Contacts of the helix formed by residues 289 - 311 (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 GLY 289 (chain B).
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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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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.5 25.6 - - + +
58B LEU* 4.2 13.9 - - + +
60B GLN* 3.8 26.2 - - + +
180B GLY* 5.5 1.3 - - - -
285B VAL* 3.8 28.4 + - + -
286B LEU* 4.2 14.1 - - + +
289B GLY* 1.3 70.1 - - - -
291B GLU* 1.3 56.5 + - + +
293B ARG* 3.1 4.9 + - - +
294B PHE* 2.8 63.8 + - + -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 4.0 20.5 - - - +
289B GLY 3.7 0.2 - - - -
290B LEU* 1.3 74.7 - - + +
292B THR* 1.3 60.6 + - - +
294B PHE* 3.3 7.7 + - + +
295B GLU* 2.9 31.4 + - - +
298B ARG* 5.0 1.4 + - - -
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 3.4 35.7 + - + +
289B GLY* 3.4 3.8 + - - -
290B LEU 3.3 0.4 - - - -
291B GLU* 1.3 76.1 - - - +
293B ARG* 1.3 58.7 + - - +
295B GLU* 3.3 8.2 + - + +
296B ARG* 2.8 32.6 + - + +
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLY* 2.8 27.8 + - - +
201B CYS 2.8 24.0 + - - -
202B LEU* 4.3 6.1 + - - +
203B SER* 5.0 1.2 - - - -
284B LEU* 4.3 5.5 + - - +
285B VAL* 3.6 51.0 - - - +
288B GLU* 2.9 40.0 + - + +
289B GLY 2.8 19.0 + - - +
290B LEU* 3.5 5.4 - - - +
292B THR* 1.3 78.2 - - - +
294B PHE* 1.3 58.7 + - + +
296B ARG* 3.3 12.2 + - - +
297B HIS* 2.9 43.5 + - + -
370B GLY* 3.8 13.5 - - - -
371B TYR 4.9 0.4 - - - +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU 5.9 1.1 - - - -
60B GLN* 4.1 7.4 - - - -
180B GLY* 4.1 9.0 - - - -
181B GLY* 3.4 34.3 - - - +
182B CYS* 3.6 23.6 - - - -
183B GLU* 3.3 52.5 - - + +
184B VAL 4.7 1.1 - - - -
290B LEU* 2.8 58.5 + - + +
291B GLU* 3.8 7.4 - - + +
293B ARG* 1.3 74.6 - - + +
295B GLU* 1.3 63.1 + - - +
297B HIS* 3.2 5.2 + - - +
298B ARG* 3.1 42.1 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU 2.9 17.4 + - - +
292B THR* 3.7 7.2 - - + +
294B PHE* 1.3 75.6 - - - +
296B ARG* 1.3 60.2 + - - +
298B ARG* 3.2 33.4 + - - +
299B HIS* 3.0 31.1 + - + +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU* 2.8 41.5 + - - +
292B THR* 2.8 20.5 + - + +
293B ARG* 3.4 23.4 + - - +
295B GLU* 1.3 79.5 - - - +
297B HIS* 1.3 73.7 + - - +
299B HIS* 3.3 14.8 + - + +
300B HIS* 3.1 45.3 + - + +
370B GLY 2.8 27.7 + - - -
371B TYR* 4.9 1.8 - - - +
373B CYS* 2.9 20.5 + - - +
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Residues in contact with HIS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLY 3.9 9.2 - - - -
181B GLY* 3.8 19.1 + - - +
201B CYS* 4.4 1.2 - - - -
293B ARG* 2.9 42.1 + - + +
294B PHE 3.2 8.3 + - - +
296B ARG* 1.3 99.6 - - - +
298B ARG* 1.3 65.8 + - - +
299B HIS 3.3 0.2 + - - -
300B HIS* 3.5 1.7 + - - +
301B GLU* 2.9 23.9 + - - +
324B PRO* 4.6 5.6 - - + +
325B VAL* 3.6 21.8 - - + -
368B THR* 3.3 25.4 + - - +
369B MET* 3.8 1.1 - - - -
370B GLY 2.9 27.1 + - - -
373B CYS* 3.8 10.6 - - - +
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Residues in contact with ARG 298 (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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183B GLU* 6.0 2.6 - - - +
291B GLU 5.0 1.0 + - - -
294B PHE* 3.1 31.9 + - - +
295B GLU* 3.2 43.6 + - - +
297B HIS* 1.3 77.2 - - - +
299B HIS* 1.3 57.6 + - - +
301B GLU* 3.5 19.4 - - - +
302B ALA* 2.9 30.1 + - - +
324B PRO* 4.6 15.7 - - + -
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.0 18.4 + - + +
296B ARG* 3.6 13.1 - - - +
297B HIS 3.2 0.4 - - - -
298B ARG* 1.3 76.3 - - - +
300B HIS* 1.3 71.6 + + - +
302B ALA* 3.2 9.6 + - + +
303B ALA* 3.0 23.4 + - - +
375B LYS* 6.0 0.7 - - - -
408B VAL* 3.8 27.4 + - + +
409B TYR* 3.6 30.7 + + - -
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 3.1 39.4 + - - +
299B HIS* 1.3 83.3 + + - +
301B GLU* 1.3 61.0 + - - +
303B ALA* 3.2 1.0 + - - +
304B LEU* 2.9 31.4 + - - +
368B THR* 4.9 2.5 - - + -
373B CYS* 3.4 42.1 + - - -
374B ARG* 3.8 2.0 - - - +
375B LYS* 3.4 27.3 + - + -
378B VAL* 4.1 12.8 - - + +
409B TYR* 2.7 40.4 + + - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B HIS 2.9 15.5 + - - +
298B ARG* 3.5 16.5 - - - +
300B HIS* 1.3 75.1 - - - +
302B ALA* 1.3 59.6 + - - +
304B LEU* 3.8 5.8 - - - +
305B ALA* 2.9 31.7 + - + +
322B LYS* 2.7 42.6 + - - +
324B PRO* 3.2 43.7 - - - +
327B THR* 4.5 4.7 + - - +
368B THR* 4.5 9.4 + - - +
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Residues in contact with ALA 302 (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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298B ARG 2.9 14.2 + - - +
299B HIS* 3.2 12.8 + - + +
301B GLU* 1.3 75.2 - - - +
303B ALA* 1.3 65.9 + - - +
305B ALA* 3.5 6.6 + - - +
306B ALA* 3.1 24.8 + - - +
408B VAL* 4.1 10.7 - - + +
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Residues in contact with ALA 303 (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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299B HIS 3.0 8.5 + - - +
300B HIS 3.2 2.0 + - - +
302B ALA* 1.3 75.7 - - - +
304B LEU* 1.3 62.7 - - - +
306B ALA* 3.4 0.5 + - - +
307B GLY 3.2 16.6 + - - -
378B VAL* 4.2 3.6 - - + -
405B ALA* 3.5 16.3 - - + +
408B VAL* 3.6 25.0 - - + +
409B TYR* 3.3 47.1 - - + +
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Residues in contact with LEU 304 (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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300B HIS 2.9 17.6 + - - +
301B GLU* 3.8 4.3 - - - +
303B ALA* 1.3 75.2 - - - +
305B ALA* 1.4 57.8 + - - +
307B GLY* 3.1 3.1 + - - -
308B ILE* 2.9 43.9 + - + +
327B THR* 3.7 35.0 - - + +
366B ILE* 3.9 23.6 - - + +
368B THR* 4.1 14.1 - - + -
378B VAL* 3.8 16.9 - - + +
381B VAL* 3.8 28.5 - - + -
382B LEU* 4.0 17.2 - - + +
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Residues in contact with ALA 305 (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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301B GLU* 2.9 21.6 + - + +
302B ALA* 3.8 7.4 - - - +
304B LEU* 1.4 75.9 - - - +
306B ALA* 1.3 53.6 + - - +
308B ILE* 3.8 7.6 - - - +
309B LYS* 2.8 35.6 + - - +
315B LEU* 5.1 15.5 - - + +
322B LYS* 6.0 2.5 - - - -
327B THR* 5.5 6.0 - - + +
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Residues in contact with ALA 306 (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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302B ALA 3.1 18.0 + - - +
303B ALA 3.9 1.6 - - - +
305B ALA* 1.3 73.0 - - - +
307B GLY* 1.4 60.7 + - - +
309B LYS* 3.7 6.4 - - - +
310B ALA* 2.8 32.6 + - - +
404B ALA* 3.5 16.5 - - + +
408B VAL* 3.7 22.4 - - + -
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Residues in contact with GLY 307 (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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303B ALA 3.2 10.4 + - - -
304B LEU 3.1 6.5 + - - -
306B ALA* 1.4 73.0 - - - +
308B ILE* 1.3 58.3 + - - +
310B ALA 3.0 1.9 + - - -
311B MET* 2.8 31.2 + - - +
382B LEU* 3.7 17.0 - - - -
401B ALA* 3.3 29.8 - - - +
404B ALA* 4.3 0.6 - - - +
405B ALA 4.4 0.8 - - - +
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Residues in contact with ILE 308 (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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304B LEU* 2.9 35.2 + - + +
305B ALA* 3.8 6.3 - - - +
307B GLY* 1.3 70.9 - - - -
309B LYS* 1.3 64.7 + - - +
311B MET* 3.2 16.6 + - + +
313B LEU* 3.3 42.9 + - + +
315B LEU* 3.9 25.1 - - + -
327B THR* 5.0 2.5 - - + -
329B VAL* 4.0 20.2 - - + -
366B ILE* 4.4 7.9 - - + -
382B LEU* 3.6 20.9 - - + +
385B LEU* 4.0 26.0 - - + -
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Residues in contact with LYS 309 (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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305B ALA 2.8 22.7 + - - +
306B ALA* 3.7 7.4 - - - +
308B ILE* 1.3 75.0 - - - +
310B ALA* 1.3 57.5 + - - +
312B GLY* 2.9 21.3 + - - -
313B LEU 4.1 9.9 + - - +
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Residues in contact with ALA 310 (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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306B ALA 2.8 21.4 + - - +
307B GLY 3.0 2.9 + - - +
309B LYS* 1.3 74.0 - - - +
311B MET* 1.3 60.4 + - - +
312B GLY* 3.1 1.8 + - - -
397B GLU* 4.9 3.6 + - - +
400B LYS* 3.7 37.8 - - + +
401B ALA 4.4 0.2 - - - -
404B ALA* 3.6 21.1 - - + -
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Residues in contact with MET 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY 2.8 10.8 + - - +
308B ILE* 3.4 9.4 - - + +
309B LYS 3.1 0.4 - - - -
310B ALA* 1.3 79.2 - - - +
312B GLY* 1.3 55.2 + - - +
313B LEU* 3.6 23.5 + - + +
382B LEU* 3.5 44.2 - - + +
385B LEU* 4.4 8.5 - - + -
386B GLU* 3.9 25.1 - - + +
389B LEU* 4.3 4.3 - - - -
396B ILE* 2.7 57.4 - - + +
397B GLU 5.3 4.7 - - - +
401B ALA* 3.7 24.6 - - + +
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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