Contacts of the helix formed by residues 266 - 283 (chain A) in PDB entry 1V1A
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 PRO 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLY 4.8 0.2 - - - +
265A LEU* 1.3 99.9 - - + +
267A VAL* 1.3 63.6 + - - +
268A GLU* 3.1 20.9 - - + +
269A GLU* 3.1 41.5 + - + +
270A ARG* 3.1 12.3 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA* 3.5 31.4 - - + -
229A VAL* 3.8 22.7 - - + -
232A ARG* 4.3 18.6 - - - +
234A VAL* 4.0 18.8 - - + -
257A TYR* 3.7 9.6 - - - +
265A LEU 3.9 0.2 + - - -
266A PRO* 1.3 73.8 - - - +
268A GLU* 1.3 67.3 + - - +
270A ARG* 3.4 26.1 + - - +
271A LEU* 3.1 24.0 + - - +
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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
----------------------------------------------------------
232A ARG* 2.8 30.4 + - - -
234A VAL* 3.7 26.4 - - + +
266A PRO* 3.2 21.9 - - + +
267A VAL* 1.3 77.1 + - - +
269A GLU* 1.3 61.3 + - + +
271A LEU* 4.1 4.0 - - - +
272A ARG* 3.5 20.8 + - - +
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.0 39.6 - - + +
266A PRO* 3.1 35.4 + - + +
268A GLU* 1.3 80.0 - - + +
270A ARG* 1.3 60.4 + - - +
271A LEU 3.2 1.3 - - - -
272A ARG* 3.1 27.2 + - - +
273A LEU* 2.8 33.8 + - - +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLU* 2.7 32.7 + - - -
229A VAL* 4.6 2.2 - - - +
257A TYR* 3.1 41.3 + - + +
260A GLY* 4.0 7.0 - - - -
261A ALA* 3.8 37.1 - - - +
264A GLY* 5.6 1.0 - - - -
265A LEU* 2.9 26.9 + - + +
266A PRO* 3.1 8.6 + - - +
267A VAL* 3.7 27.8 - - - +
269A GLU* 1.3 76.5 - - - +
271A LEU* 1.3 52.8 + - - +
273A LEU* 3.6 5.6 - - - +
274A ALA* 2.7 37.9 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 4.2 18.6 - - + -
225A ALA* 4.1 16.2 - - + +
227A ALA* 3.4 34.1 - - + +
234A VAL* 3.6 35.4 - - + +
236A GLY* 3.8 17.5 - - - +
253A PHE* 4.2 11.2 - - + -
257A TYR* 4.1 7.0 - - + -
267A VAL 3.1 14.5 + - - +
268A GLU 4.3 4.5 - - - +
270A ARG* 1.3 79.6 - - - +
272A ARG* 1.3 52.5 + - - +
274A ALA* 3.8 2.8 - - - +
275A ASN* 2.6 45.1 + - - +
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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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236A GLY* 5.9 0.2 - - - -
237A SER 5.4 2.0 - - - +
239A PHE* 3.7 13.4 - - + -
268A GLU 3.5 15.0 + - - +
269A GLU* 3.1 30.4 + - - +
271A LEU* 1.3 74.9 - - - +
273A LEU* 1.3 56.7 + - - +
275A ASN* 3.1 9.2 + - - +
276A LEU* 2.8 36.7 + - - +
301A LEU* 3.3 36.7 - - + +
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Residues in contact with LEU 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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46A LEU* 5.9 1.3 - - + -
256A GLY* 3.0 27.6 - - - +
259A ALA* 4.3 2.0 - - + -
260A GLY* 3.3 27.1 - - - +
263A TRP* 3.9 17.9 - - + -
265A LEU* 5.2 4.9 - - + -
269A GLU 2.8 17.0 + - - +
270A ARG 3.6 2.7 - - - +
272A ARG* 1.3 76.8 - - - +
274A ALA* 1.3 62.6 + - - +
276A LEU* 3.2 8.0 + - + +
277A LEU* 3.0 36.6 + - + +
297A LEU* 4.3 27.8 - - + -
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Residues in contact with ALA 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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253A PHE* 3.1 62.3 - - + +
256A GLY* 4.0 1.7 - - - -
257A TYR* 3.7 17.5 - - + +
270A ARG 2.7 22.2 + - - +
271A LEU* 3.8 2.5 - - - +
273A LEU* 1.3 74.8 - - - +
275A ASN* 1.3 60.9 + - - +
277A LEU* 3.6 0.3 + - - +
278A GLY 3.2 16.6 + - - -
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Residues in contact with ASN 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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224A GLY 4.2 9.0 - - - +
225A ALA* 4.4 0.7 - - - +
236A GLY* 3.5 17.3 + - - +
237A SER 3.1 29.5 + - - +
238A ALA* 4.3 6.8 - - - -
239A PHE* 3.8 12.4 + - + +
253A PHE* 3.7 10.8 - - - -
271A LEU* 2.6 38.8 + - - +
272A ARG* 3.1 5.8 + - - +
274A ALA* 1.3 70.9 - - - +
276A LEU* 1.3 65.2 + - - +
278A GLY 3.6 0.2 + - - -
279A ALA* 3.2 25.3 + - - +
1303A ADP 3.1 27.1 + - - +
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Residues in contact with LEU 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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239A PHE* 3.4 39.0 - - + -
272A ARG 2.8 20.1 + - - +
273A LEU* 3.2 8.7 + - + +
275A ASN* 1.3 71.5 - - - +
277A LEU* 1.3 72.7 + - + +
279A ALA* 3.8 2.1 - - - +
280A SER* 3.0 21.7 + - - -
292A PRO* 4.3 4.9 - - + -
297A LEU* 3.8 27.8 - - + -
300A LEU* 3.1 53.8 - - + +
301A LEU* 5.0 0.2 - - + -
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Residues in contact with LEU 277 (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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42A ALA* 4.4 13.7 - - + -
46A LEU* 4.0 25.1 - - + -
252A ALA* 3.2 33.8 - - + +
256A GLY* 3.9 12.6 - - - -
273A LEU* 3.0 24.6 + - + +
274A ALA 3.8 2.0 - - - +
276A LEU* 1.3 86.1 - - + +
278A GLY* 1.3 64.6 + - - +
280A SER* 3.1 5.5 + - - -
281A VAL* 3.1 20.4 + - - +
291A ALA* 4.7 3.8 - - + -
292A PRO* 3.5 39.0 - - + -
297A LEU* 4.4 8.3 - - + -
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Residues in contact with GLY 278 (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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249A ALA* 3.4 28.5 - - - +
252A ALA* 3.8 3.1 - - - +
253A PHE* 4.1 1.5 - - - +
274A ALA 3.2 13.7 + - - -
275A ASN 4.0 1.3 - - - -
276A LEU 3.3 0.2 - - - -
277A LEU* 1.3 79.7 - - - +
279A ALA* 1.3 56.2 + - - +
281A VAL* 3.3 2.3 + - - +
282A ALA* 2.9 29.1 + - - +
1303A ADP 4.0 13.7 - - - -
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Residues in contact with ALA 279 (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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239A PHE* 3.8 20.2 - - + -
241A VAL* 4.0 10.4 - - + +
275A ASN 3.2 17.9 + - - +
276A LEU 3.8 3.4 - - - +
278A GLY* 1.3 72.2 - - - +
280A SER* 1.3 66.8 + - - +
282A ALA* 3.2 2.2 + - - +
283A ALA* 2.9 26.6 + - - +
1303A ADP 3.7 32.1 + - + +
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Residues in contact with SER 280 (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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276A LEU 3.0 13.6 + - - -
277A LEU 3.1 8.5 + - - -
279A ALA* 1.3 77.8 - - - +
281A VAL* 1.3 60.6 + - - +
283A ALA* 3.4 9.4 + - - +
284A SER* 2.8 22.9 + - - -
290A GLY* 2.7 24.9 + - - -
292A PRO* 3.9 18.5 - - - +
300A LEU* 5.4 9.1 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP 3.5 0.6 - - - +
247A VAL 3.8 11.4 - - - +
248A GLY 3.8 14.4 - - - +
249A ALA* 4.5 0.2 - - - -
252A ALA* 3.4 26.2 - - + -
277A LEU 3.1 5.3 + - - +
278A GLY 3.8 6.3 - - - +
280A SER* 1.3 73.7 - - - +
282A ALA* 1.3 56.7 + - - +
283A ALA 3.0 4.3 - - - -
284A SER* 2.6 35.9 + - - +
285A ARG 6.0 0.7 - - - +
286A GLY 5.5 0.9 - - - +
287A ASP 3.6 24.7 - - - +
288A HIS* 4.3 9.6 - - + -
289A GLU 5.3 0.2 - - - +
290A GLY* 3.9 5.4 - - - +
291A ALA* 3.4 33.0 - - + +
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Residues in contact with ALA 282 (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 VAL* 5.5 0.9 - - + -
242A GLU 4.9 0.7 - - - -
243A ALA* 3.9 1.7 - - - -
244A VAL 2.9 23.7 + - - -
245A ASP 3.0 21.0 + - - -
246A PRO* 4.0 9.4 - - + -
249A ALA* 3.9 15.3 - - + -
278A GLY 2.9 18.3 + - - +
279A ALA 3.9 3.8 - - - +
281A VAL* 1.3 76.2 - - - +
283A ALA* 1.3 56.2 + - - +
284A SER 3.1 0.7 - - - -
1303A ADP 3.9 29.6 - - + +
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Residues in contact with ALA 283 (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 VAL* 3.7 29.6 - - + -
242A GLU 4.2 3.1 - - - -
244A VAL* 2.9 29.9 - - + +
279A ALA 2.9 16.5 + - - +
280A SER* 3.7 8.3 - - - +
281A VAL 3.0 0.4 - - - -
282A ALA* 1.3 75.1 - - - +
284A SER* 1.3 57.9 + - - +
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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