Contacts of the helix formed by residues 286 - 298 (chain Q) in PDB entry 3EXG
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 ASP 286 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43Q ARG* 2.8 29.8 + - - -
260Q TYR* 2.7 26.9 + - - +
281Q VAL 3.5 1.6 + - - -
282Q ARG* 3.2 25.4 + - + +
285Q SER* 1.3 75.3 - - - +
287Q PRO* 1.3 71.1 - - - +
288Q ILE* 2.9 33.8 + - - +
289Q MET* 3.2 19.4 + - + +
290Q LEU* 2.9 22.0 + - - +
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Residues in contact with PRO 287 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q MET* 3.3 15.2 - - - +
43Q ARG* 4.1 3.4 - - - +
67Q GLY* 4.2 10.8 - - - +
69Q GLU* 3.8 19.3 - - + +
70Q ALA* 3.8 24.0 - - + +
227Q GLY 5.2 0.2 - - - +
228Q MET* 3.2 39.4 - - + +
230Q ILE* 4.6 2.4 - - - +
260Q TYR* 3.9 5.2 - - - +
285Q SER 3.0 5.5 - - - +
286Q ASP* 1.3 93.1 - - - +
288Q ILE* 1.3 63.6 + - + +
290Q LEU* 3.8 4.7 - - + +
291Q LEU* 3.5 13.0 + - - +
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Residues in contact with ILE 288 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q TYR* 4.0 25.8 - - + +
39Q MET* 3.6 48.2 - - + +
40Q GLN* 3.3 33.2 - - + +
43Q ARG* 3.8 26.0 - - + +
69Q GLU* 4.9 2.0 - - + -
286Q ASP* 2.9 13.3 + - - +
287Q PRO* 1.3 77.5 - - + +
289Q MET* 1.3 60.0 + - - +
290Q LEU 3.2 0.2 - - - -
291Q LEU* 3.3 2.6 + - - +
292Q LYS* 2.9 27.1 + - + +
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Residues in contact with MET 289 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Q ARG 3.9 20.6 - - - +
283Q SER 4.0 12.1 - - - +
284Q LYS* 4.6 2.9 - - - -
285Q SER 4.0 5.6 - - - +
286Q ASP* 3.2 22.2 + - + +
288Q ILE* 1.3 79.7 - - - +
290Q LEU* 1.3 95.3 + - + +
292Q LYS* 3.2 11.9 + - + +
293Q ASP* 2.9 55.1 + - - +
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Residues in contact with LEU 290 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226Q ASP* 5.8 1.6 - - - +
228Q MET* 3.9 28.9 - - + +
229Q ASP* 4.9 9.6 - - + +
230Q ILE* 6.3 1.1 - - + -
284Q LYS 4.9 1.8 - - - +
285Q SER* 4.1 21.1 - - - +
286Q ASP 2.9 17.9 + - - +
287Q PRO* 3.8 6.1 - - + +
289Q MET* 1.3 109.6 - - + +
291Q LEU* 1.3 61.3 + - - +
293Q ASP* 3.6 5.5 + - + +
294Q ARG* 3.4 28.9 + - - +
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Residues in contact with LEU 291 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q LEU* 4.2 25.1 - - + -
32Q GLY* 4.1 10.1 - - - +
35Q TYR* 4.1 12.6 - - + -
36Q TYR* 4.0 29.2 - - + +
39Q MET* 3.8 29.8 - - + -
230Q ILE* 4.0 19.3 - - + +
231Q LEU* 5.2 4.3 - - + -
287Q PRO 3.5 3.1 + - - +
288Q ILE 3.3 7.2 + - - +
289Q MET 3.3 0.4 - - - -
290Q LEU* 1.3 76.9 - - - +
292Q LYS* 1.3 66.6 + - - +
294Q ARG* 3.1 12.9 + - + +
295Q MET* 3.0 35.6 + - + +
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Residues in contact with LYS 292 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q TYR* 3.9 18.6 - - + +
288Q ILE* 2.9 18.6 + - + +
289Q MET* 3.2 12.8 + - + +
291Q LEU* 1.3 77.5 - - - +
293Q ASP* 1.3 70.7 + - - +
295Q MET* 3.6 1.8 + - - +
296Q VAL* 3.1 29.5 + - - +
303Q VAL* 3.5 31.6 - - - +
306Q LEU* 3.3 29.1 - - + +
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Residues in contact with ASP 293 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289Q MET* 2.9 47.0 + - - +
290Q LEU* 3.9 6.3 - - - +
291Q LEU 3.3 0.2 - - - -
292Q LYS* 1.3 83.4 - - - +
294Q ARG* 1.3 61.4 + - + +
296Q VAL* 4.6 3.8 - - - -
297Q ASN* 2.8 45.4 + - - +
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Residues in contact with ARG 294 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q PHE* 3.7 40.7 - - + +
8Q GLU 3.0 27.5 + - - -
9Q ILE* 4.6 0.6 - - - +
27Q LEU* 5.6 0.9 - - + -
229Q ASP* 2.8 39.7 + - - -
230Q ILE* 5.4 1.8 - - - +
231Q LEU* 3.1 28.7 - - - +
290Q LEU* 3.4 18.3 + - - +
291Q LEU* 3.1 17.7 + - + +
293Q ASP* 1.3 77.9 - - + +
295Q MET* 1.3 64.3 + - - +
297Q ASN* 3.2 2.1 + - - -
298Q SER* 3.0 31.0 + - - -
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Residues in contact with MET 295 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q PHE* 5.1 0.2 - - - -
27Q LEU* 4.2 12.3 - - + -
29Q ARG 4.8 2.0 - - - +
32Q GLY* 3.0 46.2 - - - +
33Q LEU* 3.4 24.2 - - + +
36Q TYR* 4.5 4.7 - - + -
291Q LEU* 3.0 28.4 + - + +
292Q LYS* 3.9 6.3 - - - +
294Q ARG* 1.3 75.6 - - - +
296Q VAL* 1.3 57.7 + - - +
300Q LEU* 2.8 47.8 + - + +
301Q ALA* 3.0 18.9 + - + +
306Q LEU* 4.1 20.9 - - + -
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Residues in contact with VAL 296 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292Q LYS* 3.1 28.1 + - - +
293Q ASP* 4.0 3.8 - - - +
295Q MET* 1.3 72.5 - - - +
297Q ASN* 1.3 68.3 + - - +
298Q SER 2.7 16.6 + - - -
299Q ASN* 2.8 15.6 + - - -
301Q ALA 3.5 15.1 - - - +
302Q SER* 6.1 0.2 - - - -
303Q VAL* 4.2 29.4 - - + +
306Q LEU* 4.6 8.3 - - + -
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Residues in contact with ASN 297 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293Q ASP* 2.8 36.3 + - - +
294Q ARG* 4.3 2.0 - - - +
296Q VAL* 1.3 86.5 - - - +
298Q SER* 1.3 58.2 + - - +
299Q ASN 3.5 0.7 - - - -
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Residues in contact with SER 298 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q ALA* 4.0 9.2 - - - +
5Q ALA* 3.6 17.1 - - - +
7Q PHE* 3.4 28.2 - - - -
294Q ARG 3.0 15.8 + - - -
296Q VAL 2.7 2.4 + - - -
297Q ASN* 1.3 78.0 - - - +
299Q ASN* 1.3 70.2 + - - +
300Q LEU* 3.0 11.4 + - - +
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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