Contacts of the helix formed by residues 275 - 294 (chain A) in PDB entry 3IP7
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 TYR 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.2 7.0 - + + -
21A GLN* 2.7 29.8 - - + +
22A ILE* 4.7 12.1 - - + -
77A PHE* 3.9 27.4 - + - -
99A PRO* 2.8 30.4 - - + +
100A ALA* 3.5 20.5 + - + -
102A THR* 4.1 5.5 - - - +
118A CYS* 4.3 8.8 - - + +
226A ASP* 2.7 46.1 + - - +
229A VAL* 5.8 0.2 - - + -
248A PHE* 3.8 23.2 - + - -
274A ALA* 1.3 72.9 - - + +
276A THR* 1.3 64.0 + - - +
277A LEU 3.3 2.7 - - - -
278A TYR* 3.1 15.1 + + - +
279A SER* 3.0 25.1 + - - -
330A TYR* 5.4 0.7 + - - -
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Residues in contact with THR 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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21A GLN* 3.4 31.5 - - - +
25A GLY* 3.3 21.3 - - - +
265A PHE* 4.0 11.7 - - + -
270A PHE* 3.4 16.9 - - + -
272A PRO* 3.3 40.9 - - + -
273A GLU 2.9 15.9 + - - -
274A ALA 3.3 0.4 - - - -
275A TYR* 1.3 78.8 - - - +
277A LEU* 1.3 58.2 + - - +
279A SER* 3.4 0.9 + - - -
280A TYR* 3.0 20.4 + - - +
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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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252A PRO* 3.8 44.9 - - + +
253A THR* 4.0 14.8 - - + -
258A ASN* 3.8 15.5 - - - +
261A LEU* 3.7 27.4 - - + -
262A VAL* 4.4 9.2 - - + -
265A PHE* 4.0 22.0 - - + -
272A PRO* 4.4 9.6 + - + +
274A ALA 4.2 2.6 + - - +
275A TYR 3.3 0.4 - - - -
276A THR* 1.3 73.6 - - + +
278A TYR* 1.3 61.1 + - - +
279A SER 3.1 1.8 - - - -
280A TYR* 3.5 10.7 - - + +
281A ALA* 2.9 29.3 + - - +
313A ALA* 4.2 8.2 - - + +
314A LEU* 4.2 4.5 - - + +
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Residues in contact with TYR 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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99A PRO* 3.5 24.0 - - - +
117A THR* 2.7 53.2 + - - +
118A CYS* 4.1 10.8 - - + -
119A GLY 5.4 0.4 - - - -
248A PHE* 3.8 17.6 - + - -
249A GLY* 3.6 27.2 + - - -
250A PRO* 4.2 8.0 + - - +
252A PRO* 3.7 20.2 - - + -
274A ALA 3.4 18.4 - - - -
275A TYR* 3.1 14.9 + + + +
277A LEU* 1.3 76.4 - - - +
279A SER* 1.3 57.9 + - - +
281A ALA* 3.6 0.5 + - - +
282A ALA* 3.1 17.3 + - - +
314A LEU* 3.6 22.6 - - + +
327A LEU* 5.6 2.0 - - + -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 2.8 44.6 + - - +
25A GLY 4.3 0.9 - - - -
26A ALA* 3.5 11.5 + - - +
74A VAL* 3.6 6.2 - - - +
99A PRO* 3.7 15.4 - - - +
275A TYR 3.0 12.0 + - - -
276A THR 3.5 9.0 - - - -
278A TYR* 1.3 74.7 - - - +
280A TYR* 1.3 66.8 + - - +
281A ALA 3.1 1.3 - - - -
282A ALA* 3.1 15.6 + - - +
283A MET* 3.3 10.2 + - - +
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Residues in contact with TYR 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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25A GLY* 3.3 29.7 + - - +
28A GLN* 3.8 8.3 - - + -
29A ALA* 3.4 25.0 - - + +
32A ASP* 2.6 34.1 + - - +
261A LEU* 3.9 27.3 - - + +
265A PHE* 4.4 7.4 - + - -
276A THR 3.0 13.3 + - - +
277A LEU* 3.5 17.5 - - + +
279A SER* 1.3 74.0 - - - +
281A ALA* 1.3 58.0 + - - +
283A MET* 3.1 9.9 + - - +
284A GLN* 3.0 64.1 + - + -
313A ALA* 3.9 9.0 - - + -
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Residues in contact with ALA 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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117A THR* 4.1 5.1 - - + +
277A LEU 2.9 18.6 + - - +
278A TYR 3.7 4.3 - - - +
280A TYR* 1.3 74.8 - - - +
282A ALA* 1.3 65.1 + - - +
284A GLN* 3.1 14.8 + - - +
285A ALA* 2.8 25.8 + - - +
312A THR* 3.7 19.9 - - + +
313A ALA 4.4 1.6 - - - +
314A LEU* 3.7 27.1 - - + -
317A ILE* 5.3 0.4 - - + -
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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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74A VAL* 3.7 23.1 - - + -
97A ILE* 3.8 23.4 - - + +
99A PRO* 5.1 2.0 - - + -
117A THR* 3.6 18.3 - - + +
278A TYR 3.1 14.4 + - - +
279A SER* 3.1 10.9 + - - +
281A ALA* 1.3 74.6 - - - +
283A MET* 1.3 62.6 + - - +
285A ALA* 3.4 3.1 + - - +
286A ILE* 3.2 28.2 + - - +
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Residues in contact with MET 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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5A ILE* 3.4 50.9 - - + -
7A VAL* 5.8 0.4 - - + -
26A ALA* 4.0 21.1 - - + +
29A ALA* 3.5 23.3 - - + -
30A ALA* 4.1 4.9 - - - +
33A ILE* 3.7 12.6 - - + -
39A ILE* 5.4 0.8 - - - +
44A ILE* 4.3 12.3 - - - -
46A ILE* 4.1 8.5 - - + -
74A VAL* 3.6 18.8 - - + +
279A SER 3.3 4.8 + - - +
280A TYR 3.1 10.9 + - - +
282A ALA* 1.3 78.3 - - - +
284A GLN* 1.3 66.0 + - - +
286A ILE* 3.4 7.9 + - - +
287A ALA* 3.2 22.3 + - - +
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Residues in contact with GLN 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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29A ALA* 5.2 0.2 - - + -
33A ILE* 4.4 13.7 - - + +
280A TYR* 3.0 46.8 + - + +
281A ALA* 3.5 9.0 - - - +
283A MET* 1.3 75.6 - - - +
285A ALA* 1.3 59.8 + - - +
287A ALA* 3.2 4.9 + - - +
288A GLY* 2.8 27.0 + - - -
310A PHE* 5.3 0.6 - - - +
311A PRO* 3.7 9.7 + - - +
312A THR* 3.2 27.6 - - + +
313A ALA* 2.5 30.0 + - - +
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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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97A ILE* 4.3 6.7 - - + -
281A ALA 2.8 15.9 + - - +
282A ALA 3.6 5.8 - - - +
284A GLN* 1.3 74.3 - - - +
286A ILE* 1.3 60.1 + - - +
288A GLY 4.4 0.4 - - - +
289A ALA* 2.8 33.3 + - - +
305A LEU* 3.4 18.3 - - + +
310A PHE* 4.6 11.2 - - + -
312A THR* 4.6 1.1 - - - +
317A ILE* 4.5 10.5 - - + -
319A PHE* 4.1 19.5 - - + -
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Residues in contact with ILE 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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5A ILE* 4.3 12.8 - - + -
39A ILE* 4.1 17.5 - - + -
72A PHE* 3.8 54.5 - - + -
74A VAL* 4.4 11.7 - - + -
95A LEU* 5.0 6.5 - - + -
97A ILE* 3.9 27.4 - - + -
282A ALA 3.2 11.2 + - - +
283A MET* 3.4 9.6 + - - +
285A ALA* 1.3 76.5 - - - +
287A ALA* 1.3 59.2 + - - +
289A ALA* 3.8 1.8 - - - +
290A ALA* 2.9 30.7 + - + +
301A VAL* 3.9 10.0 - - + +
305A LEU* 4.9 2.9 - - + -
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Residues in contact with ALA 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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33A ILE* 3.9 22.2 - - + -
38A GLY 5.7 0.2 - - - +
39A ILE* 3.9 32.7 - - + +
40A ASN* 4.9 0.2 - - - +
283A MET 3.2 10.4 + - - +
284A GLN* 3.5 7.4 - - - +
286A ILE* 1.3 81.5 - - - +
288A GLY* 1.3 60.9 + - - +
290A ALA* 3.5 2.1 + - - +
291A LYS* 3.1 24.1 + - - +
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Residues in contact with GLY 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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284A GLN 2.8 18.4 + - - -
285A ALA 3.7 0.7 - - - -
287A ALA* 1.3 74.3 - - - +
289A ALA* 1.3 56.4 + - - +
291A LYS* 3.6 5.7 + - - +
292A ALA* 3.1 21.8 + - - +
310A PHE* 3.1 28.1 - - - -
311A PRO* 6.4 0.4 - - - -
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Residues in contact with ALA 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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285A ALA 2.8 11.6 + - - +
288A GLY* 1.3 68.9 - - - +
290A ALA* 1.3 61.2 + - - +
292A ALA* 3.3 0.7 + - - +
293A ALA* 2.8 24.8 + - - +
301A VAL* 3.6 17.5 - - + +
304A ALA* 3.2 14.9 - - + +
305A LEU* 3.3 40.2 - - + -
310A PHE* 3.3 16.0 - - + -
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Residues in contact with ALA 290 (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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39A ILE* 3.5 29.4 - - + -
40A ASN* 2.9 12.9 + - - +
72A PHE* 6.0 0.9 - - + -
286A ILE* 2.9 19.5 + - + +
287A ALA 3.8 0.4 - - - +
289A ALA* 1.3 76.3 - - - +
291A LYS* 1.3 58.8 + - - +
293A ALA* 3.3 0.6 + - - -
294A GLY 2.9 22.9 + - - -
295A SER 3.1 22.9 + - - +
296A VAL* 4.6 2.2 - - + -
301A VAL* 4.0 13.6 - - + +
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Residues in contact with LYS 291 (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 ASN* 3.3 15.6 + - - +
287A ALA 3.1 17.5 + - - +
288A GLY* 3.8 5.8 - - - +
289A ALA 3.2 0.2 - - - -
290A ALA* 1.3 75.2 - - - +
292A ALA* 1.3 66.9 + - - +
294A GLY* 3.1 12.5 + - - -
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Residues in contact with ALA 292 (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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288A GLY 3.1 15.5 + - - +
289A ALA* 3.6 4.7 - - - +
291A LYS* 1.3 80.2 - - - +
293A ALA* 1.3 58.7 + - - +
294A GLY 3.7 0.2 + - - -
304A ALA* 4.7 7.2 - - + +
308A GLY* 5.7 3.8 - - - -
310A PHE* 4.1 15.0 - - + -
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Residues in contact with ALA 293 (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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289A ALA 2.8 18.7 + - - +
290A ALA* 3.9 6.3 - - - +
292A ALA* 1.3 76.8 - - - +
294A GLY* 1.3 63.4 + - - +
295A SER* 3.2 13.9 + - - +
300A LYS* 3.9 19.1 - - + +
304A ALA* 3.5 17.5 - - + -
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Residues in contact with GLY 294 (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 ASN* 3.7 8.7 - - - -
290A ALA 2.9 7.5 + - - -
291A LYS 3.1 10.7 + - - -
292A ALA 3.4 0.6 + - - -
293A ALA* 1.3 77.6 - - - +
295A SER* 1.3 58.0 + - - +
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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