Contacts of the helix formed by residues 262 - 276 (chain A) in PDB entry 1R00
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 5.4 6.5 - - - -
261A TRP* 1.3 76.8 - - - +
263A ASP* 1.3 58.2 + - - +
264A GLU* 3.5 18.3 + - - +
265A ASP* 3.1 30.9 + - - +
266A ALA* 2.7 31.0 + - - +
312A MET 5.1 0.2 + - - -
313A GLY* 3.1 21.2 + - - -
314A GLY* 4.7 0.4 - - - -
317A ARG* 3.7 0.7 - - - +
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Residues in contact with ASP 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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262A SER* 1.3 71.5 - - - +
264A GLU* 1.3 74.8 + - - +
266A ALA* 3.5 0.6 + - - +
267A LEU* 3.0 25.4 + - - +
315A ARG* 2.9 32.5 + - - +
317A ARG* 2.7 26.3 + - - +
325A LEU* 3.9 17.7 - - + +
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Residues in contact with GLU 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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262A SER* 3.5 20.6 + - - +
263A ASP* 1.3 87.1 + - - +
265A ASP* 1.3 67.1 + - - +
267A LEU* 3.2 19.0 + - - +
268A THR* 3.2 15.8 + - - +
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Residues in contact with ASP 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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242A PHE* 4.0 12.4 - - + -
261A TRP* 3.6 38.6 - - + -
262A SER* 3.1 21.5 + - - +
264A GLU* 1.3 79.2 - - - +
266A ALA* 1.3 65.7 + - - +
268A THR* 3.1 15.2 + - - +
269A ILE* 3.0 26.9 + - - +
312A MET 5.6 0.3 - - - +
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Residues in contact with ALA 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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258A LEU* 4.1 16.6 - - + +
261A TRP* 3.9 10.9 - - + +
262A SER 2.7 19.6 + - - +
263A ASP 3.9 3.4 - - - +
265A ASP* 1.3 73.4 - - - +
267A LEU* 1.3 57.8 + - - +
269A ILE* 3.6 8.1 + - - +
270A LEU* 3.1 34.9 + - - +
317A ARG* 4.0 21.1 - - - +
325A LEU* 4.1 12.1 - - + -
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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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263A ASP 3.0 18.0 + - - +
264A GLU* 3.4 8.7 - - - +
265A ASP 3.0 0.2 - - - -
266A ALA* 1.3 75.8 - - - +
268A THR* 1.3 64.2 + - - +
270A LEU* 3.4 3.1 + - + +
271A ARG* 3.2 53.6 + - - +
325A LEU* 3.9 17.9 - - + +
328A SER* 3.0 30.5 - - - +
329A ALA* 3.8 24.2 - - + +
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Residues in contact with THR 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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241A PHE 4.8 1.4 - - - +
242A PHE* 3.7 28.5 + - + +
264A GLU 3.2 14.9 + - - +
265A ASP* 3.3 23.6 - - - +
267A LEU* 1.3 71.7 - - - +
269A ILE* 1.3 66.2 + - - +
271A ARG* 3.7 10.2 + - - +
272A GLY* 3.2 17.5 + - - -
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Residues in contact with ILE 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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189A VAL* 4.7 4.3 - - + -
241A PHE* 3.4 49.4 - - + +
242A PHE* 3.7 19.3 - - + -
254A LEU* 3.9 30.5 - - + -
257A VAL* 5.0 2.5 - - + -
258A LEU* 4.7 4.7 - - + -
261A TRP* 3.7 27.6 - - + -
265A ASP 3.0 19.4 + - - +
266A ALA* 3.8 9.6 - - - +
267A LEU 3.3 0.2 - - - -
268A THR* 1.3 76.4 + - - +
270A LEU* 1.3 57.0 + - - +
272A GLY* 3.1 4.0 + - - -
273A CYS* 3.1 28.7 + - - -
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Residues in contact with LEU 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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254A LEU* 3.8 22.0 - - + -
258A LEU* 4.2 25.4 - - + -
266A ALA 3.1 21.1 + - - +
267A LEU* 3.4 3.1 + - - +
268A THR 3.4 0.4 - - - -
269A ILE* 1.3 75.2 - - - +
271A ARG* 1.3 59.1 + - - +
273A CYS* 3.1 4.7 + - - +
274A VAL* 2.9 32.4 + - - +
283A LEU* 4.0 24.7 - - + -
285A VAL* 5.0 1.3 - - + -
322A VAL* 5.4 1.1 - - + +
325A LEU* 4.3 24.7 - - + +
326A ALA* 4.3 18.8 - - + +
329A ALA* 3.7 15.0 - - + -
331A LEU* 4.1 8.3 - - + -
353A PHE* 6.3 0.2 - - + -
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Residues in contact with ARG 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* 3.2 47.2 + - - +
268A THR* 4.0 9.0 - - - +
270A LEU* 1.3 76.0 - - - +
272A GLY* 1.3 62.8 + - - +
274A VAL* 3.8 8.3 - - - +
275A ARG* 3.1 24.4 + - - +
328A SER* 3.2 26.1 + - - -
329A ALA* 4.2 16.5 - - + +
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Residues in contact with GLY 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 PHE 5.4 4.7 - - - -
243A LYS 5.6 3.6 - - - -
244A PRO* 6.0 2.9 - - - -
245A LEU* 3.3 27.3 + - - +
268A THR 3.2 9.4 + - - -
269A ILE 3.1 10.0 + - - -
271A ARG* 1.3 79.4 - - - +
273A CYS* 1.3 58.7 + - - +
275A ARG* 3.7 7.9 - - - +
276A ALA* 3.3 12.8 + - - +
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Residues in contact with CYS 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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189A VAL* 3.9 18.8 - - - -
245A LEU* 3.9 7.9 - - - -
252A VAL* 3.6 22.5 - - + +
254A LEU* 3.7 30.3 - - - -
269A ILE* 3.1 20.2 + - - -
270A LEU 3.1 4.5 + - - +
272A GLY* 1.3 75.9 - - - +
274A VAL* 1.3 64.1 + - - +
276A ALA* 3.1 5.4 + - - +
277A LEU* 3.0 20.8 + - - +
283A LEU* 3.5 23.8 - - + -
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Residues in contact with VAL 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 LEU 2.9 19.8 + - - +
271A ARG* 3.8 5.2 - - - +
273A CYS* 1.3 74.5 - - - +
275A ARG* 1.3 64.1 - - - +
277A LEU* 3.0 26.6 + - + +
283A LEU* 4.4 2.9 - - + +
329A ALA 3.5 24.5 - - - +
330A GLY* 4.8 8.1 - - - +
331A LEU* 3.6 34.1 - - + -
355A ALA* 5.0 13.9 - - + -
357A SER* 6.1 0.9 - - - +
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Residues in contact with ARG 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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244A PRO* 6.1 6.3 - - + -
245A LEU 6.3 0.7 - - - +
248A THR* 4.9 4.9 - - - +
271A ARG 3.1 16.1 + - - +
272A GLY* 3.7 9.4 - - - +
274A VAL* 1.3 81.7 - - - +
276A ALA* 1.3 58.3 + - - +
277A LEU 3.5 3.1 + - - +
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Residues in contact with ALA 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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187A LEU* 3.9 8.7 - - + -
245A LEU* 3.8 21.1 - - + +
247A VAL 3.5 22.0 - - - +
248A THR* 3.0 33.4 - - - +
249A ALA 3.2 6.4 + - - -
252A VAL* 4.4 2.4 - - + +
272A GLY 3.3 10.6 + - - +
273A CYS 3.1 9.6 + - - +
275A ARG* 1.3 77.2 - - - +
277A LEU* 1.3 61.5 + - - +
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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