Contacts of the helix formed by residues 236 - 252 (chain C) in PDB entry 1G3I
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 ASN 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235C ILE* 1.3 93.5 - - - +
237C PRO* 1.3 88.0 - - - +
238C GLU* 3.3 17.1 + - - +
239C GLU* 3.1 37.2 + - - +
240C LEU* 3.1 21.8 + - - +
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Residues in contact with PRO 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ILE* 5.6 0.2 - - + -
236C ASN* 1.3 92.0 - - - +
238C GLU* 1.3 68.7 + - + +
240C LEU* 2.9 24.6 + - + +
241C LYS* 2.9 31.4 + - - +
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Residues in contact with GLU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ASN* 3.3 15.1 + - - +
237C PRO* 1.3 80.9 - - + +
239C GLU* 1.3 65.6 + - - +
240C LEU 3.0 0.7 + - - -
241C LYS* 3.2 21.7 + - - +
242C GLN* 2.9 27.5 + - - +
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ASP* 5.3 5.3 - - - +
115C GLU* 6.6 0.2 - - - -
235C ILE 4.4 9.9 - - - +
236C ASN* 3.1 18.8 + - - +
238C GLU* 1.3 76.8 - - - +
240C LEU* 1.3 55.5 + - + +
242C GLN* 3.8 3.9 - - - +
243C LYS* 2.7 79.1 + - + +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C MET* 3.9 27.8 - - + -
111C VAL* 4.2 15.7 - - + +
112C ARG* 4.5 24.2 - - + +
115C GLU* 4.2 24.0 - - + -
235C ILE* 4.0 21.8 - - + +
236C ASN 3.1 23.1 - - - +
237C PRO* 2.9 12.1 + - + +
239C GLU* 1.3 77.3 - - + +
241C LYS* 1.3 57.1 + - - +
243C LYS* 2.8 7.9 + - + +
244C ALA* 2.6 35.7 + - - +
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Residues in contact with LYS 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C MET* 4.1 15.7 - - + +
237C PRO* 2.9 47.9 + - - +
238C GLU* 3.2 25.4 + - - +
240C LEU* 1.3 77.5 - - - +
242C GLN* 1.3 58.7 + - - +
244C ALA* 3.0 3.3 + - - +
245C ILE* 2.8 35.2 + - - +
294C LYS 5.2 2.0 - - - +
295C HIS* 3.8 48.2 - - + +
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C GLU* 2.9 18.0 + - - +
239C GLU* 4.1 3.8 - - - +
241C LYS* 1.3 76.0 - - - +
243C LYS* 1.3 58.1 + - + +
245C ILE* 3.5 27.2 - - - +
246C ASP* 2.8 59.2 + - - +
249C GLU* 5.7 1.0 + - - -
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL* 3.3 22.4 - - + +
115C GLU* 5.0 19.6 + - - +
118C LYS* 6.0 1.8 - - - +
239C GLU* 2.7 63.3 + - + +
240C LEU* 2.8 6.8 + - + +
242C GLN* 1.3 71.4 - - + +
244C ALA* 1.3 62.7 + - - +
246C ASP* 3.6 15.4 - - - +
247C ALA* 3.4 13.7 + - - +
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR* 5.0 3.8 - - + +
107C ALA* 3.8 28.1 - - + +
108C MET* 3.5 27.1 - - + +
111C VAL* 3.9 11.4 - - + +
240C LEU 2.6 14.5 + - - +
241C LYS* 3.4 7.2 - - - +
243C LYS* 1.3 71.4 - - - +
245C ILE* 1.3 72.8 + - - +
247C ALA* 2.7 14.2 + - - +
248C VAL 2.8 9.9 + - - -
295C HIS* 6.0 0.9 - - + -
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR* 5.0 5.6 - - + +
241C LYS* 2.8 16.0 + - + +
242C GLN* 3.5 34.5 - - - +
244C ALA* 1.3 74.8 - - - +
246C ASP* 1.3 70.6 + - - +
248C VAL* 2.6 23.3 + - - +
249C GLU* 2.9 42.3 + - + +
295C HIS* 3.7 24.7 - - + +
296C GLY* 4.3 8.1 - - - -
297C MET 4.0 17.3 - - - +
298C VAL* 4.1 13.2 - - + -
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Residues in contact with ASP 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLN* 2.8 44.3 + - - +
243C LYS* 3.6 19.1 - - - +
245C ILE* 1.3 77.6 - - - +
247C ALA* 1.3 52.0 + - - +
249C GLU* 3.6 5.2 + - - +
250C GLN* 2.7 50.2 + - + +
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PRO* 4.0 19.5 - - + +
107C ALA* 4.9 2.5 - - + +
110C LEU* 5.7 4.0 - - + -
111C VAL* 4.7 8.5 - - + -
243C LYS 3.4 10.4 + - - +
244C ALA* 2.7 20.4 + - - +
246C ASP* 1.3 71.5 - - - +
248C VAL* 1.3 56.9 + - - +
250C GLN* 4.6 0.4 - - - -
251C ASN* 2.7 48.7 + - - +
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PRO* 4.2 6.7 - - + +
100C ILE* 5.0 1.8 - - + -
103C LEU* 3.7 26.2 - - + -
104C THR* 3.3 35.9 - - + +
107C ALA* 3.1 30.3 - - + -
244C ALA 2.8 8.1 + - - +
245C ILE* 2.6 12.8 + - - +
247C ALA* 1.3 75.8 - - - +
249C GLU* 1.3 67.1 + - - +
250C GLN 2.9 0.3 + - - -
252C GLY* 3.0 19.8 + - - +
298C VAL* 4.4 14.6 - - + -
303C ILE* 3.4 13.8 - - + +
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLN* 5.7 1.0 + - - -
245C ILE* 2.9 31.7 + - + +
246C ASP* 3.9 5.2 - - - +
248C VAL* 1.3 79.8 - - - +
250C GLN* 1.3 63.7 + - + +
297C MET 3.3 14.9 - - - +
298C VAL* 4.0 5.4 - - + -
299C LYS* 3.0 64.4 + - + +
302C HIS* 3.3 34.0 + - - +
303C ILE* 4.2 1.2 - - - +
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Residues in contact with GLN 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 3.4 23.8 + - - +
37C ARG* 3.1 42.0 + - - +
38C MET* 3.5 18.0 - - + +
45C ARG* 4.4 13.7 + - - -
46C HIS* 5.3 5.7 - - - -
246C ASP* 2.7 35.7 + - + +
247C ALA* 4.6 0.4 - - - -
248C VAL 2.9 1.0 + - - -
249C GLU* 1.3 81.8 + - + +
251C ASN* 1.3 73.5 + - - +
252C GLY 3.8 0.9 - - - -
302C HIS* 4.2 3.7 - - - +
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Residues in contact with ASN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 6.2 1.8 - - + -
34C ARG* 2.9 26.7 + - + +
38C MET* 4.5 9.9 - - - +
74C ALA* 5.5 3.4 + - + +
75C ASN 4.8 8.1 + - - -
76C ALA* 3.0 29.8 - - + +
77C PRO* 3.4 7.7 - - - +
247C ALA* 2.7 33.2 + - - +
250C GLN* 1.3 89.0 - - - +
252C GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 3.3 5.4 + - - +
77C PRO* 3.4 13.2 - - - -
103C LEU* 4.3 13.0 - - - -
248C VAL 3.0 16.2 + - - -
250C GLN 3.8 0.6 - - - -
251C ASN* 1.3 76.8 - - - +
253C ILE* 1.3 62.2 + - - -
303C ILE* 3.5 8.3 - - - +
304C LEU 2.8 26.9 + - - -
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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