Contacts of the helix formed by residues 264 - 276 (chain A) in PDB entry 1YTS
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LEU* 1.3 71.9 - - - +
265A SER* 1.3 65.1 + - - +
266A GLN 3.1 1.0 + - - -
267A LEU* 3.4 20.4 + - - +
297A GLY* 5.0 6.5 + - - +
299A PRO* 3.5 36.3 - - + +
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Residues in contact with SER 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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224A GLU* 3.2 30.9 + - - +
225A LYS* 4.1 5.9 + - - +
263A LEU* 3.8 23.8 - - - +
264A GLN* 1.3 79.3 - - - +
266A GLN* 1.3 64.3 + - - +
267A LEU 3.7 0.5 + - - -
268A GLU* 4.7 5.7 + - - +
269A SER* 5.7 0.2 + - - -
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Residues in contact with GLN 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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224A GLU* 6.6 0.2 - - + -
225A LYS 3.6 14.5 + - - +
226A LEU* 2.8 31.3 + - - +
243A ASP* 3.7 24.5 + - - +
244A LEU* 3.9 18.2 - - + +
245A ASN 4.8 0.2 + - - -
260A GLN* 3.2 18.2 + - - +
262A PRO* 3.8 8.4 - - + +
263A LEU* 3.0 28.6 + - - +
265A SER* 1.3 84.6 - - - +
267A LEU* 1.3 63.4 + - - +
268A GLU 3.3 2.8 + - - -
269A SER* 3.3 7.5 + - - +
270A HIS* 3.0 21.8 + - - +
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Residues in contact with LEU 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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262A PRO* 3.5 32.1 - - + -
263A LEU 4.1 8.1 - - - +
264A GLN* 3.4 17.2 + - - +
265A SER 3.6 0.6 - - - -
266A GLN* 1.3 76.0 - - - +
268A GLU* 1.3 61.1 + - - +
270A HIS* 4.1 4.3 - - + -
271A PHE* 2.9 35.4 + - + -
299A PRO* 3.8 27.6 - - + -
301A TYR* 3.6 29.6 - - + -
308A TYR* 3.7 36.8 - - + -
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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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265A SER 4.7 4.6 + - - +
266A GLN 3.3 0.8 - - - -
267A LEU* 1.3 77.1 - - - +
269A SER* 1.3 57.7 + - - +
271A PHE 3.3 2.6 + - - -
272A ARG* 2.9 66.5 + - - +
308A TYR* 3.0 31.2 - - + +
309A GLY* 3.1 18.4 + - - -
310A SER* 3.4 10.6 + - - -
311A ILE* 3.7 9.7 - - + +
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Residues in contact with SER 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* 4.0 20.5 + - - +
243A ASP* 2.8 29.9 + - - -
244A LEU* 3.6 15.7 - - - -
266A GLN* 3.3 7.0 + - - -
268A GLU* 1.3 76.8 - - - +
270A HIS* 1.3 58.2 + - - +
272A ARG* 3.0 12.4 + - - +
273A MET* 2.9 30.0 + - - +
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Residues in contact with HIS 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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244A LEU* 4.0 16.9 - - + +
259A CYS* 4.2 22.4 - - - +
260A GLN 5.3 0.2 + - - -
262A PRO* 3.9 29.9 - - + +
266A GLN 3.0 17.5 + - - +
267A LEU* 3.8 9.9 - - + +
268A GLU 3.2 0.2 - - - -
269A SER* 1.3 76.3 - - - +
271A PHE* 1.3 62.8 + + - +
273A MET* 3.5 18.4 + - + +
274A LEU* 3.1 39.2 + - + +
301A TYR* 2.7 49.3 + + - -
400A VAL* 5.2 1.1 - - + -
402A HIS* 4.2 2.9 - + - -
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Residues in contact with PHE 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 LEU* 2.9 37.5 + - + +
268A GLU* 3.7 3.8 - - - +
270A HIS* 1.3 75.2 - + + +
272A ARG* 1.3 62.0 + - - +
274A LEU* 3.3 15.0 + - + +
275A ALA* 3.2 24.9 + - - +
301A TYR* 3.5 47.1 - + + -
308A TYR* 3.5 36.8 - + + -
311A ILE* 3.8 25.1 - - + -
313A VAL* 3.8 16.6 - - + -
334A LEU* 4.1 18.2 - - + -
336A ILE* 4.2 15.3 - - + +
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Residues in contact with ARG 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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241A ARG* 3.6 21.1 - - - +
268A GLU* 2.9 48.9 + - - +
269A SER* 3.0 12.4 + - - +
271A PHE* 1.3 77.0 - - - +
273A MET* 1.3 57.5 + - - +
275A ALA* 3.5 3.8 + - - +
276A GLU* 3.0 37.9 + - + +
310A SER* 2.8 28.3 + - - -
311A ILE* 3.5 12.7 - - + +
338A GLU* 3.1 27.7 + - - +
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Residues in contact with MET 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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240A VAL* 3.9 27.4 - - + -
241A ARG* 4.0 17.1 - - - +
244A LEU* 3.8 18.2 - - + -
246A ALA* 4.3 6.1 - - - -
257A ILE* 4.3 19.7 - - + -
259A CYS* 4.7 2.9 - - - -
269A SER 2.9 14.6 + - - +
270A HIS* 3.7 20.9 - - + +
272A ARG* 1.3 76.3 - - - +
274A LEU* 1.3 76.8 + - + +
276A GLU* 4.3 7.5 - - - +
277A ASN* 3.3 24.6 + - + +
400A VAL* 4.0 31.6 - - + -
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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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270A HIS* 3.1 32.8 + - + +
271A PHE* 3.3 33.6 + - + +
273A MET* 1.3 83.8 - - + +
275A ALA* 1.3 58.8 + - - +
278A ARG 3.6 0.5 + - - -
279A THR* 2.4 52.9 + - + +
282A LEU* 4.2 27.4 - - + -
301A TYR* 4.5 0.7 - - + -
334A LEU* 4.7 4.0 - - + -
336A ILE* 4.0 13.9 - - + -
344A ILE* 4.6 0.2 - - - +
346A VAL* 4.2 10.1 - - + +
400A VAL* 3.9 22.7 - - + -
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Residues in contact with ALA 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 PHE 3.2 14.1 + - - +
272A ARG* 3.8 4.3 - - - +
274A LEU* 1.3 79.1 - - - +
276A GLU* 1.3 63.0 + - + +
277A ASN 3.3 0.2 - - - -
278A ARG* 3.0 30.3 + - - -
336A ILE* 4.4 17.3 - - + -
342A LYS 5.9 0.4 - - - +
344A ILE* 3.9 28.3 - - + +
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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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241A ARG* 4.3 18.4 + - - -
272A ARG* 3.0 24.4 + - + +
273A MET* 4.3 5.8 - - - +
275A ALA* 1.3 75.3 - - - +
277A ASN* 1.3 56.1 + - - +
278A ARG* 3.2 15.2 + - - +
396A LYS* 3.4 32.7 + - - +
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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