Contacts of the helix formed by residues 296 - 312 (chain C) in PDB entry 3V81
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 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C LEU* 4.0 12.1 - - - +
295C LEU* 1.3 88.4 + - - +
297C GLU* 1.3 67.5 + - + +
298C GLU* 3.2 37.2 - - + +
299C ALA* 3.2 19.6 - - + +
300C GLU* 2.7 34.9 + - - +
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Residues in contact with GLU 297 (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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296C THR* 1.3 75.8 - - + +
298C GLU* 1.3 59.3 + - - +
299C ALA 3.2 0.2 - - - -
300C GLU* 3.8 3.7 - - - +
301C LEU* 2.9 35.8 + - + +
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Residues in contact with GLU 298 (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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278C GLN* 3.0 43.2 + - + +
281C LYS* 4.7 6.4 + - - +
296C THR* 3.2 20.3 - - + +
297C GLU* 1.3 78.1 - - - +
299C ALA* 1.3 61.7 + - + +
301C LEU* 4.2 5.6 - - - +
302C GLU* 3.9 12.0 + - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C GLN* 4.0 26.7 - - + +
279C LEU* 3.4 22.8 - - + +
282C LEU* 4.5 10.1 - - + -
295C LEU* 5.1 2.2 - - + -
296C THR* 3.2 29.5 - - + +
297C GLU 3.2 0.4 - - - -
298C GLU* 1.3 83.6 - - + +
300C GLU* 1.3 60.4 + - - +
302C GLU* 3.3 17.5 - - - +
303C LEU 3.5 1.7 + - - -
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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
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252C TRP* 6.1 0.7 - - - -
279C LEU* 5.5 0.2 - - - -
295C LEU* 3.0 37.5 - - + +
296C THR 2.7 23.1 + - - +
297C GLU* 3.4 4.7 + - - +
299C ALA* 1.3 73.1 - - - +
301C LEU* 1.3 55.4 + - - +
303C LEU* 3.4 16.4 + - + +
304C ALA* 2.7 34.6 + - + +
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Residues in contact with LEU 301 (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 GLU* 2.9 21.4 + - + +
298C GLU* 4.5 7.0 - - - +
299C ALA 3.3 0.4 - - - -
300C GLU* 1.3 75.3 - - - +
302C GLU* 1.3 66.9 + - - +
304C ALA* 3.2 14.3 - - + +
305C GLU* 2.9 42.8 + - + +
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Residues in contact with GLU 302 (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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275C LYS* 3.1 37.9 - - + +
276C VAL 3.1 1.4 - - - -
277C ARG* 2.6 31.2 + - - +
278C GLN* 3.0 19.0 + - + +
279C LEU* 2.8 36.3 + - + +
298C GLU 3.9 8.3 + - - +
299C ALA 3.3 10.0 + - - +
301C LEU* 1.3 77.3 - - - +
303C LEU* 1.3 67.0 + - - +
304C ALA 2.8 0.9 + - - -
305C GLU* 3.5 9.6 + - - +
306C ASN* 2.7 29.6 + - - +
336C GLN* 4.1 0.9 + - - +
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Residues in contact with LEU 303 (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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246C LEU* 4.5 11.4 - - + -
252C TRP* 4.4 21.5 - - + -
260C LEU* 3.9 33.4 - - + -
264C LEU* 4.9 5.2 - - + -
279C LEU* 4.7 13.4 - - + +
295C LEU* 5.7 6.5 - - + -
299C ALA 3.5 7.5 + - - +
300C GLU* 3.4 23.5 + - + +
302C GLU* 1.3 78.6 - - - +
304C ALA* 1.3 59.6 + - - +
306C ASN* 4.2 6.9 - - + +
307C ARG* 2.9 63.7 + - - +
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Residues in contact with ALA 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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300C GLU* 2.7 24.0 + - + +
301C LEU* 3.2 22.0 - - + +
302C GLU 2.8 1.0 + - - -
303C LEU* 1.3 78.1 - - - +
305C GLU* 1.3 57.0 + - - +
307C ARG* 3.2 11.8 - - - +
308C GLU* 3.2 22.5 + - - +
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Residues in contact with GLU 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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275C LYS* 3.6 31.5 + - - -
301C LEU* 2.9 45.4 + - + +
302C GLU* 3.5 9.3 + - - +
304C ALA* 1.3 72.1 - - - +
306C ASN* 1.3 62.9 + - - +
308C GLU* 3.5 11.8 - - + +
309C ILE* 3.1 31.3 + - + +
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Residues in contact with ASN 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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264C LEU* 4.0 27.4 - - + +
273C GLY 4.0 3.6 - - - +
274C ILE* 3.2 20.5 - - + +
275C LYS* 2.7 50.9 + - - +
279C LEU* 4.8 0.8 - - - +
302C GLU* 2.7 23.2 + - - +
303C LEU* 3.9 7.7 - - + +
305C GLU* 1.3 75.5 - - - +
307C ARG* 1.3 61.0 + - - +
308C GLU 3.0 5.7 + - - -
309C ILE* 3.2 19.3 + - - +
310C LEU* 3.2 16.9 + - - +
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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
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246C LEU* 3.8 39.7 + - + +
247C PRO 4.5 3.0 + - - -
248C GLU* 3.4 43.2 + - - +
252C TRP* 4.9 4.2 - - - -
303C LEU* 2.9 54.8 + - - +
304C ALA* 3.2 12.3 - - - +
306C ASN* 1.3 75.3 - - - +
308C GLU* 1.3 57.9 + - - +
309C ILE 3.4 0.2 - - - -
310C LEU* 3.9 13.6 - - + +
311C LYS* 3.0 32.2 + - - +
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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
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304C ALA 3.2 16.6 + - - +
305C GLU* 3.5 15.3 - - + +
306C ASN 3.0 0.4 - - - -
307C ARG* 1.3 80.3 - - - +
309C ILE* 1.3 64.8 + - + +
311C LYS* 3.2 46.2 + - - +
312C GLU* 4.6 5.9 + - - +
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Residues in contact with ILE 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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271C TYR* 4.1 12.6 - - + -
272C PRO* 2.9 31.9 - - + +
273C GLY* 4.0 10.8 - - - +
274C ILE* 3.4 26.0 - - + -
305C GLU* 3.1 18.2 - - + +
306C ASN* 3.2 12.6 + - - +
308C GLU* 1.3 80.1 - - + +
310C LEU* 1.3 65.2 + - - +
311C LYS 3.3 0.9 - - - -
312C GLU* 3.9 23.4 + - - +
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Residues in contact with LEU 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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244C ILE* 4.8 14.4 - - + +
246C LEU* 3.4 40.6 - - + -
264C LEU* 4.2 11.4 - - + -
267C ALA* 4.1 14.8 - - + -
271C TYR* 3.1 50.1 + - + -
274C ILE* 4.8 3.4 - - + -
306C ASN 3.2 16.7 + - - +
307C ARG* 4.1 7.4 - - + +
308C GLU 3.3 0.4 - - - -
309C ILE* 1.3 76.7 - - + +
311C LYS* 1.3 68.9 + - - +
312C GLU 3.0 8.2 - - - +
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Residues in contact with LYS 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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307C ARG* 3.0 22.9 + - - +
308C GLU* 3.2 41.4 + - - +
309C ILE 3.3 0.2 - - - -
310C LEU* 1.3 82.4 - - - +
312C GLU* 1.3 65.3 + - + +
313C PRO* 3.7 1.2 - - - +
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Residues in contact with GLU 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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271C TYR* 3.4 13.3 + - - -
308C GLU 5.0 5.8 - - - +
309C ILE* 3.9 14.2 + - - +
310C LEU 3.0 15.0 - - - +
311C LYS* 1.3 78.4 - - + +
313C PRO* 1.3 77.9 - - + +
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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