Contacts of the helix formed by residues 266 - 277 (chain B) in PDB entry 1ULH
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B PRO* 3.9 17.6 + - - +
237B GLN* 2.9 27.0 + - - +
262B CYS* 4.0 12.6 - - + -
263B ALA* 3.2 10.8 + - + +
265B ASP* 1.3 106.1 + - - +
267B ASP* 1.3 59.9 + - - +
268B PRO* 3.1 9.0 - - - -
269B TYR* 3.3 22.1 + - - +
270B PHE* 3.1 33.6 - - + -
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Residues in contact with ASP 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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60B PHE* 3.9 21.0 - - + +
94B ARG* 2.6 44.6 + - - -
262B CYS* 4.8 1.2 - - - -
263B ALA 4.5 1.0 + - - -
264B ILE* 3.7 18.7 + - + +
266B GLN* 1.3 76.5 - - - +
268B PRO* 1.4 65.9 - - + +
270B PHE* 3.8 5.8 - - - -
271B ARG* 3.0 21.2 + - - +
287B LEU* 3.2 7.4 - - - +
289B HIS* 2.8 31.3 + - + +
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Residues in contact with PRO 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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38B VAL 5.2 0.4 - - - +
39B ASP* 5.0 6.1 - - - -
40B PRO* 3.7 22.7 - - + -
60B PHE* 5.1 12.8 - - + -
219B ILE* 3.6 32.7 - - + +
220B PHE* 4.0 9.2 - - + -
264B ILE 5.0 0.4 - - - +
265B ASP 3.3 13.7 - - - +
266B GLN* 3.1 8.1 - - - -
267B ASP* 1.4 89.4 - - + +
269B TYR* 1.3 62.8 + - - +
271B ARG* 3.4 6.0 + - + +
272B MET* 3.2 23.0 + - - +
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Residues in contact with TYR 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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40B PRO* 3.5 28.5 - - + +
41B TRP* 3.5 22.0 - - - -
152B GLU* 3.7 16.0 + - - -
220B PHE* 3.4 32.7 - + - -
222B PHE* 6.2 0.7 - + - -
233B PHE* 3.9 21.4 - + - -
234B PRO* 4.3 14.1 - - + +
237B GLN* 3.2 49.8 - - + +
238B ALA* 4.9 0.4 - - - +
266B GLN* 3.4 32.5 - - - +
268B PRO* 1.3 79.0 - - - +
270B PHE* 1.3 60.7 + - + +
272B MET* 3.3 9.8 - - + +
273B THR* 2.8 28.0 + - - -
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Residues in contact with PHE 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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112B TYR* 3.6 19.1 - + - -
237B GLN* 3.6 38.4 - - + -
241B SER* 4.2 5.6 - - - -
260B ILE* 3.5 41.7 - - + -
262B CYS* 4.3 4.7 - - + -
266B GLN* 3.1 39.7 - - + -
267B ASP* 3.4 4.1 + - - +
268B PRO 3.2 0.4 - - - -
269B TYR* 1.3 75.0 - - + +
271B ARG* 1.3 61.1 + - - +
272B MET 3.1 1.6 - - - -
273B THR* 3.6 11.2 - - - -
274B ARG* 3.0 34.1 + - - +
285B PRO* 5.2 2.7 - - + -
287B LEU* 3.7 38.8 - - + -
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Residues in contact with ARG 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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59B ARG 3.7 17.2 + - - -
60B PHE* 3.1 36.9 + - - +
61B GLY* 4.5 4.4 - - - +
94B ARG* 3.8 20.8 - - - +
267B ASP* 3.0 20.0 + - - +
268B PRO* 3.4 6.3 + - + +
270B PHE* 1.3 75.1 - - - +
272B MET* 1.3 64.8 + - - +
274B ARG* 3.9 6.2 + - - +
275B ASP* 3.6 23.6 + - - +
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Residues in contact with MET 272 (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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207B ILE* 4.6 4.3 - - + -
211B VAL* 4.0 41.3 - - + -
216B VAL* 4.8 0.4 - - - -
219B ILE* 4.5 18.8 - - + +
220B PHE* 3.9 22.9 - - + -
234B PRO* 3.7 34.8 - - + +
235B ALA 4.6 0.9 - - - +
238B ALA* 3.9 14.1 - - + -
268B PRO 3.2 12.6 + - - +
269B TYR* 3.3 20.0 - - + +
271B ARG* 1.3 77.3 - - - +
273B THR* 1.3 66.8 + - - +
275B ASP* 2.9 23.0 + - - +
276B VAL* 3.1 9.6 + - + +
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Residues in contact with THR 273 (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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207B ILE* 6.0 0.9 - - + -
238B ALA* 3.1 30.6 - - + +
241B SER* 3.9 19.5 - - - +
242B PHE* 3.5 27.6 - - + -
269B TYR 2.8 15.9 + - - -
270B PHE* 3.6 14.2 - - - -
271B ARG 3.4 0.2 - - - -
272B MET* 1.3 79.6 - - - +
274B ARG* 1.3 56.6 + - - +
276B VAL* 3.0 8.1 + - + +
277B ALA* 2.8 27.5 + - - +
285B PRO* 4.0 9.0 - - + -
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Residues in contact with ARG 274 (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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94B ARG* 3.5 43.4 - - - +
95B ASP* 2.8 36.6 + - - +
270B PHE 3.0 22.2 + - - +
271B ARG* 4.3 6.7 - - + +
272B MET 3.4 0.2 - - - -
273B THR* 1.3 75.5 - - - +
275B ASP* 1.3 60.7 + - - +
277B ALA 4.1 0.2 - - - -
278B PRO* 3.3 3.8 - - - +
284B LYS* 3.1 60.3 - - + +
285B PRO* 2.8 44.4 + - + +
287B LEU* 4.4 6.1 - - - -
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Residues in contact with ASP 275 (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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271B ARG* 3.6 13.3 + - - +
272B MET* 2.9 17.2 + - - +
274B ARG* 1.3 82.1 - - - +
276B VAL* 1.3 60.8 + - + +
278B PRO* 3.4 10.9 - - - +
279B ARG* 3.4 40.9 + - - +
284B LYS* 5.4 0.2 - - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.1 22.7 - - + -
210B HIS* 4.0 28.9 - - + +
211B VAL* 3.8 27.4 - - + -
242B PHE* 5.6 1.3 - - + -
272B MET* 3.1 12.5 + - + +
273B THR* 3.0 10.4 + - - +
275B ASP* 1.3 79.3 - - + +
277B ALA* 1.3 66.5 + - - +
279B ARG* 2.8 29.3 + - - +
280B ILE* 3.3 24.6 + - + -
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Residues in contact with ALA 277 (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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242B PHE* 3.7 24.0 - - + -
273B THR 2.8 19.1 + - - +
274B ARG* 4.5 0.2 - - - -
276B VAL* 1.3 70.7 - - - +
278B PRO* 1.3 68.2 - - + +
280B ILE* 3.2 11.5 + - - +
281B GLY 3.2 4.7 + - - -
282B TYR 2.8 36.7 + - - +
284B LYS* 3.7 21.8 - - + -
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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