Contacts of the helix formed by residues 302 - 327 (chain W) in PDB entry 3EXG
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 SER 302 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W PHE* 3.4 16.9 - - - -
296W VAL* 4.4 3.4 - - - -
301W ALA* 1.3 75.7 - - - +
303W VAL* 1.3 67.4 + - - +
304W GLU* 3.8 13.5 + - - +
305W GLU* 3.0 45.4 + - - +
306W LEU* 3.2 10.2 + - - +
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Residues in contact with VAL 303 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292W LYS* 4.4 17.6 + - - +
296W VAL* 4.0 24.0 - - + +
302W SER* 1.3 71.3 - - - +
304W GLU* 1.3 87.6 + - + +
306W LEU* 3.9 5.0 + - - +
307W LYS* 3.2 24.9 + - + +
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Residues in contact with GLU 304 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302W SER* 3.1 11.2 + - - +
303W VAL* 1.3 98.1 - - + +
305W GLU* 1.3 65.2 + - - +
307W LYS* 3.8 10.9 - - + +
308W GLU* 3.3 27.6 + - + +
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Residues in contact with GLU 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W PHE* 3.5 8.3 - - + -
29W ARG* 2.8 32.1 + - - -
33W LEU* 3.9 15.9 - - + +
301W ALA* 3.1 34.5 - - + +
302W SER* 3.0 26.1 + - - +
304W GLU* 1.3 77.0 - - - +
306W LEU* 1.3 63.7 + - + +
308W GLU* 3.0 18.1 + - - +
309W ILE* 3.2 17.9 + - + +
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Residues in contact with LEU 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W LEU* 3.9 25.8 - - + -
36W TYR* 3.7 36.6 - - + +
292W LYS* 3.4 51.4 - - + +
295W MET* 4.3 14.4 - - + -
296W VAL* 4.5 10.3 - - + -
301W ALA* 4.3 4.3 - - + -
302W SER 3.2 10.3 + - - +
303W VAL* 4.0 4.7 - - - +
305W GLU* 1.3 80.4 - - - +
307W LYS* 1.3 56.8 + - - +
309W ILE* 2.9 25.4 + - + +
310W ASP* 3.0 18.5 + - - +
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Residues in contact with LYS 307 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292W LYS* 5.5 2.4 - - - +
303W VAL* 3.2 18.5 + - + +
304W GLU* 4.0 10.3 - - + +
305W GLU 3.3 0.2 - - - -
306W LEU* 1.3 77.1 - - - +
308W GLU* 1.3 61.1 + - + +
310W ASP* 3.4 19.0 + - + +
311W VAL* 3.3 32.6 + - - +
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Residues in contact with GLU 308 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304W GLU* 3.3 15.3 + - + +
305W GLU* 3.0 12.6 + - - +
307W LYS* 1.3 75.2 - - + +
309W ILE* 1.3 65.6 + - + +
310W ASP 3.2 1.3 - - - -
311W VAL* 3.2 14.6 - - + +
312W GLU* 3.0 32.3 + - - +
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Residues in contact with ILE 309 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W LEU* 4.1 29.6 - - + +
36W TYR* 4.3 11.7 - - + -
37W ARG* 3.3 52.3 - - + +
40W GLN* 5.9 0.9 - - + -
305W GLU* 3.4 13.0 - - + +
306W LEU* 2.9 32.5 + - + +
308W GLU* 1.3 76.7 - - + +
310W ASP* 1.3 65.3 + - - +
312W GLU* 3.0 16.7 + - - +
313W VAL* 3.0 17.5 + - + +
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Residues in contact with ASP 310 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36W TYR* 2.7 33.3 + - - -
40W GLN* 3.5 23.2 - - - +
44W ARG* 6.0 0.2 - - - +
292W LYS* 5.1 4.9 - - - -
306W LEU 3.0 16.5 + - - +
307W LYS* 3.4 26.2 - - + +
308W GLU 3.2 0.2 - - - -
309W ILE* 1.3 76.6 - - - +
311W VAL* 1.3 53.3 + - - +
312W GLU 3.2 0.5 + - - -
313W VAL* 3.2 3.5 + - - +
314W ARG* 2.8 39.7 + - - +
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Residues in contact with VAL 311 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307W LYS* 3.3 34.3 + - - +
308W GLU* 3.2 17.0 - - + +
310W ASP* 1.3 77.1 - - - +
312W GLU* 1.3 67.1 + - + +
314W ARG* 3.3 9.1 + - - +
315W LYS* 3.2 24.9 + - - +
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Residues in contact with GLU 312 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ARG* 3.8 30.2 + - - +
308W GLU* 3.0 24.9 + - + +
309W ILE* 3.0 11.8 + - - +
311W VAL* 1.3 78.7 - - + +
313W VAL* 1.3 58.5 + - - +
315W LYS* 3.1 11.4 + - - +
316W GLU* 3.1 23.4 + - - +
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Residues in contact with VAL 313 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ARG* 4.2 25.4 - - + +
40W GLN* 3.8 19.1 - - + +
41W THR* 3.5 42.8 - - - +
44W ARG* 3.8 17.7 - - + -
309W ILE* 3.0 15.5 + - + +
310W ASP 3.8 5.6 - - - +
312W GLU* 1.3 70.9 - - - +
314W ARG* 1.3 68.6 + - - +
315W LYS 2.9 1.8 - - - -
316W GLU* 2.9 31.1 + - + +
317W ILE* 3.0 10.7 + - + +
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Residues in contact with ARG 314 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44W ARG* 3.1 41.6 - - - +
310W ASP* 2.8 25.3 + - - +
311W VAL* 3.4 11.2 - - - +
312W GLU 3.3 0.2 - - - -
313W VAL* 1.3 73.9 - - - +
315W LYS* 1.3 62.3 + - - +
317W ILE* 3.7 5.9 + - - +
318W GLU* 3.1 44.7 + - + +
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Residues in contact with LYS 315 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311W VAL* 3.2 15.0 + - - +
312W GLU* 3.1 13.8 + - - +
313W VAL 2.9 1.2 + - - -
314W ARG* 1.3 75.0 - - - +
316W GLU* 1.3 69.1 + - - +
318W GLU* 3.2 7.1 + - + -
319W ASP* 3.0 31.5 + - + +
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Residues in contact with GLU 316 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ARG* 5.5 5.0 + - - +
41W THR* 4.2 18.5 + - + +
96W PHE* 5.1 4.7 - - - -
102W VAL* 4.3 23.3 - - + +
312W GLU 3.1 6.0 + - - +
313W VAL* 2.9 25.1 + - + +
315W LYS* 1.3 77.9 - - - +
317W ILE* 1.3 62.2 + - + +
319W ASP* 3.5 5.8 + - - +
320W ALA* 3.1 26.2 + - - +
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Residues in contact with ILE 317 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41W THR* 4.1 8.1 - - + +
44W ARG* 3.6 35.7 - - + +
45W MET* 3.8 22.9 - - + +
48W LYS* 3.7 32.1 - - + -
102W VAL* 3.8 27.1 - - + -
106W LEU* 4.5 1.9 - - + +
313W VAL* 3.0 16.7 + - + +
314W ARG* 3.9 5.2 - - - +
316W GLU* 1.3 77.9 - - + +
318W GLU* 1.3 62.8 + - - +
319W ASP 3.1 2.0 - - - -
320W ALA* 3.0 6.1 + - - +
321W ALA* 2.7 33.4 + - - +
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Residues in contact with GLU 318 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48W LYS* 3.2 31.8 + - - -
314W ARG* 3.1 39.2 + - + +
315W LYS* 3.8 10.3 - - + +
317W ILE* 1.3 80.7 - - - +
319W ASP* 1.3 57.0 + - - +
321W ALA* 3.6 4.1 + - - +
322W GLN* 3.1 49.1 + - - +
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Residues in contact with ASP 319 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103W ARG* 3.5 28.7 + - - -
315W LYS* 3.0 25.0 + - + +
316W GLU* 3.7 5.2 - - - +
318W GLU* 1.3 75.6 - - - +
320W ALA* 1.3 69.2 + - - +
322W GLN* 3.3 11.6 + - - +
323W PHE* 2.9 22.5 + - - +
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Residues in contact with ALA 320 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102W VAL* 3.7 33.2 - - + +
103W ARG* 4.0 17.5 - - + +
106W LEU* 4.0 7.6 - - + -
316W GLU 3.1 11.9 + - - +
317W ILE 3.0 6.7 + - - +
319W ASP* 1.3 84.0 + - - +
321W ALA* 1.3 51.7 + - - +
323W PHE* 3.0 7.3 + - - +
324W ALA* 2.7 35.4 + - - +
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Residues in contact with ALA 321 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48W LYS* 3.7 37.9 - - + -
52W LEU* 4.5 7.9 - - + -
106W LEU* 3.7 10.7 - - + +
317W ILE 2.7 20.2 + - - +
318W GLU* 4.0 4.0 - - - +
320W ALA* 1.3 70.8 - - - +
322W GLN* 1.3 61.6 + - - +
324W ALA* 3.8 3.3 - - - -
325W THR* 2.9 32.2 + - - +
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Residues in contact with GLN 322 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318W GLU* 3.1 45.7 + - - +
319W ASP* 3.8 8.4 - - - +
320W ALA 3.3 0.2 - - - -
321W ALA* 1.3 76.3 - - - +
323W PHE* 1.3 58.2 + - - +
325W THR* 3.1 8.2 + - - -
326W ALA* 2.9 32.7 + - - +
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Residues in contact with PHE 323 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103W ARG* 3.4 73.8 - - + +
107W ALA* 3.9 12.1 - - + -
114W GLY* 4.4 15.0 - - - -
319W ASP* 2.9 14.2 + - - +
320W ALA* 3.1 10.3 - - - +
322W GLN* 1.3 78.2 - - - +
324W ALA* 1.3 64.9 + - - +
326W ALA* 4.1 3.9 - - + +
327W ASP* 3.1 49.7 + - + +
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Residues in contact with ALA 324 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52W LEU* 6.0 1.3 - - + -
106W LEU* 3.6 17.3 - - + +
107W ALA* 3.5 33.4 - - + +
110W THR* 2.8 26.7 + - + +
112W ARG* 3.4 14.2 + - - +
320W ALA 2.7 18.3 + - - +
321W ALA* 4.0 5.8 - - - +
323W PHE* 1.3 78.4 - - + +
325W THR* 1.3 59.0 + - + +
327W ASP* 4.9 0.7 - - - -
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Residues in contact with THR 325 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52W LEU* 4.1 26.0 - - + -
57W ILE* 4.1 18.2 - - + -
110W THR* 4.5 3.1 - - + -
112W ARG* 2.8 24.2 + - - +
321W ALA 2.9 19.3 + - - +
322W GLN* 3.1 10.4 + - - -
323W PHE 3.1 0.2 - - - -
324W ALA* 1.3 82.3 - - + +
326W ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 326 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322W GLN 2.9 17.4 + - - +
323W PHE* 3.4 4.0 + - - +
325W THR* 1.3 76.7 + - - +
327W ASP* 1.3 66.5 + - - +
328W PRO* 3.7 2.1 - - - +
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Residues in contact with ASP 327 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W ARG* 2.8 39.8 + - + -
113W LYS* 3.7 13.5 + - - +
114W GLY* 3.0 30.9 + - - +
323W PHE* 3.1 39.0 + - + +
324W ALA* 4.9 0.7 - - - -
325W THR 3.4 1.2 - - - -
326W ALA* 1.3 79.3 - - - +
328W PRO* 1.4 83.9 - - - +
329W GLU 3.9 0.3 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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