Contacts of the helix formed by residues 302 - 327 (chain G) in PDB entry 3EXH
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G PHE* 3.4 17.7 - - - -
296G VAL* 4.3 4.9 - - - -
301G ALA* 1.3 75.8 - - - +
303G VAL* 1.3 65.0 + - - +
304G GLU* 3.4 11.1 + - - +
305G GLU* 3.2 26.6 + - - +
306G LEU* 3.1 23.9 + - - +
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Residues in contact with VAL 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LYS* 5.5 9.4 - - + +
296G VAL* 3.7 32.3 - - + +
302G SER* 1.3 70.7 - - - +
304G GLU* 1.3 68.1 + - + +
306G LEU* 3.1 6.0 + - - +
307G LYS* 2.9 45.6 + - + +
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Residues in contact with GLU 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G SER* 3.2 10.1 + - - +
303G VAL* 1.3 77.9 - - + +
305G GLU* 1.3 58.8 + - - +
307G LYS* 3.0 11.7 + - - +
308G GLU* 2.9 46.2 + - - +
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Residues in contact with GLU 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G PHE* 3.7 13.3 - - - -
29G ARG* 2.4 38.7 + - - -
33G LEU* 4.3 12.7 - - + +
301G ALA* 3.3 16.7 - - + +
302G SER* 3.2 18.9 + - - +
304G GLU* 1.3 80.2 - - - +
306G LEU* 1.3 58.2 + - + +
308G GLU* 3.3 12.4 + - - +
309G ILE* 3.1 32.3 + - + +
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Residues in contact with LEU 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 4.2 18.8 - - + -
36G TYR* 3.9 33.7 - - + +
292G LYS* 3.7 50.0 - - + +
295G MET* 4.1 22.0 - - + -
296G VAL* 4.4 7.2 - - + -
301G ALA* 4.4 5.8 - - + -
302G SER 3.1 15.6 + - - +
303G VAL* 3.9 3.4 - - - +
305G GLU* 1.3 76.6 - - + +
307G LYS* 1.3 65.0 + - - +
308G GLU 3.2 0.2 - - - -
309G ILE* 3.2 7.6 + - + +
310G ASP* 3.2 28.5 + - - +
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Residues in contact with LYS 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LYS* 5.9 9.0 - - - +
303G VAL* 2.9 37.0 + - + +
304G GLU* 3.3 12.1 - - - +
306G LEU* 1.3 74.1 - - - +
308G GLU* 1.3 62.3 + - + +
310G ASP* 3.3 17.8 + - + +
311G VAL* 3.2 28.5 + - + +
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Residues in contact with GLU 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G GLU* 2.9 33.3 + - - +
305G GLU* 3.7 12.5 - - - +
306G LEU 3.2 0.4 - - - -
307G LYS* 1.3 74.6 - - + +
309G ILE* 1.3 67.4 + - + +
311G VAL* 4.0 8.3 - - + +
312G GLU* 3.2 35.1 + - - +
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Residues in contact with ILE 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 4.4 27.1 - - + +
36G TYR* 3.7 32.1 - - + -
37G ARG* 3.9 43.5 - - + +
40G GLN* 5.0 1.3 - - + -
305G GLU* 3.1 19.3 + - + +
306G LEU* 3.2 18.6 + - + +
308G GLU* 1.3 77.9 - - + +
310G ASP* 1.3 57.8 + - - +
312G GLU* 3.3 3.0 + - - +
313G VAL* 2.8 42.0 + - + +
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Residues in contact with ASP 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G TYR* 3.0 30.1 + - - -
40G GLN* 3.6 29.0 - - - +
44G ARG* 5.3 0.9 - - - +
306G LEU 3.2 12.9 + - - +
307G LYS* 3.3 20.3 + - + +
309G ILE* 1.3 72.0 - - - +
311G VAL* 1.3 63.7 + - + +
313G VAL* 3.5 1.0 + - - +
314G ARG* 2.8 33.6 + - - +
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Residues in contact with VAL 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G LYS* 3.2 18.7 + - + +
308G GLU* 3.5 8.0 + - + +
309G ILE 3.3 0.2 - - - -
310G ASP* 1.3 77.6 - - + +
312G GLU* 1.3 64.2 + - + +
314G ARG* 3.1 6.2 + - - +
315G LYS* 2.9 53.8 + - + +
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Residues in contact with GLU 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ARG* 2.6 37.5 + - - +
308G GLU* 3.2 28.8 + - - +
309G ILE* 3.6 5.0 - - - +
311G VAL* 1.3 80.7 - - + +
313G VAL* 1.3 63.1 + - - +
315G LYS* 3.4 9.5 + - + +
316G GLU* 3.0 29.4 + - - +
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Residues in contact with VAL 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ARG* 3.8 26.0 - - + +
40G GLN* 3.8 15.7 - - + +
41G THR* 3.7 40.8 - - - +
44G ARG* 3.8 13.2 - - + -
309G ILE* 2.8 35.9 + - + +
310G ASP 3.9 2.7 - - - +
312G GLU* 1.3 74.5 - - - +
314G ARG* 1.3 56.8 + - - +
316G GLU* 3.1 10.4 + - - +
317G ILE* 2.9 31.7 + - + +
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Residues in contact with ARG 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 3.2 56.6 - - + +
310G ASP 2.8 22.1 + - - +
311G VAL* 3.9 3.8 - - - +
313G VAL* 1.3 72.3 - - - +
315G LYS* 1.3 61.3 + - + +
317G ILE* 3.5 4.7 + - - +
318G GLU* 3.0 39.1 + - + +
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Residues in contact with LYS 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G VAL* 2.9 43.8 + - + +
312G GLU* 3.8 8.1 - - + +
314G ARG* 1.3 77.8 - - + +
316G GLU* 1.3 57.7 + - - +
318G GLU* 3.1 10.3 - - - +
319G ASP* 3.1 25.3 + - - +
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Residues in contact with GLU 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ARG* 4.0 19.6 + - - -
41G THR* 5.0 12.0 + - - +
102G VAL* 5.8 2.1 - - - +
312G GLU* 3.0 21.8 + - - +
313G VAL* 3.4 9.6 - - - +
315G LYS* 1.3 76.7 - - - +
317G ILE* 1.3 64.8 + - + +
319G ASP* 3.4 9.9 - - + +
320G ALA* 3.1 25.8 + - - +
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Residues in contact with ILE 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G THR* 4.0 26.5 - - + -
44G ARG* 3.9 13.7 - - + +
45G MET* 3.7 23.3 - - - +
48G LYS* 3.6 38.1 - - + -
102G VAL* 4.4 16.4 - - + -
106G LEU* 4.5 2.6 - - + +
313G VAL* 2.9 26.6 + - + +
314G ARG* 4.0 4.5 - - - +
316G GLU* 1.3 80.9 - - + +
318G GLU* 1.3 61.4 + - - +
320G ALA* 3.9 4.1 - - - +
321G ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G LYS* 3.1 34.3 + - - -
314G ARG* 3.0 25.1 + - + +
315G LYS* 3.1 17.3 - - - +
317G ILE* 1.3 80.1 - - - +
319G ASP* 1.3 54.1 + - - +
321G ALA* 3.6 3.2 + - - +
322G GLN* 3.2 28.4 + - - +
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Residues in contact with ASP 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ARG* 4.4 15.7 + - - +
315G LYS 3.1 11.6 + - - +
316G GLU* 3.4 13.7 - - + +
318G GLU* 1.3 73.0 - - - +
320G ALA* 1.3 67.8 + - - +
322G GLN* 3.3 12.0 + - - +
323G PHE* 3.0 22.7 + - - +
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Residues in contact with ALA 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G VAL* 3.8 29.8 - - + -
103G ARG* 4.0 29.7 - - + +
106G LEU* 4.0 6.0 - - + +
316G GLU 3.1 13.4 + - - +
317G ILE 3.4 3.6 + - - +
319G ASP* 1.3 80.1 - - - +
321G ALA* 1.3 58.2 + - - +
323G PHE* 3.3 5.8 + - - +
324G ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G LYS* 3.6 39.0 - - + +
52G LEU* 4.7 9.0 - - + -
106G LEU* 3.8 8.9 - - - +
317G ILE 2.9 19.4 + - - +
318G GLU 3.9 3.6 - - - +
320G ALA* 1.3 76.0 - - - +
322G GLN* 1.3 59.4 + - - +
324G ALA* 3.1 4.7 + - - +
325G THR* 2.8 35.4 + - + +
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Residues in contact with GLN 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G GLU 3.2 13.7 + - - +
319G ASP* 3.3 15.2 + - - +
320G ALA 3.2 0.2 - - - -
321G ALA* 1.3 77.8 - - - +
323G PHE* 1.3 67.9 + - - +
325G THR* 3.4 8.0 + - - -
326G ALA* 3.1 29.5 + - - +
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Residues in contact with PHE 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ARG* 3.2 69.8 - - + +
107G ALA* 3.7 23.1 - - + -
114G GLY* 4.4 12.1 - - - -
319G ASP 3.0 12.7 + - - +
320G ALA 3.5 7.9 - - - +
322G GLN* 1.3 77.1 - - - +
324G ALA* 1.3 63.4 + - - +
326G ALA* 3.3 2.9 + - - +
327G ASP* 2.9 59.5 + - + +
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Residues in contact with ALA 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 5.4 0.4 - - + -
106G LEU* 3.6 30.5 - - + +
107G ALA* 3.6 19.3 - - + +
110G THR* 3.0 24.6 + - + +
112G ARG* 3.5 13.3 + - - +
320G ALA 2.9 17.2 + - - +
321G ALA* 3.1 4.9 + - - +
323G PHE* 1.3 85.1 - - + +
325G THR* 1.3 62.0 + - + +
326G ALA 3.3 0.2 - - - -
327G ASP* 4.2 0.7 - - - -
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Residues in contact with THR 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 3.9 28.9 - - + -
55G GLN* 5.8 0.2 - - - +
57G ILE* 4.3 22.7 - - + -
112G ARG* 2.7 23.7 + - - +
321G ALA* 2.8 25.4 + - + +
322G GLN* 3.7 10.6 + - - +
323G PHE 3.3 0.2 - - - -
324G ALA* 1.3 75.1 - - - +
326G ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G ARG* 4.1 0.8 + - - -
322G GLN* 3.1 26.4 + - - +
323G PHE* 4.1 2.7 - - - +
325G THR* 1.3 79.8 - - - +
327G ASP* 1.3 65.1 + - - +
328G PRO* 3.3 9.2 - - - +
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Residues in contact with ASP 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ALA* 4.3 0.9 - - + +
112G ARG* 2.9 46.2 + - + +
113G LYS* 3.5 11.0 + - - +
114G GLY* 2.6 38.3 + - - -
323G PHE* 2.9 40.8 + - + +
324G ALA* 4.3 2.5 - - - +
325G THR 3.5 1.0 - - - -
326G ALA* 1.3 74.5 - - - +
328G PRO* 1.4 78.9 - - - +
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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