Contacts of the helix formed by residues 229 - 246 (chain I) 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 ASP 229 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ILE* 3.7 11.6 - - - +
10I LYS 4.5 1.4 + - - -
70I ALA* 4.2 1.3 - - - -
226I ASP* 3.5 17.2 + - - +
228I MET* 1.3 78.3 - - - +
230I ILE* 1.3 55.8 + - - +
231I LEU* 2.7 22.0 + - - -
232I CYS* 3.2 35.8 + - - -
233I VAL* 3.3 13.2 + - - +
290I LEU* 4.6 11.9 - - + +
294I ARG* 2.8 41.2 + - - -
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Residues in contact with ILE 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I TYR* 4.4 26.5 - - + -
39I MET* 4.1 17.7 - - + -
70I ALA* 3.9 19.1 - - + +
73I VAL* 3.9 18.8 - - + +
74I GLY* 3.3 37.7 - - - +
77I ALA* 5.5 0.4 - - + -
228I MET 3.1 5.0 + - - +
229I ASP* 1.3 73.2 + - - +
231I LEU* 1.3 64.0 + - + +
232I CYS 3.6 0.2 - - - -
233I VAL* 3.6 3.8 - - - +
234I ARG* 3.1 24.1 + - + +
287I PRO 4.5 5.6 - - - +
290I LEU* 6.0 1.1 - - + -
291I LEU* 4.1 33.4 - - + +
294I ARG* 5.5 1.3 - - - +
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Residues in contact with LEU 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I PHE* 3.7 33.4 - - + -
9I ILE* 3.7 12.0 - - + +
25I THR* 4.2 7.7 - - + +
27I LEU* 4.2 19.5 - - + -
35I TYR* 5.0 5.2 - - + -
229I ASP* 2.7 11.8 + - - +
230I ILE* 1.3 95.4 - - + +
232I CYS* 1.3 58.6 + - - -
234I ARG* 3.9 29.7 + - + +
235I GLU* 3.2 30.5 + - - +
291I LEU* 5.3 3.4 - - + -
294I ARG* 3.0 29.8 - - - +
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Residues in contact with CYS 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 4.0 16.6 - - + -
10I LYS 4.3 16.8 - - - +
12I CYS* 5.6 3.6 - - - -
225I VAL* 3.6 17.3 - - + -
226I ASP* 3.6 19.7 - - - +
229I ASP* 3.2 35.2 - - - -
231I LEU* 1.3 74.6 - - - +
233I VAL* 1.3 60.0 + - - +
235I GLU* 4.0 7.0 - - + -
236I ALA* 2.5 36.7 + - + +
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Residues in contact with VAL 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I ALA* 3.4 26.7 - - + +
71I CYS* 4.0 3.8 - - - +
74I GLY 3.5 10.3 - - - -
75I LEU* 3.5 28.0 - - + +
225I VAL* 4.5 7.9 - - + -
226I ASP 4.0 1.6 - - - +
227I GLY* 4.0 26.9 - - - -
229I ASP 3.4 13.9 - - - +
230I ILE 3.6 7.9 - - - +
232I CYS* 1.3 77.3 - - - +
234I ARG* 1.3 57.0 + - - +
236I ALA* 4.1 1.6 - - - +
237I THR* 2.8 34.8 + - - -
253I MET* 5.2 0.2 - - - +
255I LEU* 4.8 9.2 - - + -
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Residues in contact with ARG 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I THR* 2.8 29.7 + - - +
26I VAL 3.1 21.6 + - - -
27I LEU* 4.4 6.3 - - - +
31I ASP* 4.4 10.9 + - - -
35I TYR* 3.4 37.1 + - - -
74I GLY* 3.3 13.2 + - - +
77I ALA* 3.4 20.4 - - + +
230I ILE* 3.1 16.1 + - + +
231I LEU* 4.0 22.7 + - + +
232I CYS 3.3 0.2 - - - -
233I VAL* 1.3 79.8 - - - +
235I GLU* 1.3 61.0 + - - +
237I THR* 3.7 1.5 - - - -
238I ARG* 2.9 71.5 + - - +
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Residues in contact with GLU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 3.6 22.9 - - + -
21I PRO* 4.3 6.6 - - + +
22I PRO* 3.3 30.1 - - - +
24I THR 4.6 0.2 - - - +
25I THR* 3.3 26.0 + - - +
231I LEU 3.2 21.2 + - - +
232I CYS* 3.0 7.3 + - - +
234I ARG* 1.3 75.9 + - - +
236I ALA* 1.3 61.2 + - - +
238I ARG* 3.2 29.8 + - - +
239I PHE* 2.9 29.6 + - - +
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Residues in contact with ALA 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I CYS* 4.7 1.3 - - - -
21I PRO* 4.2 9.7 - - + +
223I LEU* 4.0 11.4 - - + +
225I VAL* 3.5 32.8 - - + -
232I CYS* 2.5 20.0 + - - +
233I VAL* 4.1 2.2 - - - +
235I GLU* 1.3 69.0 - - - +
237I THR* 1.3 65.5 + - - +
239I PHE* 3.3 10.0 + - - +
240I ALA* 2.9 24.9 + - - +
253I MET* 4.0 9.7 - - + +
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Residues in contact with THR 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I LEU* 3.1 38.7 - - - +
78I GLY* 3.5 29.2 - - - +
79I ILE* 3.8 11.4 - - + -
162I LEU* 4.4 9.4 - - + -
190I ILE* 5.7 3.1 - - + -
233I VAL 2.8 23.5 + - - -
234I ARG 3.7 4.0 - - - -
236I ALA* 1.3 74.3 - - - +
238I ARG* 1.3 58.6 + - - +
240I ALA* 2.9 4.7 + - - +
241I ALA* 2.8 27.9 + - + +
253I MET* 3.8 10.3 - - + +
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Residues in contact with ARG 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I THR* 5.2 0.4 + - - -
26I VAL 5.3 1.2 + - - -
35I TYR* 4.9 1.6 + - - -
77I ALA 2.8 25.3 + - - -
78I GLY* 3.3 24.2 - - - +
234I ARG* 2.9 59.0 + - - +
235I GLU* 3.2 19.9 + - - +
237I THR* 1.3 75.0 - - - +
239I PHE* 1.3 61.5 + - - +
241I ALA* 4.2 2.2 - - - +
242I ALA* 3.3 23.2 + - - +
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Residues in contact with PHE 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I LEU* 4.1 16.4 - - + -
19I GLU* 3.9 12.3 - - - -
20I GLY* 3.4 32.3 - - - -
21I PRO* 3.5 35.4 - - + -
22I PRO* 5.1 3.6 - - + -
223I LEU* 3.9 18.2 - - + -
235I GLU 2.9 17.1 + - - +
236I ALA 3.3 3.1 - - - +
238I ARG* 1.3 76.1 - - - +
240I ALA* 1.3 61.3 + - + +
242I ALA* 3.4 6.5 + - - +
243I TYR* 3.0 34.5 + + + +
251I ILE* 4.1 19.3 - - + -
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Residues in contact with ALA 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I ILE* 4.1 21.3 - - + -
223I LEU* 5.4 0.9 - - + -
236I ALA 2.9 17.2 + - - +
237I THR* 3.6 3.1 - - - +
239I PHE* 1.3 82.2 - - + +
241I ALA* 1.3 61.2 + - - +
242I ALA 3.1 1.3 - - - -
243I TYR* 3.1 7.0 + - - +
244I CYS* 2.8 32.7 + - - +
251I ILE* 4.1 19.3 - - + -
253I MET* 4.5 9.0 - - - -
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Residues in contact with ALA 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I GLY 3.9 13.7 - - - +
79I ILE* 4.6 6.1 - - + -
160I VAL* 4.1 11.2 - - + +
190I ILE* 4.0 10.6 - - + +
237I THR* 2.8 18.3 + - + +
238I ARG* 4.3 2.7 - - - +
240I ALA* 1.3 73.3 - - - +
242I ALA* 1.3 57.6 + - - +
244I CYS* 3.5 1.7 + - - +
245I ARG* 2.8 60.5 + - - +
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Residues in contact with ALA 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I ARG 3.3 18.4 + - - +
239I PHE* 3.5 6.7 - - - +
240I ALA 3.1 0.4 - - - -
241I ALA* 1.3 74.5 - - - +
243I TYR* 1.3 60.9 + - - +
245I ARG* 3.0 9.5 + - - +
246I SER* 2.8 31.8 + - - -
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Residues in contact with TYR 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LEU* 4.1 23.1 - - + -
221I PRO* 3.3 24.8 - - + +
239I PHE* 3.0 24.0 + + + +
240I ALA* 3.1 11.0 + - - +
242I ALA* 1.3 76.0 - - - +
244I CYS* 1.3 64.6 + - - +
246I SER* 3.2 19.6 + - - -
248I LYS* 3.3 55.4 + - + +
249I GLY 3.3 22.0 - - - -
250I PRO 3.7 10.1 - - - -
251I ILE* 4.1 20.9 - - + -
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Residues in contact with CYS 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I VAL* 3.7 22.0 - - + -
188I PRO* 3.9 17.5 - - + +
189I CYS 4.0 14.4 - - - -
190I ILE* 3.7 27.1 - - + -
240I ALA 2.8 17.1 + - - +
241I ALA 4.5 0.2 - - - -
243I TYR* 1.3 71.4 - - - +
245I ARG* 1.3 60.8 + - - +
246I SER 3.1 1.6 - - - -
247I GLY* 3.0 19.6 + - - -
248I LYS 4.3 0.2 + - - -
249I GLY 3.2 25.6 + - - +
251I ILE* 3.8 12.6 - - - -
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Residues in contact with ARG 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I GLY 4.7 1.0 + - - -
79I ILE* 4.5 4.4 - - - +
80I ASN* 3.6 21.3 + - - +
83I ASP* 2.9 39.4 + - - -
158I ASP* 3.0 64.6 + - + +
159I GLU* 4.0 0.2 - - - +
160I VAL* 3.9 10.6 - - + +
188I PRO* 5.7 0.4 - - - -
241I ALA* 2.8 46.8 + - - +
242I ALA* 3.0 7.5 + - - +
244I CYS* 1.3 70.6 - - - +
246I SER* 1.3 60.6 + - - +
247I GLY* 3.0 7.0 + - - -
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Residues in contact with SER 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I ALA 2.8 14.4 + - - -
243I TYR* 3.2 7.0 + - - -
244I CYS 3.1 0.8 - - - -
245I ARG* 1.3 76.8 - - - +
247I GLY* 1.3 58.4 + - - +
248I LYS* 3.2 37.0 + - - +
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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
------------------------------------------------------------
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