Contacts of the helix formed by residues 286 - 306 (chain B) in PDB entry 2AX1
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 THR 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLU* 4.2 0.6 + - - -
175B LEU* 3.7 30.5 - - + -
179B VAL* 4.0 18.4 - - + -
236B GLU* 5.4 0.7 - - - -
240B TYR* 3.6 26.2 - - + +
261B TYR* 3.3 35.3 - - + +
280B ARG* 4.4 9.0 + - - -
284B VAL* 3.8 3.4 - - - +
285B LEU* 1.3 74.9 - - + +
287B THR* 1.3 59.9 + - - +
288B SER 3.4 1.6 - - - -
289B CYS 4.1 1.1 - - - +
290B GLY* 2.7 31.9 + - - +
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ASP* 4.7 1.8 - - - +
280B ARG* 4.0 12.3 - - + +
281B ALA 2.7 26.4 + - - +
282B SER* 3.4 21.2 + - - +
284B VAL* 3.1 28.1 + - - +
285B LEU 3.3 0.4 - - - -
286B THR* 1.3 76.5 + - - +
288B SER* 1.3 60.6 + - - +
291B ASN* 2.9 53.4 + - - +
556B SER* 3.9 11.4 - - - +
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 5.0 0.9 + - - -
193B PHE* 3.6 16.1 - - - -
285B LEU 4.5 3.8 + - - -
286B THR 3.4 0.2 - - - -
287B THR* 1.3 76.4 - - - +
289B CYS* 1.3 58.8 + - - +
291B ASN* 3.9 3.7 - - - +
292B THR* 2.7 38.0 + - - -
317B GLY* 4.2 3.6 + - - -
554B GLY* 3.3 40.4 + - - -
555B TYR* 4.1 2.5 - - - -
556B SER* 3.9 22.4 + - - -
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Residues in contact with CYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL 5.2 0.4 - - - -
179B VAL* 3.9 35.0 - - + +
182B LEU* 5.3 1.3 - - - -
183B PRO* 3.5 31.6 - - + -
191B TYR* 5.5 4.0 - - - +
240B TYR* 4.0 15.5 - - - +
285B LEU 5.0 1.4 + - - +
286B THR 3.6 3.9 + - - +
288B SER* 1.3 79.6 + - - +
290B GLY* 1.3 58.2 + - - +
292B THR* 3.4 4.7 + - - -
293B LEU* 2.9 54.1 + - - +
554B GLY 4.8 3.0 + - - +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 3.6 23.5 - - - -
240B TYR* 3.8 7.3 + - - -
280B ARG* 3.5 7.9 - - - -
286B THR 2.7 23.8 + - - -
289B CYS* 1.3 74.0 - - - +
291B ASN* 1.3 59.6 + - - -
293B LEU* 4.0 1.7 - - - +
294B THR* 2.9 30.7 + - - -
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Residues in contact with ASN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 3.3 30.2 - - + -
225B ASP* 2.9 21.4 + - - +
228B VAL* 4.0 0.9 - - - +
280B ARG* 2.8 26.8 + - - +
287B THR* 2.9 38.6 + - - +
288B SER* 3.9 3.1 - - - +
290B GLY* 1.3 74.4 - - - +
292B THR* 1.3 54.2 + - - +
295B CYS* 2.8 37.4 + - - +
317B GLY* 3.8 16.1 - - - -
318B ASP* 4.3 3.8 - - - +
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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
----------------------------------------------------------
187B MET* 3.6 26.5 - - + -
191B TYR* 3.7 19.7 - - + -
193B PHE* 3.9 7.6 - - - -
288B SER 2.7 24.9 + - - -
289B CYS* 3.7 3.8 - - - -
290B GLY 3.3 0.2 - - - -
291B ASN* 1.3 74.1 - - - +
293B LEU* 1.3 59.8 + - - +
295B CYS* 3.8 0.9 - - - +
296B TYR* 2.9 32.2 + - - +
315B VAL* 3.9 23.8 - - + +
317B GLY* 2.9 23.8 + - - -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.7 23.7 - - + +
182B LEU* 4.7 3.6 - - + -
183B PRO* 4.7 3.6 - - + -
186B VAL* 4.0 20.4 - - + -
187B MET* 3.6 25.1 - - + -
236B GLU* 5.1 6.5 - - + -
239B ILE* 4.6 21.8 - - + -
240B TYR* 3.9 19.5 - - + +
289B CYS* 2.9 40.9 + - - +
290B GLY* 4.0 3.8 - - - +
292B THR* 1.3 75.8 - - - +
294B THR* 1.3 54.6 + - - +
296B TYR* 3.3 2.1 + - - +
297B LEU* 2.7 37.3 + - - +
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 4.1 15.0 - - + -
228B VAL* 4.8 4.5 - - + -
232B ASP* 4.3 15.5 + - + +
236B GLU* 2.6 34.8 + - - +
280B ARG* 4.9 0.4 - - - -
290B GLY 2.9 11.1 + - - -
291B ASN* 3.9 2.7 - - - -
293B LEU* 1.3 73.6 - - - +
295B CYS* 1.3 66.2 + - - +
297B LEU* 3.8 9.8 - - + +
298B LYS* 3.0 54.3 + - + +
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Residues in contact with CYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 5.9 0.9 - - - -
221B THR* 5.5 1.8 - - - -
224B PHE* 3.8 20.2 - - + -
291B ASN 2.8 23.1 + - - +
292B THR 3.9 1.3 - - - +
294B THR* 1.3 74.5 - - - +
296B TYR* 1.3 58.0 + - - +
298B LYS* 4.1 3.1 - - - +
299B ALA* 3.0 33.4 + - - +
315B VAL* 3.9 11.0 - - + -
317B GLY 3.4 19.1 - - - +
318B ASP* 4.1 11.9 - - - -
320B LEU* 4.0 27.1 - - - -
343B MET* 4.8 6.6 - - - +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.7 2.0 - - + -
71B MET* 3.7 31.0 - - + -
74B LYS* 5.1 6.9 + - - -
186B VAL 4.3 4.4 + - - -
187B MET* 3.6 48.0 + - + -
190B SER* 3.7 28.8 + - - -
292B THR 2.9 18.8 + - - +
293B LEU 3.5 2.5 - - - +
295B CYS* 1.3 74.9 - - - +
297B LEU* 1.3 62.5 + - - +
300B SER* 2.8 53.8 + - - -
313B MET* 3.5 23.6 - - + -
315B VAL* 4.2 8.9 - - + +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.5 63.9 - - + +
67B VAL* 3.6 18.1 - - + +
68B LEU* 3.7 15.3 - - + +
71B MET* 3.7 16.6 - - + -
235B VAL* 3.8 20.9 - - + -
293B LEU 2.7 21.6 + - - +
294B THR* 3.8 9.6 - - + +
296B TYR* 1.3 73.7 - - - +
298B LYS* 1.3 64.9 + - + +
300B SER* 3.8 1.7 - - - -
301B ALA* 3.1 19.9 + - - +
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Residues in contact with LYS 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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58B GLN* 3.7 2.6 - - - +
64B TYR* 4.4 14.4 - - + -
224B PHE* 5.5 3.8 - - + -
227B THR* 4.0 5.3 + - - -
228B VAL* 4.9 0.6 - - - +
232B ASP* 2.8 38.6 + - - -
294B THR* 3.0 31.8 + - + +
295B CYS* 4.2 2.9 - - - +
297B LEU* 1.3 78.3 - - + +
299B ALA* 1.3 57.4 + - - +
301B ALA* 3.4 0.6 + - - -
302B ALA* 2.9 28.1 + - - +
343B MET* 3.6 16.2 - - + -
346B TYR* 2.9 53.1 + - + +
347B SER 3.1 14.8 + - - -
348B ALA* 4.2 13.0 - - + +
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Residues in contact with ALA 299 (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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295B CYS 3.0 19.7 + - - +
298B LYS* 1.3 74.7 - - - +
300B SER* 1.3 60.9 + - - +
302B ALA* 4.2 0.9 - - - -
303B CYS* 2.9 34.3 + - - -
313B MET* 3.9 15.9 - - + -
320B LEU* 3.4 31.0 - - + -
339B PHE* 3.6 7.9 - - + -
343B MET* 3.6 12.5 - - + -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.8 22.0 - - - -
296B TYR* 2.8 40.3 + - - -
297B LEU 3.8 3.1 - - - -
299B ALA* 1.3 77.3 - - - +
301B ALA* 1.3 63.7 + - - +
303B CYS* 3.3 6.5 + - - +
304B ARG* 3.3 29.2 + - - +
313B MET* 3.7 20.0 - - - +
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Residues in contact with ALA 301 (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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63B HIS* 3.8 9.1 - - - +
64B TYR* 3.7 27.8 - - + +
67B VAL* 3.8 8.6 - - + +
297B LEU 3.1 14.5 + - - +
298B LYS* 3.6 4.5 - - - +
300B SER* 1.3 80.2 - - - +
302B ALA* 1.3 57.2 + - - +
304B ARG* 3.1 7.2 + - - +
305B ALA* 2.9 27.2 + - - +
346B TYR* 3.6 22.4 - - + +
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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 LYS 2.9 17.7 + - - +
299B ALA 3.8 0.2 - - - +
300B SER 3.3 0.2 - - - -
301B ALA* 1.3 75.8 - - - +
303B CYS* 1.3 56.9 + - - +
305B ALA* 3.2 2.1 + - - +
306B ALA* 2.9 31.0 + - - +
339B PHE* 3.6 41.4 - - + +
342B ALA* 3.7 18.6 - - + -
343B MET* 3.8 11.2 - - + +
346B TYR* 3.8 1.5 - - + -
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Residues in contact with CYS 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 ALA 2.9 21.0 + - - -
300B SER* 3.4 9.9 - - - +
301B ALA 3.2 0.2 - - - -
302B ALA* 1.3 75.8 - - - +
304B ARG* 1.3 59.1 + - + +
306B ALA 3.3 1.6 + - - -
307B LYS 2.9 21.7 + - - -
308B LEU* 3.1 22.6 + - - +
311B CYS* 3.7 33.7 - - + -
313B MET* 4.0 19.1 - - - -
322B VAL* 4.4 8.1 - - - -
339B PHE* 3.7 17.7 - - - -
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Residues in contact with ARG 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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63B HIS* 3.6 33.0 + - + +
66B ASP* 4.0 14.3 + - - +
67B VAL* 3.8 27.8 - - - +
70B GLU* 2.8 43.0 + - - -
300B SER* 3.3 14.9 + - - +
301B ALA* 3.1 8.0 + - - +
303B CYS* 1.3 75.2 - - + +
305B ALA* 1.3 64.4 + - - +
307B LYS* 2.9 22.1 + - - +
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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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63B HIS* 3.7 19.9 - - + -
301B ALA 2.9 13.8 + - - +
302B ALA 3.4 8.5 - - - +
304B ARG* 1.3 77.1 - - - +
306B ALA* 1.3 59.9 + - - +
307B LYS* 3.6 9.5 + - - +
338B VAL* 3.6 15.1 - - + +
342B ALA* 3.8 23.1 - - + -
345B ARG* 4.4 10.1 - - - +
346B TYR* 4.7 1.8 - - - +
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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
----------------------------------------------------------
302B ALA 2.9 15.8 + - - +
304B ARG 3.1 0.2 - - - -
305B ALA* 1.3 75.8 - - - +
307B LYS* 1.3 71.6 + - - +
308B LEU* 3.4 21.8 + - + +
335B SER* 3.3 34.4 - - - +
338B VAL* 3.8 9.7 - - + +
339B PHE* 3.7 14.6 - - + +
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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