - - + -
297A THR* 4.2 6.2 - - + +
301A MET* 3.5 25.6 - - + -
303A PHE* 4.6 5.2 - - + -
319A LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 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 ALA 2.8 16.1 + - - +
266A GLU 3.0 6.5 + - - +
268A ILE* 1.3 73.7 - - - +
270A ILE* 1.3 63.1 + - - +
272A ALA* 3.2 3.6 + - - -
273A GLY 3.2 4.7 + - - -
274A CYS* 2.9 32.5 + - + +
275A LYS 4.0 4.5 - - - +
276A THR* 3.8 20.0 - - + -
282A MET* 3.8 21.1 - - + -
286A LEU* 4.6 14.3 - - + +
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Residues in contact with ILE 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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266A GLU* 2.8 25.9 + - + +
267A GLN* 4.0 6.1 - - - +
269A ALA* 1.3 76.1 - - - +
271A THR* 1.3 57.8 + - - +
273A GLY* 2.8 21.3 + - - -
274A CYS 4.1 10.1 - - - +
276A THR* 4.0 20.2 - - + +
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Residues in contact with THR 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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267A GLN 2.9 17.7 + - - -
268A ILE 3.3 4.9 + - - -
270A ILE* 1.3 79.4 - - - +
272A ALA* 1.3 60.3 + - - +
273A GLY* 3.1 1.1 + - - -
297A THR* 3.7 19.2 + - + -
300A LYS* 4.1 43.2 + - + +
301A MET* 3.4 23.1 - - - -
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Residues in contact with ALA 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 ILE* 3.1 12.8 + - + +
269A ALA 3.7 2.7 - - - +
270A ILE 3.1 0.4 - - - -
271A THR* 1.3 76.0 - - - +
273A GLY* 1.3 57.9 + - - +
274A CYS* 4.8 0.2 - - - -
286A LEU* 3.6 31.0 - - + -
289A LYS* 3.0 28.4 + - + +
293A GLU* 5.3 2.6 - - + +
294A LEU* 4.7 4.3 - - + -
297A THR* 3.4 26.0 - - + +
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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