Contacts of the helix formed by residues 302 - 326 (chain A) in PDB entry 3EXF
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE* 4.0 17.8 - - - -
296A VAL* 4.4 3.1 - - - -
301A ALA* 1.3 75.8 - - - +
303A VAL* 1.3 56.6 + - - +
304A GLU* 2.6 35.1 + - - +
305A GLU* 2.7 36.5 + - - +
306A LEU* 3.3 12.7 + - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LYS* 4.6 16.3 + - + +
296A VAL* 4.0 24.5 - - + +
302A SER* 1.3 69.9 - - - +
304A GLU* 1.3 88.9 + - - +
306A LEU* 4.3 5.6 - - - +
307A LYS* 3.5 28.0 + - + +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A SER* 2.6 20.2 + - - +
303A VAL* 1.3 99.8 - - - +
305A GLU* 1.3 64.3 + - + +
307A LYS* 3.2 8.2 + - - +
308A GLU* 3.2 27.0 + - - +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 3.7 17.1 - - - -
29A ARG* 2.8 41.9 + - - -
33A LEU* 4.4 6.9 - - + +
301A ALA* 4.3 7.3 - - + +
302A SER* 2.7 30.2 + - - +
304A GLU* 1.3 73.9 - - + +
306A LEU* 1.3 63.8 + - + +
308A GLU* 3.3 10.2 + - - +
309A ILE* 3.1 31.5 + - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.2 25.6 - - + -
36A TYR* 3.5 44.4 + - + +
292A LYS* 3.3 44.4 - - + +
295A MET* 5.0 9.2 - - + -
296A VAL* 4.6 13.0 - - + -
301A ALA* 4.2 11.0 - - + -
302A SER 3.3 10.8 + - - +
303A VAL* 4.7 3.1 - - - +
305A GLU* 1.3 76.9 - - - +
307A LYS* 1.3 59.6 - - - +
308A GLU 3.3 0.2 - - - -
309A ILE* 3.4 7.8 + - + +
310A ASP* 2.9 27.7 + - - +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LYS* 3.7 24.0 - - - +
303A VAL* 3.5 18.0 + - + +
304A GLU* 3.3 12.1 - - - +
305A GLU 3.1 0.2 - - - -
306A LEU* 1.3 76.0 - - - +
308A GLU* 1.3 61.5 + - - +
309A ILE 3.1 1.6 - - - -
310A ASP* 3.2 25.3 + - - +
311A VAL* 3.0 32.0 + - - +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLU* 3.2 14.1 + - - +
305A GLU* 3.3 14.4 - - - +
307A LYS* 1.3 82.0 - - - +
309A ILE* 1.3 58.8 + - + +
311A VAL* 3.3 11.0 - - + +
312A GLU* 2.9 44.6 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.6 31.0 - - + +
36A TYR* 4.3 14.8 - - + -
37A ARG* 3.6 50.3 - - + +
305A GLU* 3.1 18.8 + - + +
306A LEU* 3.7 13.9 - - + +
307A LYS 3.1 0.4 - - - -
308A GLU* 1.3 77.3 - - + +
310A ASP* 1.3 69.8 + - - +
311A VAL 2.8 0.9 - - - -
312A GLU* 4.1 6.7 - - - +
313A VAL* 2.8 30.7 + - + +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.2 16.8 + - - -
40A GLN* 2.8 31.2 - - - +
44A ARG* 5.9 0.2 - - - +
292A LYS* 4.6 1.2 + - - -
306A LEU 2.9 15.3 + - - +
307A LYS* 3.2 42.7 + - + +
309A ILE* 1.3 75.7 - - - +
311A VAL* 1.3 53.2 + - + +
313A VAL* 3.2 7.0 + - - +
314A ARG* 2.6 38.9 + - - +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LYS 3.0 16.9 + - - +
308A GLU* 3.3 16.6 - - + +
309A ILE 2.8 1.6 - - - -
310A ASP* 1.3 76.0 - - + +
312A GLU* 1.3 68.4 + - + +
314A ARG* 3.1 10.5 + - + +
315A LYS* 3.0 40.3 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 2.8 35.4 + - - +
308A GLU* 2.9 41.9 + - - +
309A ILE* 3.1 4.2 + - - +
311A VAL* 1.3 75.3 - - + +
313A VAL* 1.3 57.2 + - - +
315A LYS* 3.1 14.2 - - + +
316A GLU* 3.0 32.8 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.1 24.5 - - - +
40A GLN* 3.5 29.4 - - + +
41A THR* 3.6 24.7 - - - +
44A ARG* 3.6 19.7 - - + -
309A ILE* 2.8 25.8 + - + +
310A ASP* 3.3 4.7 - - - +
312A GLU* 1.3 72.9 - - - +
314A ARG* 1.3 68.0 + - - +
315A LYS 2.9 2.3 + - - -
316A GLU* 3.0 17.4 + - + -
317A ILE* 3.0 15.4 + - + +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.4 39.2 - - - +
310A ASP* 2.6 18.4 + - - +
311A VAL* 3.2 16.4 - - + +
313A VAL* 1.3 74.2 - - - +
315A LYS* 1.3 58.4 + - - +
317A ILE* 3.6 6.5 + - - +
318A GLU* 3.0 27.5 + - - +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A VAL* 3.0 31.9 + - + +
312A GLU* 3.1 17.9 - - + +
313A VAL 2.9 0.8 + - - -
314A ARG* 1.3 75.2 - - - +
316A GLU* 1.4 67.4 + - - +
317A ILE 3.0 2.1 + - - -
318A GLU* 3.0 14.0 + - + +
319A ASP* 2.7 30.3 + - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.5 21.5 + - - +
41A THR* 5.1 5.8 - - + +
102A VAL* 5.4 7.0 - - + -
103A ARG* 4.3 4.9 + - - +
312A GLU* 3.0 24.2 + - - +
313A VAL* 3.0 18.8 + - + +
315A LYS* 1.4 73.0 - - - +
317A ILE* 1.3 71.6 + - + +
319A ASP* 3.5 6.9 + - - +
320A ALA* 3.0 25.7 + - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 4.2 17.0 - - + +
44A ARG* 3.5 33.2 - - + +
45A MET* 4.4 2.2 - - - +
48A LYS* 3.6 42.2 - - + -
102A VAL* 4.0 31.0 - - + -
106A LEU* 4.9 2.7 - - + -
313A VAL* 3.0 18.9 + - + +
314A ARG* 4.0 5.6 - - - +
315A LYS 3.0 0.6 - - - -
316A GLU* 1.3 81.6 - - + +
318A GLU* 1.3 68.1 + - - +
320A ALA* 3.1 3.9 + - - +
321A ALA* 2.9 22.2 + - - +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.8 12.7 + - - +
314A ARG 3.0 18.1 + - - +
315A LYS* 3.0 6.6 + - + +
317A ILE* 1.3 75.5 - - - +
319A ASP* 1.3 65.3 + - - +
321A ALA* 3.2 13.8 + - - +
322A GLN* 2.8 44.7 + - + +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.0 30.0 + - - +
315A LYS* 2.7 34.2 + - - +
316A GLU* 4.0 4.1 + - - +
318A GLU* 1.3 82.0 - - - +
320A ALA* 1.3 52.7 + - - +
322A GLN* 3.5 11.6 - - + +
323A PHE* 2.7 37.2 + - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 3.8 20.2 - - + -
103A ARG* 3.5 41.3 - - - +
106A LEU* 3.8 6.1 - - + +
316A GLU 3.0 18.7 + - - +
317A ILE 3.6 3.1 - - - +
319A ASP* 1.3 73.9 - - - +
321A ALA* 1.3 65.8 + - - +
323A PHE* 3.4 2.8 + - - +
324A ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.7 30.5 - - + +
52A LEU* 4.6 9.9 - - + +
106A LEU* 3.8 8.5 - - - +
317A ILE 2.9 11.7 + - - +
318A GLU* 3.2 23.1 - - - +
320A ALA* 1.3 75.8 - - - +
322A GLN* 1.3 55.9 + - - +
324A ALA* 3.3 2.1 + - - +
325A THR* 2.4 36.9 + - - +
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Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU* 2.8 34.0 + - + +
319A ASP* 3.1 17.2 + - + +
321A ALA* 1.3 77.9 - - - +
323A PHE* 1.3 64.4 + - - +
325A THR* 3.5 5.6 + - - -
326A ALA* 3.5 26.2 + - - +
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.5 64.2 - - + +
107A ALA* 3.6 13.2 - - + -
114A GLY* 4.2 14.6 - - - -
319A ASP 2.7 19.8 + - - +
320A ALA 4.0 2.0 - - - +
321A ALA 3.3 0.2 - - - -
322A GLN* 1.3 77.8 - - + +
324A ALA* 1.3 62.7 + - + +
325A THR 3.4 0.2 - - - -
326A ALA* 4.1 3.1 - - - -
327A ASP* 3.4 40.7 + - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 6.2 1.1 - - + -
106A LEU* 3.6 7.2 - - + +
107A ALA* 3.4 36.6 - - + +
110A THR* 2.9 24.6 + - + +
112A ARG* 3.1 18.6 + - - +
320A ALA 3.0 17.2 + - - +
321A ALA* 3.8 2.2 - - - +
323A PHE* 1.3 82.0 - - + +
325A THR* 1.3 62.2 + - - +
326A ALA 3.4 0.7 - - - -
327A ASP* 4.1 3.6 - - - -
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.6 20.4 - - + +
55A GLN* 5.8 0.7 - - - +
57A ILE* 3.4 40.6 - - + +
110A THR* 4.9 0.4 - - + -
112A ARG* 3.0 23.2 + - - +
321A ALA 2.4 31.9 + - - +
322A GLN* 3.5 8.5 + - - -
323A PHE 3.4 0.2 - - - -
324A ALA* 1.3 78.4 - - - +
326A ALA* 1.3 56.6 + - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A GLN* 3.5 22.3 + - - +
323A PHE* 4.2 2.7 - - - +
324A ALA 3.4 0.2 - - - -
325A THR* 1.3 80.3 - - - +
327A ASP* 1.3 60.3 + - - +
328A PRO* 3.9 5.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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