Contacts of the helix formed by residues 296 - 310 (chain C) in PDB entry 1C7G
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 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ASP 3.9 9.2 - - - -
69C GLU* 2.7 20.8 + - - +
76C ASN* 3.0 40.4 - - - +
291C TYR* 5.9 0.2 - - - +
294C LEU 3.7 1.2 + - - -
295C ALA* 1.3 70.4 - - - +
297C ARG* 1.3 59.7 + - - +
299C MET* 3.1 23.7 + - - +
300C GLU 3.2 0.9 + - - -
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Residues in contact with ARG 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET* 3.6 16.4 - - - +
61A TRP* 4.7 5.5 - - - -
64A MET* 3.4 29.0 - - - +
261A VAL* 6.1 1.0 - - - +
262A ASN* 3.1 33.5 + - - +
263A ILE* 4.3 10.9 - - - +
297A ARG* 5.0 0.2 - - - +
298A ASP* 2.7 29.7 + - - -
63C GLY 4.3 2.7 - - - +
64C MET* 3.7 45.8 - - - +
67C GLY* 3.8 12.9 - - - -
69C GLU* 3.3 16.5 + - - +
295C ALA* 3.8 10.9 - - + +
296C GLY* 1.3 75.2 - - - +
298C ASP* 1.3 70.0 + - - +
300C GLU* 3.2 7.5 + - - +
301C ALA* 3.0 27.2 + - - +
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Residues in contact with ASP 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 5.2 1.0 - - - +
297A ARG* 2.7 29.1 + - - -
298A ASP* 4.0 12.5 - - - +
64C MET* 4.3 2.4 - - - +
261C VAL* 4.9 3.3 - - - +
263C ILE* 3.5 24.4 - - + +
294C LEU* 4.2 17.3 - - + -
295C ALA* 3.1 27.3 + - - +
297C ARG* 1.3 87.2 + - - +
299C MET* 1.3 60.5 + - - +
300C GLU 3.2 0.4 - - - -
301C ALA* 3.8 6.0 - - - +
302C MET* 3.0 29.5 + - - +
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Residues in contact with MET 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER* 4.5 6.7 - - - +
76C ASN* 4.0 12.7 - - + +
77C PHE* 4.0 30.1 - - + +
80C LEU* 3.8 19.9 - - + +
95C PRO* 4.3 7.2 - - - -
290C SER 3.4 22.0 - - - +
291C TYR* 3.6 30.3 - - + +
294C LEU* 4.2 20.2 - - + +
295C ALA 3.9 5.4 - - - +
296C GLY* 3.1 25.9 + - - +
298C ASP* 1.3 78.1 - - - +
300C GLU* 1.3 59.4 + - - +
302C MET* 4.0 5.5 - - - +
303C ALA* 3.1 27.7 + - - +
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLY* 3.7 32.3 - - - +
66C ILE* 4.4 10.1 - - + +
76C ASN* 2.7 34.6 + - - +
79C HIS* 2.5 42.6 + - - +
296C GLY 3.2 4.9 + - - +
297C ARG 3.4 9.4 - - - +
298C ASP 3.2 0.2 - - - -
299C MET* 1.3 77.5 - - - +
301C ALA* 1.3 64.9 + - - +
303C ALA* 3.3 6.2 + - - +
304C ILE* 3.1 40.9 + - + +
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Residues in contact with ALA 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 5.8 0.2 - - - +
56C MET* 4.0 25.6 - - - -
60C GLN* 3.0 24.4 + - - +
63C GLY 5.3 0.2 + - - -
64C MET* 4.1 13.7 - - + -
261C VAL* 3.8 5.8 - - + -
297C ARG 3.0 16.3 + - - +
298C ASP* 4.0 7.6 - - - +
300C GLU* 1.3 76.9 - - - +
302C MET* 1.3 56.6 + - - +
304C ILE* 3.5 7.3 + - - -
305C GLY 2.9 23.4 + - - -
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Residues in contact with MET 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.8 30.2 - - + +
255C GLY* 4.0 13.0 - - - -
259C CYS* 4.1 18.4 - - + +
261C VAL* 3.5 15.9 - - + +
263C ILE 5.2 0.4 - - - +
264C GLY* 3.9 8.7 - - - -
265C GLY 3.7 27.8 - - - +
266C PHE* 4.0 13.9 - - + -
294C LEU* 3.7 30.1 - - + -
298C ASP 3.0 17.5 + - - +
299C MET* 4.0 2.7 - - - +
300C GLU 3.2 0.2 - - - -
301C ALA* 1.3 75.1 - - - +
303C ALA* 1.3 66.3 + - - +
305C GLY* 3.9 0.2 - - - -
306C LEU* 3.0 24.1 + - + +
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C HIS* 4.1 11.4 - - + +
80C LEU* 3.7 33.6 - - - +
83C THR* 3.6 22.5 + - - +
299C MET 3.1 19.5 + - - +
300C GLU* 3.3 7.6 + - - +
302C MET* 1.3 78.9 - - - +
304C ILE* 1.3 62.5 + - + +
306C LEU* 3.6 1.0 + - - -
307C ARG* 3.5 16.6 + - - +
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Residues in contact with ILE 304 (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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59C LYS* 3.7 26.9 - - + +
60C GLN* 3.5 28.3 - - + +
63C GLY* 4.2 5.8 - - - -
300C GLU* 3.1 41.9 + - + +
301C ALA 3.8 3.8 - - - +
303C ALA* 1.3 75.1 - - + +
305C GLY* 1.3 63.9 + - - +
307C ARG* 3.2 9.3 + - - +
308C GLU* 3.0 35.4 + - + +
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Residues in contact with GLY 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLN* 3.2 26.0 - - - +
259C CYS 3.2 16.1 - - - +
260C LEU* 3.5 5.7 - - - +
301C ALA 2.9 11.7 + - - -
304C ILE* 1.3 77.6 - - - +
306C LEU* 1.3 56.5 + - - +
308C GLU* 3.2 7.0 + - - +
309C ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 5.6 1.3 - - + -
83C THR* 4.3 5.6 - - + -
84C VAL* 3.9 30.5 - - + -
87C LEU* 3.8 17.3 - - + -
88C PHE* 4.0 28.0 - - + -
219C VAL* 5.0 2.9 - - + -
253C MET* 4.9 1.8 - - + -
258C ASP 4.8 5.6 - - - +
259C CYS* 3.7 25.4 + - - +
266C PHE* 4.5 7.2 - - + -
302C MET* 3.0 18.1 + - + +
303C ALA* 3.8 5.8 - - - +
305C GLY* 1.3 77.3 - - - +
307C ARG* 1.3 60.3 + - - +
309C ALA* 3.6 6.2 + - - +
310C MET* 3.5 34.2 - - + +
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LYS* 4.7 5.1 - - - +
83C THR* 3.1 42.3 + - - +
86C GLU* 3.1 41.0 + - - -
87C LEU* 4.2 20.4 - - + +
238C LYS* 5.8 1.6 - - - +
303C ALA 3.5 7.3 + - - +
304C ILE* 3.2 11.1 + - - +
306C LEU* 1.3 78.0 - - - +
308C GLU* 1.3 64.7 + - + +
310C MET* 3.2 19.5 + - + +
311C GLN* 4.2 1.6 + - - +
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Residues in contact with GLU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER* 2.4 29.3 + - - -
59C LYS* 4.0 7.8 - - - +
60C GLN* 3.7 4.8 - - - +
260C LEU* 4.0 7.7 - - + +
304C ILE* 3.0 32.3 + - + +
305C GLY 3.2 7.4 + - - +
307C ARG* 1.3 77.1 - - + +
309C ALA* 1.3 61.4 + - - +
310C MET 3.1 1.6 + - - -
311C GLN* 3.1 22.8 + - - +
314C TYR* 4.1 6.8 - - - +
410C ARG* 2.8 38.3 + - - +
15D THR* 4.1 13.2 + - + +
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Residues in contact with ALA 309 (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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219C VAL* 3.3 31.9 - - + +
237C ILE* 4.5 0.2 - - - +
258C ASP 3.4 25.4 - - - +
260C LEU* 3.9 4.4 - - + +
305C GLY 2.9 13.3 + - - +
306C LEU* 3.7 9.2 - - + +
308C GLU* 1.3 76.5 - - - +
310C MET* 1.3 60.2 + - - +
311C GLN 3.2 2.5 + - - +
314C TYR* 3.7 29.0 - - + -
315C ILE* 4.3 1.4 - - - +
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Residues in contact with MET 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 4.2 26.0 - - + -
88C PHE* 5.1 1.6 - - + -
219C VAL* 3.7 30.3 - - + -
237C ILE* 3.5 21.3 - - - +
238C LYS* 4.1 28.7 + - + +
241C VAL* 4.1 30.1 - - + -
306C LEU* 3.5 35.7 - - + +
307C ARG* 3.5 11.4 - - + +
308C GLU 3.1 1.6 - - - -
309C ALA* 1.3 76.3 - - - +
311C GLN* 1.3 63.1 + - - +
312C TYR 3.2 4.0 + - - -
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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
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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