Contacts of the helix formed by residues 271 - 289 (chain A) in PDB entry 3ISL
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 ALA 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.1 22.4 + - + +
207A GLY 6.0 0.4 - - - +
208A MET* 4.1 3.8 - - + +
269A THR 3.4 0.2 + - - -
270A GLU* 1.3 73.2 - - - +
272A THR* 1.3 65.6 + - - +
273A THR 3.5 1.3 - - - -
274A MET* 3.4 21.2 + - + +
275A LEU* 3.0 23.7 + - - +
206B SER 3.3 26.9 - - - +
207B GLY* 4.1 8.1 - - - -
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.7 19.9 - - + +
37A VAL 3.3 40.0 + - - +
38A GLY 5.6 0.5 - - - -
44A PHE* 3.6 23.3 - - + -
270A GLU 3.2 8.9 + - - -
271A ALA* 1.3 72.3 - - - +
273A THR* 1.3 62.5 + - - +
275A LEU* 3.3 4.0 + - - +
276A TYR* 3.1 35.4 + - + -
21B PRO* 4.2 15.6 - - - +
205B PRO* 5.7 0.2 - - - -
206B SER* 4.3 10.3 + - - +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 3.9 35.1 + - + +
34A THR 4.9 1.4 + - - -
36A VAL* 3.8 13.9 - - - +
272A THR* 1.3 76.5 - - - +
274A MET* 1.3 64.2 + - - +
276A TYR* 3.3 15.8 + - + +
277A ALA* 3.0 20.4 + - - +
29B LEU* 5.0 0.2 - - - +
32B MET* 3.9 27.0 - - - +
205B PRO* 3.5 30.5 - - - +
206B SER 5.4 0.2 + - - -
273B THR* 5.6 0.2 - - + -
274B MET* 5.3 3.1 - - - -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 5.0 4.3 - - - +
204A VAL* 4.3 9.0 - - + -
205A PRO* 2.8 50.7 - - + +
206A SER 3.8 9.6 - - - +
207A GLY 4.4 14.1 - - - +
208A MET* 3.9 19.2 - - + +
271A ALA* 3.4 21.3 + - + +
272A THR 3.3 0.8 - - - -
273A THR* 1.3 80.1 - - - +
275A LEU* 1.3 57.9 + - - +
277A ALA* 3.4 5.5 + - + +
278A LEU* 2.9 27.4 + - - +
206B SER 5.7 0.2 + - - -
207B GLY* 6.4 0.2 - - - -
273B THR* 5.2 3.6 - - - -
274B MET* 3.9 34.5 - - + +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.2 36.1 - - + -
47A ILE* 3.5 21.3 - - + -
48A MET* 3.9 18.2 - - + +
51A THR* 4.1 18.6 - - + +
68A PRO* 4.3 6.5 - - + -
208A MET* 3.9 15.8 - - + +
260A TRP* 3.9 21.3 - - + -
270A GLU* 4.6 1.6 - - + -
271A ALA 3.0 13.4 + - - +
272A THR 3.4 9.0 - - - +
274A MET* 1.3 74.7 - - - +
276A TYR* 1.4 65.1 + - - +
278A LEU* 4.3 3.1 - - + -
279A ARG* 2.9 25.0 + - - +
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Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.1 15.0 - - + +
34A THR* 3.6 40.6 - - + -
35A PRO 2.8 20.7 + - - -
36A VAL* 4.3 0.9 - - - -
37A VAL* 3.3 26.7 + - + +
44A PHE* 4.7 2.2 - + - -
47A ILE* 3.6 30.5 - - + -
272A THR* 3.1 30.3 + - + -
273A THR* 3.3 22.4 + - + +
275A LEU* 1.4 75.9 - - - +
277A ALA* 1.3 57.7 + - - +
279A ARG* 3.5 5.6 - - - +
280A GLU* 2.9 34.7 + - - +
9B LEU* 3.7 19.7 - - + +
11B THR* 4.1 11.1 - - + +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.0 16.9 - - + +
31A VAL* 4.3 5.6 - - - -
32A MET* 3.7 28.5 - - + -
204A VAL* 3.7 8.8 - - + +
205A PRO* 4.1 10.5 - - + -
273A THR 3.0 13.0 + - - +
274A MET* 3.7 8.5 - - + +
275A LEU 3.2 0.4 - - - -
276A TYR* 1.3 78.0 - - - +
278A LEU* 1.3 57.7 + - - +
280A GLU* 3.4 1.0 + - - -
281A GLY* 2.9 27.4 + - - -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 4.0 15.7 - - + -
55A LEU* 4.7 4.0 - - + -
68A PRO* 3.6 37.9 - - + -
198A THR* 3.8 24.5 - - + -
202A LEU* 4.7 5.4 - - + -
204A VAL* 3.9 11.6 - - + +
208A MET* 4.1 9.2 - - + -
210A PRO* 4.3 16.6 - - + -
274A MET 2.9 17.5 + - - +
275A LEU* 3.7 6.7 - - + +
277A ALA* 1.3 73.0 - - - +
279A ARG* 1.3 66.2 + - - +
281A GLY 3.1 0.3 + - - -
282A VAL* 2.8 54.2 + - + +
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 3.9 20.3 - - + +
50A GLU* 2.9 38.9 + - - +
51A THR* 3.5 25.7 + - - +
54A MET* 3.4 22.5 - - + +
275A LEU 2.9 21.4 + - - +
276A TYR* 3.5 5.2 - - - +
278A LEU* 1.3 74.5 - - - +
280A GLU* 1.3 85.9 + - - +
283A ARG* 2.9 34.6 + - - +
7B ARG* 2.6 35.6 + - - +
8B GLU 4.8 2.2 + - - -
9B LEU* 3.6 25.5 - - + +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG 4.8 4.1 - - - +
28A VAL* 4.0 15.0 - - + -
31A VAL* 3.7 28.7 - - + +
276A TYR 2.9 24.2 + - - +
277A ALA 4.0 2.2 - - - +
279A ARG* 1.3 102.2 + - - +
281A GLY* 1.3 63.2 + - - +
283A ARG* 2.9 35.8 + - - +
284A LEU* 3.1 27.4 + - + +
8B GLU* 3.5 2.4 - - - +
9B LEU* 2.9 29.7 + - + +
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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
----------------------------------------------------------
28A VAL* 3.6 12.2 - - - +
202A LEU* 4.6 6.6 - - - +
204A VAL* 3.6 26.0 - - - -
277A ALA 2.9 15.0 + - - -
280A GLU* 1.3 72.6 - - - +
282A VAL* 1.3 61.5 + - - +
284A LEU* 3.3 6.4 + - - +
285A VAL* 3.1 25.9 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 5.5 1.1 - - + -
54A MET* 3.9 41.7 - - + +
55A LEU* 4.0 13.9 - - + -
58A LEU* 4.3 17.5 - - + -
202A LEU* 4.8 10.8 - - + -
204A VAL* 5.9 0.2 - - + -
278A LEU* 2.8 42.2 + - + +
279A ARG 4.1 1.6 - - - +
281A GLY* 1.3 69.5 - - - -
283A ARG* 1.3 68.4 + - - +
285A VAL* 3.2 8.3 + - + +
286A LEU* 3.1 25.7 + - + +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 5.2 9.1 + - - +
54A MET* 3.7 19.0 - - + -
279A ARG* 2.9 23.0 + - - +
280A GLU* 2.9 43.4 + - - +
282A VAL* 1.3 79.4 - - - +
284A LEU* 1.3 74.3 + - - +
286A LEU* 3.3 4.4 + - - +
287A GLU* 3.0 69.5 + - + +
7B ARG* 3.5 35.6 + - - +
8B GLU* 3.5 22.8 - - - +
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Residues in contact with LEU 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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25A ASP* 3.6 37.2 - - + +
27A ARG* 3.7 43.3 - - + +
28A VAL* 4.1 11.4 - - + -
280A GLU* 3.1 16.7 + - + +
281A GLY* 3.7 6.7 - - - +
282A VAL 3.1 0.2 - - - -
283A ARG* 1.3 105.7 - - - +
285A VAL* 1.3 66.6 + - - +
287A GLU* 3.3 7.8 + - + +
288A GLU* 3.1 22.9 + - - +
293A ARG* 4.4 6.0 + - - +
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Residues in contact with VAL 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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58A LEU* 4.1 14.8 - - + -
180A GLY* 4.7 2.2 - - - -
202A LEU* 3.8 26.7 - - + +
281A GLY 3.1 18.0 + - - +
282A VAL* 3.2 8.9 + - + +
284A LEU* 1.3 78.6 - - - +
286A LEU* 1.3 61.0 + - + +
288A GLU* 3.3 5.2 + - - +
289A GLY 3.0 26.2 + - - -
290A LEU* 3.4 30.1 - - + -
293A ARG* 3.8 38.5 - - - +
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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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54A MET* 3.7 47.6 - - + +
57A GLU* 3.8 37.2 - - + +
58A LEU* 4.3 8.1 - - + +
282A VAL* 3.1 18.7 + - + +
283A ARG* 3.7 4.3 - - - +
285A VAL* 1.3 81.6 - - + +
287A GLU* 1.3 64.9 + - + +
289A GLY* 3.4 10.9 + - - +
290A LEU* 4.2 24.0 - - + -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 4.3 9.1 + - - +
283A ARG* 3.0 61.8 + - + +
284A LEU* 3.3 13.8 + - + +
285A VAL 3.2 0.2 - - - -
286A LEU* 1.3 74.6 - - - +
288A GLU* 1.3 66.2 + - - +
289A GLY* 3.5 0.3 + - - -
7B ARG* 3.8 17.5 - - - +
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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
----------------------------------------------------------
284A LEU 3.1 12.5 + - - +
285A VAL 3.3 8.9 + - - +
287A GLU* 1.3 79.5 - - - +
289A GLY* 1.3 58.2 + - - +
292A THR* 3.4 25.6 + - + +
293A ARG* 2.8 44.6 + - + +
296A ARG* 2.7 55.5 + - - +
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Residues in contact with GLY 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 VAL 3.0 10.7 + - - -
286A LEU 3.4 8.2 + - - -
287A GLU 3.3 3.4 - - - -
288A GLU* 1.3 78.7 - - - +
290A LEU* 1.3 55.7 + - - -
291A GLU 3.4 2.2 - - - -
292A THR* 4.0 5.6 - - - -
293A ARG* 2.6 38.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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