Contacts of the helix formed by residues 261 - 272 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C SER* 3.6 19.6 - - - +
181C GLY* 3.5 34.1 - - - +
257C LYS* 3.9 22.7 - - + +
258C LYS 4.7 1.1 - - - +
259C GLY 3.4 7.8 + - - +
260C ASP* 1.3 73.1 + - - +
262C LYS* 1.3 69.2 + - - +
263C PRO* 3.0 5.3 - - - -
264C LEU* 3.0 21.2 + - + +
265C ALA* 3.3 8.8 + - - +
322C VAL* 3.8 27.1 - - + -
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Residues in contact with LYS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282B SIA 2.9 44.3 + - - +
180C THR* 3.7 19.6 + - - +
182C ASP* 4.6 2.4 + - - -
260C ASP* 3.3 23.9 + - - +
261C VAL* 1.3 81.5 - - - +
263C PRO* 1.3 64.8 - - + +
265C ALA* 3.1 8.2 - - - +
266C GLU* 3.0 38.2 + - - +
276C THR 5.9 1.1 - - - -
278C THR 5.3 0.2 - - - -
279C SER* 3.3 24.8 + - - +
282C MET* 3.6 23.3 - - + -
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Residues in contact with PRO 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASP* 3.2 27.6 - - + +
261C VAL 3.0 4.2 - - - -
262C LYS* 1.3 86.8 - - + +
264C LEU* 1.3 63.1 + - - +
265C ALA 2.9 4.4 + - - -
266C GLU* 2.9 14.9 + - + +
267C GLN* 2.9 24.7 + - - +
316C GLN* 5.4 3.4 - - - +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LYS* 5.6 4.0 - - + +
261C VAL* 3.0 13.2 + - + +
263C PRO* 1.3 78.1 - - - +
265C ALA* 1.3 57.0 + - - +
267C GLN* 3.6 11.2 - - + +
268C ILE* 3.0 61.1 + - + +
301C MET* 4.8 7.6 - - + -
303C PHE* 5.5 1.8 - - + -
316C GLN* 3.7 41.6 + - + +
318C LEU 3.6 15.3 - - - +
319C LEU* 3.5 25.6 - - + -
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C PHE* 3.9 26.2 - - + -
179C SER 3.6 23.8 - - - +
180C THR* 4.4 3.4 - - - -
261C VAL 3.3 3.0 + - - -
262C LYS* 3.1 15.7 + - - +
263C PRO 2.9 0.2 - - - -
264C LEU* 1.3 77.8 - - - +
266C GLU* 1.3 54.8 + - - +
268C ILE* 3.1 3.2 + - - +
269C ALA* 2.6 36.7 + - - +
282C MET* 4.2 13.7 - - + -
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1282B SIA 4.8 2.9 - - - +
262C LYS* 3.0 41.3 + - - +
263C PRO* 2.9 12.8 + - + +
265C ALA* 1.3 77.9 - - - +
267C GLN* 1.3 56.7 + - - +
269C ALA* 3.2 1.1 + - - +
270C ILE* 2.8 42.0 + - + +
276C THR* 4.0 27.6 + - + +
282C MET* 3.9 17.0 - - + -
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Residues in contact with GLN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C PRO 2.9 11.7 + - - +
264C LEU* 3.6 15.4 - - + +
266C GLU* 1.3 77.8 - - - +
268C ILE* 1.3 63.0 + - - +
270C ILE* 3.4 8.0 + - - +
271C THR* 2.9 33.6 + - - +
301C MET* 5.1 10.7 - - + +
316C GLN* 2.6 47.6 - - - +
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Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.0 27.6 - - + -
178C PHE* 4.0 24.9 - - + -
264C LEU* 3.0 39.6 + - + +
265C ALA* 3.6 3.6 - - - +
267C GLN* 1.3 74.9 - - - +
269C ALA* 1.3 65.4 + - - +
271C THR* 3.2 2.1 + - - -
272C ALA* 2.9 22.7 + - - +
286C LEU* 4.7 8.7 - - + -
297C THR* 4.2 7.1 - - + +
301C MET* 3.3 29.8 - - + -
303C PHE* 5.1 0.4 - - + -
319C LEU* 3.5 23.3 - - + -
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Residues in contact with ALA 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C PHE* 5.5 0.2 - - + -
265C ALA 2.6 21.0 + - - +
266C GLU* 3.3 5.8 - - - +
268C ILE* 1.3 75.0 - - - +
270C ILE* 1.3 56.9 + - - +
272C ALA* 3.2 2.6 + - - +
273C GLY 3.0 5.5 + - - -
274C CYS* 2.8 40.9 + - + +
276C THR* 4.0 7.6 - - + -
282C MET* 3.5 31.0 - - + -
286C LEU* 4.6 14.1 - - + +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C GLU* 2.8 29.6 + - + +
267C GLN* 3.8 6.5 - - - +
269C ALA* 1.3 73.2 - - - +
271C THR* 1.3 58.1 + - - +
273C GLY* 2.6 24.3 + - - -
274C CYS 4.0 7.4 - - - +
276C THR* 3.6 21.3 - - + +
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLN* 2.9 24.0 + - - +
268C ILE 3.7 3.6 - - - -
270C ILE* 1.3 77.9 - - - +
272C ALA* 1.3 61.3 + - - +
273C GLY 3.0 0.9 + - - -
297C THR* 3.8 20.0 + - + -
300C LYS* 4.0 42.6 + - + +
301C MET* 4.1 17.2 - - - +
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ILE 2.9 15.4 + - - +
269C ALA 3.6 4.7 - - - +
271C THR* 1.3 76.2 - - - +
273C GLY* 1.3 61.1 + - - +
274C CYS* 4.6 1.6 - - - -
286C LEU* 3.6 27.6 - - + -
289C LYS* 3.4 23.4 + - + +
294C LEU* 4.7 3.6 - - + -
297C THR* 3.3 25.7 - - + +
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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