Contacts of the helix formed by residues 271 - 289 (chain A) in PDB entry 3V50
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 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A PRO 3.9 0.6 + - - -
270A ALA* 1.3 78.0 - - - +
272A MET* 1.3 65.0 + - - +
273A ALA* 3.6 9.6 + - - +
274A GLU* 2.8 42.8 + - - +
275A ARG* 3.0 21.9 + - - +
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Residues in contact with MET 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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237A ALA* 5.1 6.5 - - + -
244A ARG* 3.1 53.8 - - - +
271A SER* 1.3 71.1 - - - +
273A ALA* 1.3 63.6 + - - +
275A ARG* 3.3 26.5 + - - +
276A ASN* 2.9 43.3 + - - +
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Residues in contact with ALA 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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271A SER* 3.2 9.4 + - - +
272A MET* 1.3 80.0 - - - +
274A GLU* 1.3 58.1 + - + +
276A ASN* 3.3 9.8 + - - +
277A GLN* 2.8 45.7 + - - +
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Residues in contact with GLU 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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40A LEU* 4.2 6.9 - - + +
270A ALA* 4.3 13.1 - - + +
271A SER* 2.8 33.0 + - - +
273A ALA* 1.3 74.2 - - + +
275A ARG* 1.3 60.8 + - - +
277A GLN* 3.7 18.8 - - - +
278A GLN* 2.9 37.1 + - + +
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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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40A LEU* 4.3 5.2 - - + -
237A ALA* 4.9 2.4 - - - +
238A GLY 3.8 9.7 + - - +
242A GLY* 2.8 34.8 + - - +
243A ALA 3.0 25.1 + - - -
244A ARG* 4.3 15.9 - - + +
265A LEU* 3.9 25.0 - - + +
268A THR* 4.1 10.1 - - + -
270A ALA* 3.1 37.2 + - + +
271A SER 3.0 9.7 + - - +
272A MET* 3.4 33.1 - - - +
274A GLU* 1.3 75.6 - - - +
276A ASN* 1.3 63.4 + - - +
278A GLN* 3.4 1.3 + - - +
279A ILE* 3.1 30.4 + - - +
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Residues in contact with ASN 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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220A LEU* 6.1 1.8 - - - +
244A ARG* 2.8 36.3 + - - +
272A MET* 2.9 43.2 + - - +
273A ALA* 3.5 7.7 - - - +
275A ARG* 1.3 75.8 - - - +
277A GLN* 1.3 59.1 + - + +
279A ILE* 3.4 5.8 + - - +
280A ALA* 3.0 28.6 + - - +
303A MA4 4.0 33.1 - - + +
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Residues in contact with GLN 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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273A ALA* 2.8 37.2 + - - +
274A GLU* 3.7 21.1 - - - +
276A ASN* 1.3 75.0 - - + +
278A GLN* 1.3 60.3 + - + +
280A ALA* 3.4 7.4 + - - +
281A GLY* 2.8 24.9 + - - -
303A MA4 5.6 2.9 - - + -
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Residues in contact with GLN 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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32A GLN* 3.7 8.1 - - - +
36A SER* 2.8 40.7 + - - +
39A GLN* 2.6 40.3 + - - +
40A LEU* 3.7 33.0 - - + +
265A LEU* 5.3 1.6 - - + -
274A GLU* 2.9 23.8 + - + +
275A ARG 3.9 1.8 - - - +
277A GLN* 1.3 74.5 - - + +
279A ILE* 1.3 66.2 + - - +
281A GLY* 3.2 3.1 + - - -
282A ILE* 3.1 28.0 + - - +
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Residues in contact with ILE 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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244A ARG* 3.7 35.0 - - + -
245A GLY* 4.5 6.3 - - - +
246A ILE* 3.9 9.9 - - + -
263A ILE* 4.1 16.7 - - + +
265A LEU* 3.9 32.5 - - + -
275A ARG 3.1 14.0 + - - +
276A ASN 3.8 3.6 - - - +
278A GLN* 1.3 74.8 - - - +
280A ALA* 1.3 62.8 + - - +
282A ILE* 3.1 12.0 + - - +
283A GLY* 3.1 17.7 + - - -
302A MA4 3.9 18.2 - - + +
303A MA4 3.5 27.8 - - + -
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Residues in contact with ALA 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 ASN 3.0 17.0 + - - +
277A GLN* 3.6 8.5 - - - +
279A ILE* 1.3 76.6 - - - +
281A GLY* 1.3 57.0 + - - +
283A GLY* 3.1 2.6 + - - -
284A ALA* 2.8 24.1 + - - -
302A MA4 3.4 39.6 - - + +
303A MA4 4.2 22.1 - - + +
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Residues in contact with GLY 281 (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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26A SER* 5.0 1.2 + - - -
32A GLN* 3.4 24.1 + - - +
277A GLN 2.8 14.9 + - - -
278A GLN* 3.2 4.7 + - - -
279A ILE 3.2 0.6 - - - -
280A ALA* 1.3 73.4 - - - +
282A ILE* 1.3 65.0 + - - +
284A ALA* 3.3 10.1 + - - +
285A ALA* 3.1 17.5 + - - +
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Residues in contact with ILE 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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29A PRO* 5.1 2.9 - - + +
32A GLN* 3.8 11.2 - - + -
33A ILE* 4.0 38.1 - - + -
36A SER* 4.0 18.8 - - - +
44A VAL* 4.1 20.4 - - + -
46A MET* 4.6 5.4 - - + -
263A ILE* 3.7 33.2 - - + -
265A LEU* 5.2 1.6 - - + -
278A GLN 3.1 16.2 + - - +
279A ILE* 3.1 9.2 + - - +
281A GLY* 1.3 75.0 - - - +
283A GLY* 1.3 62.3 + - - +
285A ALA* 3.2 5.2 + - + +
286A LEU* 3.0 30.7 + - + +
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Residues in contact with GLY 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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250A LEU* 5.3 1.5 - - - +
279A ILE 3.1 12.3 + - - -
280A ALA 3.1 4.9 + - - -
282A ILE* 1.3 77.9 - - - +
284A ALA* 1.3 60.9 + - - +
286A LEU* 3.2 15.1 + - - +
287A ILE* 3.0 33.9 + - - +
302A MA4 4.2 24.6 - - - +
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Residues in contact with ALA 284 (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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26A SER* 3.8 13.2 - - - +
280A ALA 2.8 11.8 + - - +
281A GLY* 3.6 13.2 - - - +
282A ILE 3.2 0.2 - - - -
283A GLY* 1.3 75.6 - - - +
285A ALA* 1.3 58.1 + - - +
287A ILE* 3.3 2.2 + - - +
288A GLU* 3.0 34.0 + - - +
302A MA4 3.4 40.7 - - - +
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Residues in contact with ALA 285 (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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26A SER* 4.1 9.5 - - - -
27A PRO 3.3 25.1 - - - +
29A PRO* 3.8 22.7 - - + +
32A GLN* 3.9 11.9 - - + -
281A GLY 3.1 12.5 + - - +
282A ILE 3.2 8.5 + - - +
284A ALA* 1.3 72.5 - - - +
286A LEU* 1.3 65.8 + - - +
289A HIS* 3.1 31.0 + - - +
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Residues in contact with LEU 286 (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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29A PRO* 3.9 15.3 - - + -
46A MET* 3.8 19.1 - - + -
48A GLU* 3.6 32.3 - - - +
250A LEU* 4.7 7.4 - - + -
261A VAL* 4.0 35.7 - - + -
282A ILE* 3.0 23.6 + - + +
283A GLY* 3.2 13.9 + - - +
285A ALA* 1.3 76.7 - - - +
287A ILE* 1.3 60.9 + - - +
289A HIS 3.3 0.3 - - - -
290A TRP* 3.0 45.0 + - + -
292A ARG* 3.7 6.2 + - - +
302A MA4 4.9 1.6 - - + -
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Residues in contact with ILE 287 (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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225A LEU* 3.6 31.2 - - + -
226A PRO* 4.1 13.5 - - + -
229A TRP* 3.7 48.2 - - + +
250A LEU* 4.8 7.4 - - + -
283A GLY* 3.0 24.9 + - - +
284A ALA 3.6 3.8 - - - +
286A LEU* 1.3 78.2 - - - +
288A GLU* 1.3 62.7 + - - +
289A HIS 3.4 0.5 + - - -
290A TRP* 3.8 10.6 + - - +
302A MA4 3.8 45.9 - - + +
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Residues in contact with GLU 288 (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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26A SER* 2.8 46.3 + - - +
284A ALA 3.0 14.5 + - - +
287A ILE* 1.3 76.7 - - - +
289A HIS* 1.3 80.6 + - + +
290A TRP 3.6 1.2 + - - -
302A MA4 2.5 48.4 + - - +
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Residues in contact with HIS 289 (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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26A SER 2.9 26.5 + - - -
27A PRO* 3.2 23.3 + - + -
28A GLN* 3.3 38.0 + - - +
29A PRO* 4.1 4.9 - - + -
285A ALA* 3.1 21.5 + - - +
286A LEU 3.3 4.3 - - - -
287A ILE 3.2 0.2 - - - -
288A GLU* 1.3 97.4 + - + +
290A TRP* 1.3 55.7 + - - +
291A GLN 3.5 2.6 + - - -
292A ARG* 2.5 38.2 + - - -
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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