Contacts of the helix formed by residues 302 - 327 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K PHE* 3.2 16.8 - - - -
296K VAL* 4.8 1.3 - - - -
301K ALA* 1.3 72.8 - - - +
303K VAL* 1.3 65.1 + - - +
304K GLU* 3.3 24.6 + - - +
305K GLU* 2.8 49.6 + - - +
306K LEU* 3.2 8.8 + - - +
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Residues in contact with VAL 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292K LYS* 4.6 21.3 - - - +
296K VAL* 4.3 21.4 - - + +
301K ALA 4.0 1.2 + - - -
302K SER* 1.3 72.1 - - - +
304K GLU* 1.3 89.7 + - + +
306K LEU* 4.2 5.6 - - + +
307K LYS* 3.2 28.4 + - + +
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Residues in contact with GLU 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302K SER* 3.0 20.5 + - - +
303K VAL* 1.3 99.3 + - + +
305K GLU* 1.3 64.2 + - - +
307K LYS* 3.9 7.3 + - - +
308K GLU* 3.1 31.4 + - - +
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Residues in contact with GLU 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K PHE* 3.1 18.6 - - + -
29K ARG* 3.4 20.1 + - - -
33K LEU* 4.4 10.9 - - + +
301K ALA* 3.1 18.4 - - + +
302K SER* 2.8 42.8 + - - +
304K GLU* 1.3 74.5 - - - +
306K LEU* 1.3 62.2 + - + +
308K GLU* 2.9 32.7 + - - +
309K ILE* 3.1 12.6 + - + +
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Residues in contact with LEU 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 4.4 13.5 - - + -
36K TYR* 3.7 40.3 - - + +
292K LYS* 3.6 42.2 - - + +
295K MET* 4.7 9.6 - - + -
296K VAL* 4.5 11.2 - - + -
301K ALA* 4.2 18.8 - - + -
302K SER 3.2 13.5 + - - +
303K VAL* 4.2 3.8 - - + +
305K GLU* 1.3 75.8 - - + +
307K LYS* 1.3 53.5 + - - +
308K GLU 2.8 14.3 + - - -
309K ILE* 2.9 10.9 + - + +
310K ASP* 2.8 30.5 + - - +
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Residues in contact with LYS 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K VAL* 3.2 21.5 + - + +
304K GLU* 4.0 8.5 - - - +
305K GLU 3.3 0.2 - - - -
306K LEU* 1.3 77.7 - - - +
308K GLU* 1.3 57.5 + - + +
310K ASP* 3.4 22.8 + - + +
311K VAL* 3.3 24.5 - - + +
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Residues in contact with GLU 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304K GLU* 3.1 22.2 - - - +
305K GLU* 2.9 14.5 + - - +
306K LEU 2.8 1.8 + - - -
307K LYS* 1.3 79.8 - - + +
309K ILE* 1.3 62.3 + - + +
310K ASP 3.1 1.1 - - - -
311K VAL* 3.2 16.8 + - + +
312K GLU* 3.2 20.2 + - - +
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Residues in contact with ILE 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 4.1 40.8 - - + +
36K TYR* 4.5 11.0 - - + -
37K ARG* 3.5 56.1 - - + +
40K GLN* 5.4 0.9 - - + -
305K GLU* 3.1 13.4 + - + +
306K LEU* 2.9 17.5 + - + +
308K GLU* 1.3 75.0 - - - +
310K ASP* 1.3 62.8 + - - +
312K GLU* 3.1 5.1 + - - +
313K VAL* 3.0 27.0 + - + +
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Residues in contact with ASP 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K TYR* 3.0 25.8 + - - -
40K GLN* 3.4 28.7 - - - +
44K ARG* 5.9 0.2 - - - -
306K LEU 2.8 11.6 + - - -
307K LYS* 3.4 32.1 + - + +
309K ILE* 1.3 77.4 - - - +
311K VAL* 1.3 61.7 + - + +
313K VAL* 3.7 3.6 + - - +
314K ARG* 3.1 25.6 + - - +
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Residues in contact with VAL 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K LYS* 3.3 27.4 - - - +
308K GLU* 3.2 10.9 + - + +
310K ASP* 1.3 76.7 - - + +
312K GLU* 1.3 66.0 + - - +
314K ARG* 3.3 13.4 - - + +
315K LYS* 3.3 31.9 + - - +
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Residues in contact with GLU 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ARG* 3.4 30.5 + - - +
308K GLU* 3.2 14.5 + - - +
309K ILE* 3.1 9.2 + - - +
311K VAL* 1.3 75.5 - - - +
313K VAL* 1.3 60.1 + - - +
315K LYS* 3.0 10.0 + - - +
316K GLU* 2.8 28.2 + - - +
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Residues in contact with VAL 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ARG* 4.1 16.8 - - - +
40K GLN* 4.2 14.6 - - + +
41K THR* 3.7 37.0 - - + +
44K ARG* 3.4 36.1 - - + -
309K ILE* 3.0 21.6 + - + +
310K ASP* 3.9 5.4 - - - +
312K GLU* 1.3 74.7 - - - +
314K ARG* 1.3 65.7 + - - +
316K GLU* 3.0 10.8 + - + +
317K ILE* 2.8 24.8 + - + +
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Residues in contact with ARG 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K ARG* 2.9 45.8 - - - +
310K ASP 3.1 15.3 + - - +
311K VAL* 3.3 21.9 - - + +
313K VAL* 1.3 78.5 - - - +
315K LYS* 1.3 57.1 + - - +
317K ILE* 3.4 8.2 + - - +
318K GLU* 3.0 28.8 + - - +
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Residues in contact with LYS 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311K VAL* 3.3 20.3 + - - +
312K GLU* 3.0 12.0 + - - +
314K ARG* 1.3 75.1 - - - +
316K GLU* 1.3 68.1 + - - +
318K GLU* 3.1 9.0 + - + -
319K ASP* 2.9 45.4 + - - +
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Residues in contact with GLU 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ARG* 6.3 1.8 - - - +
41K THR* 5.2 11.9 - - + -
102K VAL* 5.0 9.7 - - + +
312K GLU 2.8 15.2 + - - +
313K VAL* 3.1 16.4 - - + +
315K LYS* 1.3 72.5 - - - +
317K ILE* 1.3 63.3 + - + +
319K ASP* 3.8 6.0 + - - +
320K ALA* 3.3 22.0 + - - +
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Residues in contact with ILE 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K THR* 4.0 10.5 - - + +
44K ARG* 3.5 29.8 - - + +
45K MET* 3.7 26.0 - - + +
48K LYS* 3.8 40.2 - - + -
102K VAL* 3.8 24.5 - - + -
106K LEU* 4.9 1.5 - - + +
313K VAL* 2.8 18.3 + - + +
314K ARG* 3.6 9.2 - - - +
316K GLU* 1.3 69.9 - - - +
318K GLU* 1.3 56.7 - - - +
320K ALA* 2.9 7.3 + - - +
321K ALA* 2.7 32.1 + - - +
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Residues in contact with GLU 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K LYS* 3.2 27.2 + - - -
314K ARG* 3.0 17.0 + - + +
315K LYS* 3.1 9.8 + - + +
317K ILE* 1.3 76.9 - - - +
319K ASP* 1.3 61.4 + - - +
321K ALA* 4.5 4.3 - - - +
322K GLN* 3.2 30.5 + - - +
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Residues in contact with ASP 319 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 4.3 11.4 + - - +
315K LYS* 2.9 46.7 + - - +
316K GLU* 4.2 5.6 - - - +
318K GLU* 1.3 77.2 - - - +
320K ALA* 1.3 58.4 + - - +
322K GLN* 3.2 14.1 - - + +
323K PHE* 3.2 23.9 + - - +
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Residues in contact with ALA 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K VAL* 3.6 28.3 - - + +
103K ARG* 4.0 28.5 - - + +
106K LEU* 4.4 4.2 - - + +
316K GLU 3.3 13.0 + - - +
317K ILE 2.9 10.3 + - - +
319K ASP* 1.3 76.6 - - - +
321K ALA* 1.3 64.9 + - - +
322K GLN 3.1 1.6 - - - -
323K PHE* 3.0 6.2 + - - +
324K ALA* 2.9 22.5 + - - +
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Residues in contact with ALA 321 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K LYS* 3.7 40.4 - - + +
52K LEU* 5.0 7.2 - - + -
106K LEU* 4.2 9.3 - - - +
317K ILE 2.7 18.1 + - - +
318K GLU* 4.2 7.4 - - - +
320K ALA* 1.3 72.5 - - - +
322K GLN* 1.3 52.8 + - - +
324K ALA* 3.2 4.5 + - - +
325K THR* 2.8 41.5 + - + +
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Residues in contact with GLN 322 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 5.8 1.8 - - - +
318K GLU* 3.2 19.9 + - - +
319K ASP* 3.2 20.4 - - + +
320K ALA 3.1 0.4 - - - -
321K ALA* 1.3 79.9 - - - +
323K PHE* 1.3 63.5 + - - +
325K THR* 3.7 6.2 + - - -
326K ALA* 2.9 46.6 + - - +
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Residues in contact with PHE 323 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 3.3 69.3 - - + +
104K GLU 4.9 0.2 - - - -
107K ALA* 3.9 11.2 - - + -
114K GLY* 3.8 24.5 - - - -
319K ASP 3.2 4.2 + - - +
320K ALA 3.0 8.4 + - - +
322K GLN* 1.3 90.6 - - + +
324K ALA* 1.3 58.4 + - - +
326K ALA* 5.0 0.4 - - - -
327K ASP* 2.8 66.2 + - + +
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Residues in contact with ALA 324 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K LEU* 5.5 1.1 - - + -
103K ARG 4.8 0.7 - - - +
106K LEU* 3.6 13.0 - - + -
107K ALA* 3.4 37.0 - - + +
110K THR* 3.2 17.2 + - + +
112K ARG* 3.0 31.0 + - - +
320K ALA 2.9 10.8 + - - +
321K ALA* 3.6 7.4 - - - +
323K PHE* 1.3 77.0 - - - +
325K THR* 1.3 60.1 + - + +
327K ASP 4.0 0.2 + - - -
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Residues in contact with THR 325 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K LEU* 3.8 28.7 - - + -
57K ILE* 4.4 17.0 - - + -
110K THR* 4.6 2.5 - - + -
112K ARG* 3.0 18.5 + - - +
321K ALA* 2.8 26.3 + - + +
322K GLN* 3.7 7.8 + - - -
324K ALA* 1.3 75.9 - - + +
326K ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 326 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322K GLN* 2.9 31.9 + - - +
323K PHE* 4.4 0.9 - - - +
325K THR* 1.3 77.7 - - - +
327K ASP* 1.3 64.9 + - - +
328K PRO* 3.6 6.1 - - - +
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Residues in contact with ASP 327 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K ALA* 5.7 0.2 - - + -
112K ARG* 3.0 39.8 + - + -
113K LYS* 3.9 8.2 + - - +
114K GLY* 3.1 35.0 + - - -
323K PHE* 2.8 41.5 + - + +
324K ALA* 4.0 0.6 + - - -
325K THR 3.5 0.2 - - - -
326K ALA* 1.3 78.6 - - - +
328K PRO* 1.3 86.5 - - - +
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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