Contacts of the helix formed by residues 295 - 307 (chain Y) in PDB entry 2Q4G
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 LEU 295 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267Y ILE* 4.2 9.2 - - + +
268Y THR 4.1 9.0 - - - +
269Y ALA* 3.8 15.3 + - - +
272Y CYS* 4.0 24.7 - - + -
290Y LEU* 4.0 23.3 - - + +
293Y ASN* 2.8 32.9 + - + +
294Y GLU* 1.3 73.5 - - - +
296Y GLY* 1.3 66.0 + - - +
298Y GLU* 4.2 1.0 + - - +
299Y GLY* 3.2 21.0 + - - -
303Y LEU* 4.1 17.3 - - + -
319Y VAL* 4.3 0.9 - - + -
322Y CYS* 3.1 13.8 + - - +
324Y PHE* 3.5 29.2 - - + -
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Residues in contact with GLY 296 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294Y GLU* 3.5 2.9 - - - -
295Y LEU* 1.3 82.5 - - - +
297Y ASP* 1.3 63.5 + - - -
298Y GLU 3.2 0.9 - - - -
300Y ALA 3.0 3.6 + - - -
322Y CYS 2.9 9.5 + - - -
323Y SER* 3.3 20.6 - - - -
324Y PHE* 2.9 23.8 - - - -
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Residues in contact with ASP 297 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296Y GLY* 1.3 68.6 - - - -
298Y GLU* 1.3 60.6 + - - +
300Y ALA* 3.2 7.3 + - - +
301Y ARG* 2.8 28.6 + - - +
323Y SER 4.0 1.2 + - - -
324Y PHE* 3.4 5.2 - - - -
325Y THR* 2.7 53.9 + - - +
327Y ALA* 3.3 19.1 - - + +
328Y CYS* 3.7 18.4 - - + +
331Y HIS* 5.7 0.2 - - - -
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Residues in contact with GLU 298 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269Y ALA* 3.7 22.4 - - + -
295Y LEU 4.7 1.1 - - - +
296Y GLY 3.2 1.0 - - - -
297Y ASP* 1.3 77.7 - - - +
299Y GLY* 1.3 57.8 + - - +
301Y ARG* 2.9 23.4 + - - +
302Y LEU* 2.8 54.4 + - + +
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Residues in contact with GLY 299 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269Y ALA* 4.0 4.2 - - - +
272Y CYS* 4.1 19.5 - - - -
295Y LEU* 3.2 22.8 + - - -
296Y GLY 3.7 0.4 - - - -
298Y GLU* 1.3 75.8 - - - +
300Y ALA* 1.3 67.2 + - - +
302Y LEU* 3.1 8.3 + - - +
303Y LEU* 2.9 30.1 + - - +
324Y PHE* 4.5 2.0 - - - -
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Residues in contact with ALA 300 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296Y GLY 3.0 5.7 + - - -
297Y ASP 3.4 8.7 - - - +
299Y GLY* 1.3 75.4 - - - +
301Y ARG* 1.3 57.5 + - - +
303Y LEU* 3.7 4.8 + - - +
304Y CYS* 3.2 34.4 + - - -
324Y PHE* 3.6 31.8 - - + -
328Y CYS* 3.5 33.4 - - + -
331Y HIS* 5.7 0.2 - - - -
332Y PHE* 3.8 8.7 - - + -
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Residues in contact with ARG 301 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297Y ASP 2.8 12.2 + - - +
298Y GLU* 2.9 24.5 + - - +
300Y ALA* 1.3 76.9 - - - +
302Y LEU* 1.3 65.2 + - - +
304Y CYS* 3.3 4.2 + - - +
305Y GLU* 3.0 54.7 + - + +
331Y HIS* 3.7 42.8 + - + +
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Residues in contact with LEU 302 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269Y ALA* 3.5 24.9 - - + +
272Y CYS* 4.6 2.0 - - - -
273Y GLY* 3.8 18.6 - - - +
276Y CYS* 3.6 14.5 - - + -
298Y GLU* 2.8 46.1 + - + +
299Y GLY* 3.7 11.4 - - - +
301Y ARG* 1.3 74.2 - - + +
303Y LEU* 1.3 61.4 + - - +
305Y GLU* 3.6 18.2 + - - +
306Y THR* 2.9 28.8 + - - -
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Residues in contact with LEU 303 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272Y CYS* 3.9 11.7 - - - -
275Y LEU* 5.6 0.4 - - + -
276Y CYS* 4.1 16.8 - - - -
279Y LEU* 4.3 10.3 - - + -
288Y LEU* 4.1 24.9 - - + -
290Y LEU* 4.7 2.9 - - + -
295Y LEU* 4.1 16.4 - - + -
299Y GLY 2.9 20.0 + - - +
300Y ALA* 3.9 4.9 - - - +
302Y LEU* 1.3 78.2 - - - +
304Y CYS* 1.3 59.1 + - - +
306Y THR* 2.9 5.4 + - - -
307Y LEU* 2.8 42.4 + - + +
314Y LEU* 6.1 0.2 - - + -
317Y LEU* 4.4 10.1 - - + -
319Y VAL* 4.0 26.9 - - + -
324Y PHE* 4.7 5.2 - - + -
332Y PHE* 4.9 6.1 - - + -
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Residues in contact with CYS 304 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Y ALA 3.2 19.9 + - - +
301Y ARG 3.3 3.3 + - - +
303Y LEU* 1.3 78.8 - - - +
305Y GLU* 1.3 62.3 + - + +
307Y LEU* 3.2 3.9 + - - -
308Y LEU* 3.1 34.0 + - + +
331Y HIS* 4.0 16.8 - - + +
332Y PHE* 3.4 58.8 - - - -
335Y VAL* 3.7 14.3 - - + +
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Residues in contact with GLU 305 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301Y ARG* 3.0 51.9 + - + +
302Y LEU* 3.9 21.0 - - - +
304Y CYS* 1.3 75.7 - - + +
306Y THR* 1.3 59.1 + - - +
308Y LEU* 3.0 22.2 + - - +
309Y GLU* 3.4 27.1 + - - +
331Y HIS* 6.1 1.3 - - - +
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Residues in contact with THR 306 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276Y CYS* 3.2 28.2 + - + +
279Y LEU* 3.7 35.2 - - + -
280Y ARG* 4.1 12.0 - - + +
302Y LEU 2.9 12.8 + - - -
303Y LEU* 2.9 9.8 + - - -
305Y GLU* 1.3 74.8 - - - +
307Y LEU* 1.3 59.0 + - + +
308Y LEU 2.9 9.6 + - - -
309Y GLU* 3.2 25.1 + - - +
312Y CYS* 4.1 14.9 - - + +
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Residues in contact with LEU 307 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279Y LEU* 5.6 2.7 - - + -
303Y LEU* 2.8 33.4 + - + +
304Y CYS* 3.2 8.7 + - - +
306Y THR* 1.3 72.2 - - + +
308Y LEU* 1.3 62.5 + - - +
309Y GLU 3.6 2.9 - - - +
312Y CYS* 3.8 25.1 - - - -
314Y LEU* 4.8 19.3 - - + +
317Y LEU* 4.3 23.1 - - + -
332Y PHE* 4.6 9.0 - - + -
335Y VAL* 4.0 18.6 - - + -
339Y ASN* 2.8 41.4 + - - +
342Y LEU* 4.7 14.8 - - + -
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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