Contacts of the helix formed by residues 271 - 289 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A SER* 3.3 24.7 - - - +
207A GLY* 4.0 11.4 - - - -
70B ASP* 2.9 21.8 + - + +
207B GLY 6.0 0.2 - - - +
208B MET* 3.8 4.0 - - + +
270B GLU* 1.3 74.6 - - - +
272B THR* 1.3 53.6 + - - +
273B THR 3.6 1.1 - - - -
274B MET* 3.3 21.7 + - + +
275B LEU* 2.8 36.0 + - - +
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 4.3 16.2 - - + -
205A PRO* 4.0 7.6 - - - +
206A SER* 3.6 20.0 + - - +
36B VAL* 3.3 30.2 - - + +
37B VAL 3.6 22.7 - - - +
38B GLY* 5.4 0.7 - - - -
39B GLN 5.6 0.4 - - - +
44B PHE* 3.8 18.7 - - + -
270B GLU 3.2 5.7 + - - +
271B ALA* 1.3 67.6 - - - +
273B THR* 1.3 73.3 + - - -
275B LEU* 3.1 6.6 + - - +
276B TYR* 3.0 27.2 + - - -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 5.1 0.2 - - - +
32A MET* 3.8 16.5 - - - +
205A PRO* 3.4 30.0 - - - +
273A THR* 5.6 0.7 - - + -
274A MET* 5.2 3.6 - - - -
32B MET* 3.8 45.0 + - + +
34B THR 5.0 1.2 + - - -
36B VAL* 3.9 9.4 - - - +
272B THR* 1.3 83.5 + - - +
274B MET* 1.3 59.6 + - + +
276B TYR* 3.1 16.5 + - + +
277B ALA* 2.9 27.4 + - - +
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER 5.7 0.2 + - - -
273A THR* 5.3 2.9 - - - -
274A MET* 3.9 35.9 - - + +
32B MET* 5.1 6.5 - - - +
204B VAL* 4.4 10.5 - - + -
205B PRO* 2.9 47.6 - - + +
206B SER 3.6 12.1 - - - +
207B GLY 4.2 16.2 - - - +
208B MET* 3.8 19.6 - - + +
271B ALA* 3.3 24.2 + - + +
272B THR 3.3 1.0 - - - -
273B THR* 1.3 80.8 - - - +
275B LEU* 1.3 57.8 + - - +
277B ALA* 3.4 3.7 + - - +
278B LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.6 26.0 - - + -
47B ILE* 3.7 23.3 - - + -
48B MET* 3.8 24.0 - - + +
51B THR* 4.0 20.4 - - + +
68B PRO* 4.1 14.1 - - + -
208B MET* 3.6 8.4 - - + +
260B TRP* 4.1 19.3 - - + -
270B GLU* 4.6 2.2 - - + -
271B ALA 2.8 18.4 + - - +
272B THR 3.6 4.5 - - - +
274B MET* 1.3 73.1 - - - +
276B TYR* 1.3 66.6 + - - +
278B LEU* 3.2 3.9 + - + -
279B ARG* 3.0 26.4 + - - +
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.7 21.1 - - + +
11A THR* 3.6 15.2 + - - +
31B VAL* 4.1 15.0 - - + +
34B THR* 3.6 41.5 - - + -
35B PRO 2.8 20.1 + - - -
36B VAL* 4.4 7.0 - - + -
37B VAL* 3.4 17.7 + - + +
44B PHE* 4.5 10.8 - + - -
47B ILE* 3.6 30.1 - - + -
272B THR 3.0 16.8 + - - -
273B THR* 3.1 22.2 + - + +
275B LEU* 1.3 77.9 - - - +
277B ALA* 1.3 57.7 + - - +
279B ARG* 3.5 6.1 - - - +
280B GLU* 3.1 33.1 + - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.7 23.4 - - + +
31B VAL* 4.1 6.9 - - - +
32B MET* 3.7 30.7 - - + -
204B VAL* 3.7 14.2 - - + +
205B PRO* 4.0 2.5 - - + -
273B THR 2.9 10.9 + - - +
274B MET* 3.8 8.3 - - - +
275B LEU 3.2 0.4 - - - -
276B TYR* 1.3 75.6 - - - +
278B LEU* 1.3 55.1 + - - +
280B GLU 3.3 0.7 + - - -
281B GLY* 2.8 31.5 + - - -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 4.0 19.7 - - + -
55B LEU* 4.7 8.3 - - + -
68B PRO* 3.8 31.0 - - + -
198B THR* 3.7 24.7 - - + -
202B LEU* 4.6 6.7 - - + -
204B VAL* 3.9 13.6 - - + +
208B MET* 4.3 9.2 - - - -
210B PRO* 4.5 14.4 - - + -
274B MET 3.0 18.6 + - - +
275B LEU* 3.8 4.5 - - + +
277B ALA* 1.3 72.5 - - - +
279B ARG* 1.3 59.7 + - - +
282B VAL* 2.7 62.4 + - + +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 2.8 34.1 + - - +
8A GLU 4.7 2.6 + - - -
9A LEU* 3.5 26.2 - - + +
10A CYS 5.7 0.2 - - - +
47B ILE* 3.9 22.0 - - + +
50B GLU* 3.0 38.6 + - - +
51B THR* 3.3 26.8 + - - +
54B MET* 3.3 22.5 - - + +
275B LEU 3.0 17.4 + - - +
276B TYR* 3.5 6.3 - - - +
278B LEU* 1.3 76.6 - - - +
280B GLU* 1.3 79.4 + - - +
283B ARG* 2.9 32.2 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 3.7 2.9 - - - +
9A LEU* 3.0 27.3 + - + +
27B ARG 4.7 4.3 - - - +
28B VAL* 4.2 15.0 - - + -
31B VAL* 3.7 29.1 - - + +
276B TYR 3.1 20.9 + - - +
277B ALA 3.8 3.8 - - - +
279B ARG* 1.3 104.6 + - - +
281B GLY* 1.4 58.0 + - - +
283B ARG* 3.0 35.7 + - - +
284B LEU* 3.0 32.4 + - + +
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.5 18.3 - - - +
202B LEU* 4.5 6.5 - - - +
204B VAL* 3.6 15.5 - - - -
277B ALA 2.8 18.4 + - - -
280B GLU* 1.4 76.3 - - - +
282B VAL* 1.3 62.4 + - - +
284B LEU* 3.4 6.6 + - - +
285B VAL* 3.2 26.5 + - - +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 5.5 2.0 - - + -
54B MET* 3.6 42.2 - - + +
55B LEU* 4.1 14.1 - - + +
58B LEU* 4.3 20.9 - - + -
202B LEU* 4.9 4.9 - - + -
204B VAL* 5.8 0.2 - - + -
278B LEU* 2.7 51.4 + - + +
279B ARG* 4.7 1.3 - - - +
281B GLY* 1.3 69.5 - - - +
283B ARG* 1.3 67.7 + - - +
284B LEU 3.1 1.7 + - - -
285B VAL* 3.1 15.7 + - + -
286B LEU* 3.2 17.7 + - + +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.3 43.5 + - - +
8A GLU* 3.8 19.4 - - - +
27B ARG* 5.2 9.9 + - - +
54B MET* 3.6 18.1 - - + -
279B ARG* 2.9 27.9 + - - +
280B GLU* 3.0 43.7 + - - +
282B VAL* 1.3 72.2 - - - +
284B LEU* 1.4 76.8 + - - +
286B LEU* 3.2 3.6 + - - +
287B GLU* 2.8 71.1 + - + +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASP* 3.6 37.5 - - + +
27B ARG* 3.6 45.5 - - + +
28B VAL* 4.0 13.0 - - + -
280B GLU* 3.0 17.7 + - + +
281B GLY* 3.7 6.7 - - - +
282B VAL 3.1 0.4 - - - -
283B ARG* 1.4 102.1 - - - +
285B VAL* 1.3 67.4 + - + +
287B GLU* 3.5 8.2 + - + +
288B GLU* 3.1 22.3 + - - +
293B ARG* 4.3 5.5 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.9 17.0 - - + -
180B GLY* 4.8 2.5 - - - -
202B LEU* 3.8 26.0 - - + +
281B GLY 3.2 16.8 - - - +
282B VAL* 3.1 7.2 + - + +
284B LEU* 1.3 79.1 - - + +
286B LEU* 1.3 60.9 + - + +
288B GLU* 3.2 6.4 + - - +
289B GLY 3.0 25.5 + - - -
290B LEU* 3.8 25.4 - - + -
293B ARG* 3.6 42.3 - - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 6.1 0.4 - - - +
54B MET* 3.8 47.1 - - + +
57B GLU* 3.8 37.5 - - + +
58B LEU* 4.4 6.7 - - - +
282B VAL* 3.2 17.5 + - + +
283B ARG* 3.8 3.8 - - - +
285B VAL* 1.3 76.0 - - + +
287B GLU* 1.3 65.4 + - - +
289B GLY* 3.2 12.8 + - - +
290B LEU* 4.2 26.7 - - + +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 5.0 6.8 - - - +
27B ARG* 4.1 16.5 + - - -
283B ARG* 2.8 58.7 + - + +
284B LEU* 3.7 8.5 - - - +
285B VAL 3.3 0.2 - - - -
286B LEU* 1.3 75.7 - - - +
288B GLU* 1.3 65.3 + - - +
289B GLY* 3.4 0.3 + - - -
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU 3.1 13.5 + - - +
285B VAL 3.5 8.3 - - - +
287B GLU* 1.3 78.6 - - - +
289B GLY* 1.3 60.8 + - - +
292B THR* 3.4 27.7 + - + +
293B ARG* 2.9 36.8 + - + +
296B ARG* 2.8 53.3 + - - +
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Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B VAL 3.0 11.4 + - - -
286B LEU* 3.2 11.4 + - - -
287B GLU 3.2 3.2 - - - -
288B GLU* 1.3 78.8 - - - +
290B LEU* 1.3 54.0 + - - -
291B GLU 3.7 1.8 - - - -
292B THR* 3.4 5.6 + - - -
293B ARG* 2.8 34.7 + - - +
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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