Contacts of the helix formed by residues 302 - 327 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S PHE* 3.4 18.6 - - - -
296S VAL* 4.2 2.0 - - - -
301S ALA* 1.4 73.2 - - - +
303S VAL* 1.3 66.5 + - - +
304S GLU* 3.9 14.2 + - - +
305S GLU* 2.8 40.1 + - - +
306S LEU* 2.8 21.8 + - - +
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Residues in contact with VAL 303 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292S LYS* 3.5 29.8 - - - +
296S VAL* 3.8 20.5 - - + +
302S SER* 1.3 71.9 - - - +
304S GLU* 1.3 82.2 + - + +
306S LEU* 3.2 5.2 + - - +
307S LYS* 2.6 42.8 + - + +
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Residues in contact with GLU 304 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302S SER* 3.2 12.0 + - - +
303S VAL* 1.3 98.7 - - + +
305S GLU* 1.3 65.9 + - - +
307S LYS* 3.3 10.6 - - + +
308S GLU* 2.8 36.2 + - - +
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Residues in contact with GLU 305 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S PHE* 3.1 21.5 - - + -
29S ARG* 3.3 24.3 + - - -
33S LEU* 5.1 7.5 - - + +
301S ALA* 3.1 14.7 - - + +
302S SER* 2.8 46.4 + - - +
304S GLU* 1.3 75.8 - - - +
306S LEU* 1.3 63.2 + - + +
308S GLU* 2.9 27.4 + - - +
309S ILE* 3.2 16.7 + - + +
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Residues in contact with LEU 306 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU* 4.4 14.8 - - + -
36S TYR* 3.7 42.1 - - + +
292S LYS* 3.6 44.9 - - + +
295S MET* 4.5 16.2 - - + -
296S VAL* 5.0 7.0 - - + -
301S ALA* 4.4 16.6 - - + -
302S SER 2.8 14.6 + - - +
303S VAL* 3.7 7.4 - - - +
305S GLU* 1.3 72.5 - - - +
307S LYS* 1.3 58.1 + - - +
308S GLU 2.9 10.6 + - - -
309S ILE* 3.3 4.8 + - + +
310S ASP* 3.0 28.9 + - - +
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Residues in contact with LYS 307 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292S LYS* 5.7 6.4 - - - +
303S VAL* 2.6 25.8 + - + +
304S GLU* 3.3 18.4 - - - +
306S LEU* 1.3 72.7 - - - +
308S GLU* 1.3 56.9 + - + -
310S ASP* 3.4 37.4 + - - +
311S VAL* 3.0 32.4 + - + +
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Residues in contact with GLU 308 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304S GLU* 2.8 27.7 - - - +
305S GLU* 2.9 15.1 + - - +
307S LYS* 1.3 79.7 - - + +
309S ILE* 1.3 61.8 + - + +
310S ASP 3.2 0.7 - - - -
311S VAL* 3.4 10.1 + - + +
312S GLU* 3.0 35.2 + - + +
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Residues in contact with ILE 309 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU* 4.2 39.5 - - + +
36S TYR* 4.4 14.6 - - + -
37S ARG* 2.9 65.1 - - + +
40S GLN* 6.0 1.1 - - + -
305S GLU* 3.2 14.0 + - + +
306S LEU* 3.3 5.8 + - + +
308S GLU* 1.3 74.4 - - + +
310S ASP* 1.3 66.2 + - - +
312S GLU* 4.1 4.7 - - - +
313S VAL* 2.9 28.2 + - + +
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Residues in contact with ASP 310 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S TYR* 2.2 35.2 + - - -
40S GLN* 3.9 22.3 - - - +
44S ARG* 5.9 0.3 - - - +
292S LYS* 5.2 4.2 - - - -
306S LEU* 3.0 25.9 + - - +
307S LYS* 3.4 38.7 + - - +
309S ILE* 1.3 77.0 - - - +
311S VAL* 1.3 61.3 + - + +
313S VAL* 4.0 3.5 - - - +
314S ARG* 3.1 22.7 + - - +
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Residues in contact with VAL 311 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307S LYS* 3.0 24.5 - - + +
308S GLU* 3.4 11.6 + - + +
309S ILE 3.2 0.6 - - - -
310S ASP* 1.3 73.5 - - + +
312S GLU* 1.3 67.0 + - + +
314S ARG* 3.3 8.9 + - + +
315S LYS* 3.3 24.6 + - - +
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Residues in contact with GLU 312 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 2.8 36.5 + - - +
308S GLU* 3.0 26.9 + - + +
309S ILE* 3.2 6.0 + - - +
311S VAL* 1.3 73.2 - - + +
313S VAL* 1.3 66.2 + - - +
315S LYS* 3.3 10.7 + - - +
316S GLU* 3.2 17.3 + - - +
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Residues in contact with VAL 313 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ARG* 3.9 20.6 - - - +
40S GLN* 4.2 7.0 - - + +
41S THR* 3.2 39.3 - - + +
44S ARG* 3.5 30.1 - - + -
309S ILE* 2.9 20.6 + - + +
310S ASP* 4.0 3.8 - - - +
312S GLU* 1.3 73.1 - - - +
314S ARG* 1.3 59.7 + - - +
315S LYS 2.9 1.8 - - - -
316S GLU* 2.7 30.1 + - + +
317S ILE* 2.9 18.5 + - + +
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Residues in contact with ARG 314 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S ARG* 4.0 43.1 - - - +
48S LYS* 6.0 3.4 - - - +
310S ASP 3.1 15.5 + - - +
311S VAL* 3.3 12.7 + - + +
313S VAL* 1.3 78.1 - - - +
315S LYS* 1.3 56.4 + - - +
317S ILE* 3.7 8.5 + - - +
318S GLU* 3.0 41.5 + - + +
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Residues in contact with LYS 315 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311S VAL* 3.3 13.9 + - - +
312S GLU* 3.4 13.4 - - - +
313S VAL 2.9 0.4 - - - -
314S ARG* 1.3 77.1 - - - +
316S GLU* 1.3 59.8 + - - +
318S GLU* 3.3 6.1 + - + +
319S ASP* 2.9 55.1 + - - +
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Residues in contact with GLU 316 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S THR* 5.8 4.5 - - + -
102S VAL* 5.2 13.1 - - + +
103S ARG* 5.9 2.1 + - - -
312S GLU 3.2 8.4 + - - +
313S VAL* 2.7 21.1 + - + +
315S LYS* 1.3 75.7 - - - +
317S ILE* 1.3 66.5 + - + +
319S ASP* 3.4 11.6 + - - +
320S ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 317 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S THR* 4.1 11.7 - - + +
44S ARG* 3.5 38.4 - - + +
45S MET* 3.9 19.3 - - + +
48S LYS* 3.7 30.3 - - + -
102S VAL* 3.8 29.6 - - + -
106S LEU* 4.8 1.5 - - + +
313S VAL* 2.9 18.5 + - + +
314S ARG* 3.9 12.1 - - - +
316S GLU* 1.3 77.4 - - + +
318S GLU* 1.3 63.0 + - - +
320S ALA* 3.1 3.9 + - - +
321S ALA* 2.7 28.8 + - - +
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Residues in contact with GLU 318 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S LYS* 3.2 31.8 + - - -
314S ARG* 3.0 30.4 + - + +
315S LYS* 3.8 7.2 - - + +
317S ILE* 1.3 79.8 - - - +
319S ASP* 1.3 57.2 + - - +
321S ALA* 3.8 5.6 - - - +
322S GLN* 3.0 32.9 + - - +
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Residues in contact with ASP 319 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S ARG* 4.4 11.9 + - - +
315S LYS* 2.9 47.5 + - - +
316S GLU* 3.8 14.3 - - - +
318S GLU* 1.3 78.4 - - - +
320S ALA* 1.3 57.9 + - - +
322S GLN* 3.2 28.1 + - - +
323S PHE* 3.3 9.5 + - - +
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Residues in contact with ALA 320 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S VAL* 4.1 14.4 - - + -
103S ARG* 3.7 45.0 - - + +
106S LEU* 4.3 5.4 - - + -
316S GLU* 3.0 18.0 + - + +
317S ILE 3.7 2.5 - - - +
319S ASP* 1.3 73.1 - - - +
321S ALA* 1.3 66.0 + - - +
322S GLN 2.9 1.6 - - - -
323S PHE* 2.8 2.4 + - - +
324S ALA* 2.7 27.3 + - - +
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Residues in contact with ALA 321 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S LYS* 3.7 40.2 - - + +
52S LEU* 5.2 7.9 - - + +
106S LEU* 3.8 11.9 - - - +
317S ILE 2.7 19.9 + - - +
318S GLU* 3.8 9.2 - - - +
320S ALA* 1.3 71.5 - - - +
322S GLN* 1.3 59.9 + - - +
324S ALA* 3.6 2.7 + - - +
325S THR* 3.1 32.4 + - - +
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Residues in contact with GLN 322 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S ARG* 5.9 1.8 - - - +
318S GLU* 3.0 18.2 + - - +
319S ASP* 3.2 27.0 + - - +
320S ALA 2.9 0.8 - - - -
321S ALA* 1.3 78.0 - - - +
323S PHE* 1.3 63.2 + - - +
325S THR* 3.4 5.9 + - - -
326S ALA* 3.0 38.8 + - - +
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Residues in contact with PHE 323 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S ARG* 3.5 57.4 - - + +
107S ALA* 3.9 14.1 - - + -
114S GLY* 3.8 35.2 - - - -
319S ASP 3.3 9.8 + - - +
320S ALA 2.8 10.2 + - - +
322S GLN* 1.3 82.9 - - - +
324S ALA* 1.3 67.1 + - - +
326S ALA* 4.0 2.8 - - - +
327S ASP* 3.1 46.0 + - + +
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Residues in contact with ALA 324 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S LEU* 5.2 1.3 - - + -
103S ARG 4.8 0.7 - - - +
106S LEU* 3.7 15.3 - - + -
107S ALA* 3.5 34.8 - - + +
110S THR* 2.6 33.6 + - + +
112S ARG* 3.5 10.2 + - - +
320S ALA 2.7 18.9 + - - +
321S ALA* 3.9 6.1 - - - +
323S PHE* 1.3 78.0 - - - +
325S THR* 1.3 58.2 + - - +
327S ASP* 4.6 0.9 - - - -
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Residues in contact with THR 325 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S LEU* 4.3 21.5 - - + -
57S ILE* 3.9 26.5 - - + -
112S ARG* 3.1 21.0 + - - +
321S ALA 3.1 18.7 + - - +
322S GLN* 3.5 6.6 + - - -
323S PHE 3.2 0.2 - - - -
324S ALA* 1.3 79.4 - - - +
326S ALA* 1.3 62.6 + - - +
327S ASP 3.3 2.0 - - - -
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Residues in contact with ALA 326 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322S GLN* 3.0 28.3 + - - +
323S PHE* 3.3 4.9 + - - +
325S THR* 1.3 77.4 - - - +
327S ASP* 1.3 63.2 + - - +
328S PRO* 3.6 6.1 - - - +
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Residues in contact with ASP 327 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107S ALA* 5.7 0.4 - - + -
112S ARG* 2.5 38.0 + - + +
113S LYS* 3.4 12.6 + - - +
114S GLY* 2.6 39.9 + - - -
323S PHE* 3.1 34.1 + - + +
324S ALA* 5.0 0.7 - - - -
325S THR 3.3 1.4 - - - -
326S ALA* 1.3 76.9 - - - +
328S PRO* 1.3 83.6 - - - +
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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