Contacts of the helix formed by residues 304 - 315 (chain C) in PDB entry 2R7D
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 THR 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302C GLY* 5.7 1.3 - - - -
303C ASP* 1.3 89.2 - - - +
305C LEU* 1.3 58.5 + - - +
306C PRO* 3.3 14.9 - - - +
307C ALA* 3.1 22.1 + - + +
308C MSE 2.9 27.4 + - - +
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Residues in contact with LEU 305 (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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240C LEU* 3.8 7.3 - - + +
241C PRO* 3.7 30.7 - - + -
304C THR* 1.3 72.5 - - - +
306C PRO* 1.3 62.5 - - + +
307C ALA 3.2 0.2 + - - -
308C MSE 3.2 17.6 + - + +
309C TRP* 2.7 38.1 + - - +
410C VAL* 4.0 31.9 - - + -
412C VAL* 4.0 11.4 - - + -
422C LEU* 4.5 7.6 - - + -
424C PRO* 4.3 16.8 - - + -
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Residues in contact with PRO 306 (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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304C THR* 3.3 16.8 - - - +
305C LEU* 1.3 95.5 - - + +
307C ALA* 1.3 59.1 + - - +
309C TRP* 3.7 2.3 - - + +
310C ALA* 3.1 24.8 + - - +
410C VAL* 4.9 1.8 - - + -
411C VAL 4.2 3.4 - - - +
412C VAL* 4.0 33.8 - - + +
438C PRO* 4.1 18.2 - - + +
439C GLY* 4.3 19.3 - - - +
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Residues in contact with ALA 307 (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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300C VAL* 3.5 17.8 - - - +
301C ALA 3.9 11.0 - - - +
302C GLY* 3.5 23.3 - - - +
304C THR* 3.1 35.5 + - - +
306C PRO* 1.3 80.2 - - - +
308C MSE 1.3 61.2 + - - +
311C ARG* 3.1 18.8 + - - +
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Residues in contact with MSE 308 (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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237C SER* 3.9 19.7 - - - +
238C ILE* 4.1 8.6 - - - +
239C ASP* 3.3 40.8 - - - +
240C LEU* 4.2 13.4 - - + +
241C PRO* 5.3 0.2 - - + -
303C ASP* 3.4 30.1 - - + +
304C THR 2.9 16.2 + - - +
305C LEU* 3.8 28.0 - - + +
307C ALA* 1.3 72.4 - - - +
309C TRP* 1.3 66.9 + - - +
311C ARG* 3.0 16.7 + - - +
312C ARG* 2.9 26.2 + - - +
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Residues in contact with TRP 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C LEU* 4.1 16.5 - - + +
305C LEU 2.7 22.8 + - - +
306C PRO 3.7 4.7 - - - +
308C MSE 1.3 75.1 - - - +
310C ALA* 1.3 60.5 + - - +
312C ARG* 3.5 36.1 + - - +
313C LYS* 3.4 39.1 + - + +
412C VAL* 3.4 45.3 - - + +
413C ASP* 4.2 13.0 + - + +
420C THR* 4.4 5.3 + - - +
422C LEU* 3.7 34.1 - - + -
429C ASP* 3.7 41.7 - - + -
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Residues in contact with ALA 310 (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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298C ARG* 4.5 15.3 - - - +
300C VAL* 4.4 12.3 - - + -
306C PRO 3.1 16.2 + - - +
307C ALA* 3.8 3.8 - - - +
309C TRP* 1.3 77.5 - - - +
311C ARG* 1.3 66.9 + - - +
313C LYS* 3.2 24.9 + - - +
314C THR* 3.2 19.2 + - - +
412C VAL 5.7 1.3 - - - +
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Residues in contact with ARG 311 (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 LEU* 3.5 42.7 - - + +
237C SER* 2.7 41.3 + - - +
238C ILE* 3.8 10.1 - - + -
296C PRO* 6.4 0.4 - - + -
300C VAL* 2.9 35.4 + - + +
301C ALA* 3.8 0.6 - - - +
302C GLY 2.6 35.9 + - - +
303C ASP* 4.7 2.0 - - - +
307C ALA 3.1 14.8 + - - +
308C MSE 3.0 22.2 + - - +
310C ALA* 1.3 77.2 - - - +
312C ARG* 1.3 61.8 + - - +
314C THR* 2.7 26.7 + - - +
315C LEU* 3.0 22.7 + - + +
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Residues in contact with ARG 312 (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 ILE* 4.3 25.8 - - + +
240C LEU* 3.8 25.1 - - + +
308C MSE 2.9 15.4 + - - +
309C TRP* 3.5 48.8 + - - +
311C ARG* 1.3 77.6 - - - +
313C LYS* 1.3 65.0 + - + +
314C THR 3.3 0.5 + - - -
315C LEU* 3.4 27.4 + - + +
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Residues in contact with LYS 313 (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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297C THR* 4.8 1.7 + - - -
298C ARG* 5.2 7.5 - - - +
309C TRP* 3.4 27.6 - - + +
310C ALA* 3.2 24.7 + - - +
312C ARG* 1.3 79.9 - - + +
314C THR* 1.3 61.8 + - + +
315C LEU 3.8 3.3 + - - +
413C ASP* 3.5 32.9 + - - +
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Residues in contact with THR 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PRO* 3.4 7.4 - - - +
297C THR* 3.0 41.5 + - + -
298C ARG* 3.5 60.4 + - + +
300C VAL* 4.2 3.0 - - + +
310C ALA 3.4 12.1 - - - +
311C ARG* 2.7 25.0 + - - +
313C LYS* 1.3 76.8 - - + +
315C LEU* 1.3 68.1 + - - +
316C ALA* 4.3 0.7 - - - -
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Residues in contact with LEU 315 (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 ILE* 3.6 36.1 - - + -
293C GLN* 4.3 23.3 - - - +
296C PRO* 4.3 9.2 - - + -
311C ARG* 3.0 33.8 + - + +
312C ARG* 3.4 21.6 + - + +
313C LYS 4.4 4.0 - - - +
314C THR* 1.3 79.3 + - - +
316C ALA* 1.3 69.0 + - - +
317C ARG* 3.7 2.8 + - - +
328C HIS* 5.9 3.1 - - + +
329C GLY* 5.3 6.7 - - - -
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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