Contacts of the helix formed by residues 260 - 271 (chain B) in PDB entry 1YXU
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 SER 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B GLU* 2.8 33.7 + - - -
258B ARG* 3.8 22.1 - - - +
259B VAL* 1.3 77.1 - - - +
261B SER* 1.3 63.6 + - - +
262B GLU* 3.7 5.0 + - - +
263B CYS* 3.3 14.0 + - - +
264B GLN* 3.0 20.4 + - - +
289B TRP* 3.7 5.9 - - - -
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Residues in contact with SER 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 4.9 4.8 + - - +
259B VAL 3.7 1.5 + - - -
260B SER* 1.3 73.4 - - - +
262B GLU* 1.3 60.3 + - - +
264B GLN* 3.4 11.7 + - - +
265B HIS* 2.8 30.0 + - - +
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B SER* 3.2 6.3 + - - +
261B SER* 1.3 80.1 - - - +
263B CYS* 1.3 58.9 + - - +
265B HIS* 3.5 5.2 + - - +
266B LEU* 3.1 20.8 + - - +
287B HIS* 3.2 17.1 + - - +
288B PRO* 3.4 36.4 - - - +
289B TRP* 3.8 18.6 - - + +
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Residues in contact with CYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU* 3.8 2.5 - - - +
232B LEU* 4.4 8.3 - - - -
236B VAL* 3.9 21.3 - - - -
259B VAL* 3.6 20.9 - - + -
260B SER* 3.3 18.7 + - - +
262B GLU* 1.3 72.3 - - - +
264B GLN* 1.3 67.2 + - - +
265B HIS 3.1 0.9 - - - -
266B LEU* 3.1 5.1 + - - +
267B ILE* 2.9 41.2 + - - +
289B TRP* 3.7 34.5 - - - +
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Residues in contact with GLN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B PHE* 3.6 53.3 - - + +
257B GLN 5.2 0.2 + - - -
259B VAL* 3.0 29.1 + - + +
260B SER 3.0 18.0 + - - +
261B SER* 3.6 9.3 + - - +
263B CYS* 1.3 75.5 - - - +
265B HIS* 1.3 61.6 + - - +
267B ILE* 3.8 1.4 - - - +
268B ARG* 3.1 46.3 + - - +
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Residues in contact with HIS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B SER 2.8 19.0 + - - +
262B GLU* 3.7 6.7 - - - +
263B CYS 3.1 0.6 - - - -
264B GLN* 1.3 78.1 - - - +
266B LEU* 1.3 55.5 + - - +
268B ARG* 3.3 8.5 + - - +
269B TRP* 3.0 41.0 + + + +
287B HIS* 2.9 35.8 - + - -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 4.3 6.1 - - + -
232B LEU* 4.0 16.8 - - + -
262B GLU 3.1 7.9 + - - +
263B CYS* 3.1 8.6 + - - +
265B HIS* 1.3 73.4 - - - +
267B ILE* 1.3 65.6 + - - +
269B TRP* 3.2 11.3 + - + +
270B CYS* 3.0 34.9 + - - -
279B PRO* 5.0 0.4 - - + -
284B ILE* 4.2 22.0 - - + +
287B HIS* 3.7 35.9 - - + +
289B TRP* 3.8 17.0 - - + -
290B MET* 3.7 29.8 - - + -
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLY* 3.9 8.7 - - - +
232B LEU* 3.8 24.9 - - + -
233B TYR* 4.0 24.9 - - + +
236B VAL* 4.0 3.4 - - + -
253B VAL* 4.5 5.4 - - + -
255B PHE* 3.6 38.4 - - + -
263B CYS* 2.9 34.7 + - - +
264B GLN 3.8 4.0 - - - +
266B LEU* 1.3 75.0 - - - +
268B ARG* 1.3 63.3 + - - +
270B CYS* 3.3 7.4 + - - +
271B LEU* 3.1 44.0 + - + +
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B GLN* 4.5 7.7 + - - -
253B VAL* 3.0 52.6 + - + +
255B PHE* 3.5 25.0 - - + +
264B GLN* 3.1 37.4 + - - +
265B HIS* 3.8 6.7 - - - +
267B ILE* 1.3 74.3 - - - +
269B TRP* 1.3 64.5 + - - +
271B LEU* 3.3 8.4 + - - +
272B ALA* 3.3 19.1 + - - +
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Residues in contact with TRP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B HIS* 3.0 26.0 + + + +
266B LEU* 3.2 12.3 + - + +
268B ARG* 1.3 77.3 - - - +
270B CYS* 1.3 61.9 + - - +
272B ALA* 3.2 17.2 + - + +
277B ASP 3.0 28.3 + - - -
278B ARG* 3.7 0.7 - - - -
279B PRO* 3.2 33.7 - - + +
283B GLU* 3.5 52.9 - - + -
287B HIS* 4.0 29.4 - + - -
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 4.9 6.7 - - - -
225B VAL* 3.6 22.2 - - - +
226B TRP* 3.6 12.3 - - - -
228B LEU 4.9 1.6 - - - -
229B GLY* 3.5 29.4 - - - -
232B LEU* 5.8 0.7 - - - -
266B LEU* 3.0 26.7 + - - -
267B ILE* 3.5 5.6 - - - +
269B TRP* 1.3 76.9 - - - +
271B LEU* 1.3 59.1 + - - +
272B ALA 3.3 0.2 - - - -
278B ARG* 3.3 23.4 - - - -
279B PRO* 3.8 11.0 - - - -
284B ILE* 4.0 18.2 - - - -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TRP* 3.3 65.4 - - + +
229B GLY* 3.9 14.6 - - - +
230B ILE* 3.9 9.6 - - + +
241B PRO* 4.6 6.1 - - + -
242B PHE* 4.2 13.9 - - + -
251B GLY 4.7 8.9 - - - +
253B VAL* 3.9 21.5 - - + -
267B ILE* 3.1 34.9 + - + +
268B ARG* 3.4 9.4 - - - +
269B TRP 3.2 0.4 - - - -
270B CYS* 1.3 77.4 - - - +
272B ALA* 1.3 65.2 + - - -
273B LEU* 3.4 4.5 + - - +
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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