Contacts of the helix formed by residues 240 - 255 (chain C) in PDB entry 1C3Q
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 GLY 240 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASN* 3.1 15.2 - - - +
253A SER* 5.1 0.2 - - - -
254A THR* 5.0 4.3 - - - -
189C LEU* 5.0 5.2 - - - -
236C THR 3.2 7.4 + - - +
237C ALA 4.3 4.2 + - - -
238C ASP 3.7 0.8 - - - -
239C LYS* 1.3 81.5 - - - +
241C PRO* 1.3 73.0 - - - +
242C GLY 3.2 0.5 + - - -
243C SER* 3.3 1.0 + - - -
244C PHE* 3.1 23.7 + - - +
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Residues in contact with PRO 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 3.7 31.4 - - + -
249A LEU* 3.9 4.5 - - + +
250A ASN* 4.2 1.3 - - - +
253A SER* 3.6 24.7 - - - +
189C LEU* 4.7 10.3 - - + -
192C LYS* 3.7 36.8 - - + +
193C VAL* 3.9 6.9 - - + +
240C GLY* 1.3 81.1 - - - +
242C GLY* 1.3 64.3 + - - +
244C PHE* 3.9 8.7 - - + -
245C GLN* 3.1 24.1 + - - +
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Residues in contact with GLY 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 3.5 23.3 - - - +
249A LEU* 3.9 21.5 - - - +
250A ASN* 2.8 9.7 + - - -
241C PRO* 1.3 79.1 - - - +
243C SER* 1.3 64.5 + - - +
245C GLN* 3.3 13.8 + - - +
246C ILE* 3.3 18.0 + - - +
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Residues in contact with SER 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 3.6 10.3 - - - +
247A GLU* 4.8 1.6 + - - -
250A ASN* 2.8 28.7 + - - -
236C THR* 3.5 21.6 - - - +
239C LYS* 3.5 26.0 - - - +
240C GLY 3.9 0.9 - - - -
242C GLY* 1.3 74.8 - - - +
244C PHE* 1.3 57.4 + - - +
246C ILE* 3.2 6.5 + - - +
247C GLU* 2.8 29.5 + - - +
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Residues in contact with PHE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C HIS* 5.1 2.0 - - + -
189C LEU* 3.8 42.8 - - + -
190C LEU* 3.7 35.2 - - + -
193C VAL* 3.7 18.6 - - + -
229C ALA* 3.6 28.7 - - + -
232C ALA* 3.7 10.3 - - + -
233C ALA* 3.7 13.9 - - + -
236C THR* 3.2 23.5 + - - +
240C GLY 3.1 15.5 + - - +
241C PRO* 3.9 7.4 - - + +
243C SER* 1.3 77.9 - - - +
245C GLN* 1.3 54.6 + - - +
247C GLU* 3.1 2.8 + - - +
248C LEU* 2.7 42.7 + - + +
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Residues in contact with GLN 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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30A ASN* 4.5 5.2 - - - +
34A ASN* 3.6 31.3 + - - +
246A ILE* 5.1 3.6 - - - +
249A LEU* 4.1 18.2 - - - +
31C PHE* 3.8 29.9 - - + -
193C VAL* 3.9 20.6 - - + +
241C PRO 3.1 19.1 + - - +
242C GLY 3.5 4.8 + - - +
244C PHE* 1.3 78.0 - - - +
246C ILE* 1.3 75.9 + - + +
248C LEU* 3.3 6.7 + - - +
249C LEU* 3.3 23.9 + - + +
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Residues in contact with ILE 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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246A ILE* 3.6 28.9 - - + -
242B GLY* 3.5 26.6 - - - +
243B SER* 3.7 10.5 - - - +
245B GLN* 5.4 3.4 - - - +
246B ILE* 3.6 26.2 - - + -
242C GLY 3.3 14.1 + - - +
243C SER* 3.2 8.6 + - - +
245C GLN* 1.3 88.9 - - + +
247C GLU* 1.3 63.0 + - - +
249C LEU* 3.2 18.4 + - + +
250C ASN* 3.1 23.2 + - - +
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Residues in contact with GLU 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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232C ALA* 3.6 29.8 - - + +
235C GLN* 2.4 31.3 + - + +
236C THR* 4.0 12.6 - - + +
243C SER 2.8 18.0 + - - +
244C PHE 3.6 3.4 - - - +
246C ILE* 1.3 74.8 - - - +
248C LEU* 1.3 60.7 + - - +
250C ASN* 3.1 19.9 + - - +
251C LYS* 2.3 60.1 + - - +
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 4.2 19.7 - - + -
190C LEU* 3.9 17.5 - - + -
193C VAL* 5.7 2.2 - - + -
196C ALA* 5.6 1.8 - - + -
199C LEU* 4.9 0.9 - - + -
225C TYR* 3.8 28.5 - - + +
228C ALA* 4.3 3.4 - - + -
229C ALA* 4.0 33.2 - - + +
232C ALA* 3.8 9.4 - - + +
244C PHE* 2.7 27.8 + - + +
245C GLN* 3.6 7.6 - - - +
246C ILE 3.3 0.2 - - - -
247C GLU* 1.3 72.8 - - - +
249C LEU* 1.3 63.8 + - - +
251C LYS* 3.3 1.0 + - - +
252C LEU* 3.0 49.4 + - + +
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PRO* 4.1 2.0 - - + +
242B GLY* 3.9 19.7 - - - +
245B GLN* 4.2 22.0 - - - +
31C PHE* 3.7 29.8 - - + -
34C ASN* 4.1 12.8 - - + +
35C GLY* 3.8 32.8 - - - +
38C ALA* 3.3 25.8 - - + +
245C GLN* 3.6 16.2 - - + +
246C ILE* 3.2 18.3 + - + +
248C LEU* 1.3 80.1 - - - +
250C ASN* 1.3 64.3 + - - +
252C LEU* 3.4 7.7 + - + -
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Residues in contact with ASN 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS* 3.2 23.9 + - - +
240B GLY 3.1 6.9 - - - -
241B PRO* 4.4 2.5 - - - -
242B GLY 2.8 30.0 + - - -
243B SER* 3.0 29.8 + - - +
246C ILE* 3.1 15.0 + - - +
247C GLU* 3.1 31.8 + - - +
249C LEU* 1.3 76.1 - - - +
251C LYS* 1.3 60.5 + - - +
253C SER* 2.7 31.3 + - - -
254C THR* 3.1 11.4 + - - +
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Residues in contact with LYS 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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239B LYS 5.3 2.4 + - - -
228C ALA* 3.4 31.4 - - - +
231C LEU* 3.8 31.9 - - + -
232C ALA* 3.7 9.9 - - + +
235C GLN* 2.8 16.9 + - - -
247C GLU* 2.3 52.2 + - - +
248C LEU 3.3 3.1 + - - +
250C ASN* 1.3 71.1 - - - +
252C LEU* 1.3 57.3 + - - +
253C SER 2.9 4.9 - - - -
254C THR* 3.4 15.9 + - - +
255C VAL* 2.7 34.9 + - - +
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Residues in contact with LEU 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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14C ARG* 3.0 17.5 + - - -
35C GLY* 3.9 21.3 - - - +
38C ALA* 3.9 8.3 - - + -
39C LEU* 3.4 31.6 - - + +
199C LEU* 4.0 25.4 - - + -
203C VAL* 5.5 4.7 - - + -
224C SER 5.3 0.4 - - - +
225C TYR* 3.9 25.1 - - + -
228C ALA* 3.8 21.3 - - + -
248C LEU* 3.0 33.0 + - + +
249C LEU* 3.8 9.6 - - + +
250C ASN 3.3 0.4 - - - -
251C LYS* 1.3 76.2 - - - +
253C SER* 1.3 56.7 + - - +
255C VAL* 4.0 3.5 - - + +
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Residues in contact with SER 253 (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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240B GLY* 4.4 0.5 - - - -
241B PRO* 3.3 29.8 - - - +
14C ARG* 3.5 12.2 + - - +
38C ALA* 3.1 23.8 - - - -
249C LEU 3.6 1.2 + - - -
250C ASN* 2.7 17.8 + - - -
251C LYS 2.9 0.8 - - - -
252C LEU* 1.3 82.5 - - - +
254C THR* 1.3 65.4 + - - +
255C VAL 3.7 0.2 - - - -
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Residues in contact with THR 254 (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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238B ASP 4.8 9.0 - - - +
239B LYS 4.6 13.2 - - - +
240B GLY* 5.3 1.3 - - - -
250C ASN 3.1 16.2 + - - +
251C LYS* 3.4 24.1 + - - +
253C SER* 1.3 85.7 - - - +
255C VAL* 1.3 68.8 + - - +
256C THR* 3.2 16.5 + - - +
259C ASP* 4.2 1.2 - - - +
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Residues in contact with VAL 255 (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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10C LEU* 4.2 14.6 - - + -
14C ARG* 3.0 34.4 + - - +
39C LEU* 5.7 0.4 - - + -
224C SER* 4.8 4.9 - - - +
227C VAL* 4.1 17.5 - - + -
228C ALA* 4.5 14.1 - - + +
231C LEU* 4.2 11.0 - - + -
251C LYS 2.7 24.2 + - - +
252C LEU* 4.0 8.1 - - + +
253C SER 4.6 0.2 - - - +
254C THR* 1.3 74.6 + - - +
256C THR* 1.3 67.1 + - - +
259C ASP* 3.6 24.0 - - + +
260C VAL* 4.3 7.9 - - + -
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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
------------------------------------------------------------
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