Contacts of the helix formed by residues 298 - 311 (chain B) in PDB entry 2G9Y
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 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B ARG* 5.5 5.8 - - - +
292B ARG* 6.0 9.6 - - + +
296B VAL 4.5 5.4 - - - +
297B PRO* 1.3 76.9 - - - +
299B LEU* 1.3 65.5 + - - +
300B ALA* 3.6 9.0 + - - +
301B GLN* 2.9 43.2 + - - +
302B MET* 2.9 22.8 + - - +
344B ASP* 4.6 7.0 - - - -
347B GLU* 5.3 3.8 - - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.2 6.5 - - + -
148B THR* 3.8 20.9 - - + +
297B PRO 4.1 0.2 + - - -
298B THR* 1.3 73.7 - - - +
300B ALA* 1.3 56.7 + - - +
302B MET* 3.4 17.2 + - + +
303B THR* 2.9 33.7 + - - -
321B VAL* 3.5 22.4 - - + -
322B GLU 3.8 6.7 - - - +
323B GLY* 3.8 25.4 - - - +
344B ASP* 3.4 31.5 + - - +
345B LEU* 3.9 29.4 - - + +
348B ALA* 3.8 11.0 - - + -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 3.1 7.7 - - - +
299B LEU* 1.3 79.5 - - - +
301B GLN* 1.3 56.9 + - + +
303B THR* 3.5 2.3 + - - -
304B ASP* 2.9 29.1 + - - +
344B ASP* 4.6 1.4 + - - -
347B GLU* 4.0 34.5 - - + +
348B ALA* 4.0 17.1 - - - +
351B ARG* 3.4 25.5 + - + +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ALA* 5.4 5.4 - - - +
243B LEU* 5.4 2.5 - - + -
296B VAL 4.2 2.1 - - - +
297B PRO* 3.4 13.7 - - + +
298B THR* 2.9 50.4 + - - +
300B ALA* 1.3 75.3 - - + +
302B MET* 1.3 61.9 + - - +
304B ASP* 3.2 6.8 + - - +
305B LYS* 2.9 30.7 + - - +
351B ARG* 4.5 7.4 - - - +
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.9 20.4 - - + -
147B SER 3.9 11.9 - - - +
148B THR* 4.4 4.3 - - + -
204B LEU* 3.8 25.3 - - + +
205B GLY 4.4 1.6 - - - -
243B LEU* 4.5 3.6 - - + -
259B PHE* 3.7 33.7 - - + -
264B MET* 3.7 27.6 - - + +
297B PRO* 3.6 16.8 - - + -
298B THR 2.9 13.9 + - - +
299B LEU* 3.8 25.1 - - + +
301B GLN* 1.3 75.6 - - - +
303B THR* 1.3 58.2 + - - +
305B LYS* 3.5 3.4 + - - +
306B ALA* 3.0 30.7 + - - +
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 5.6 0.9 - - + -
48B LEU* 5.3 0.7 - - + -
146B VAL* 4.9 1.5 - - - +
299B LEU* 2.9 22.1 + - - +
300B ALA* 3.5 8.3 - - - +
302B MET* 1.3 77.7 - - - +
304B ASP* 1.3 62.6 + - - +
306B ALA* 3.2 6.8 + - - +
307B ILE* 3.0 40.3 + - + +
319B LEU* 4.4 1.9 - - + +
321B VAL* 3.3 40.4 - - + +
348B ALA* 3.6 24.4 - - + +
351B ARG* 4.4 5.2 - - + -
352B ALA* 4.7 5.2 - - + +
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Residues in contact with ASP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA 2.9 16.4 + - - +
301B GLN* 3.5 7.0 - - - +
303B THR* 1.3 78.8 - - - +
305B LYS* 1.3 61.0 + - - +
307B ILE* 3.4 10.8 + - - +
308B GLU* 3.2 20.6 + - - +
351B ARG* 2.8 41.6 + - + +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 5.2 2.2 - - + -
243B LEU* 3.6 31.9 - - + +
244B ASN* 3.6 20.5 + - - +
246B VAL* 2.7 44.1 + - - -
247B THR* 4.8 1.6 - - - +
301B GLN 2.9 16.7 + - - +
302B MET* 3.9 5.8 - - - +
304B ASP* 1.3 73.2 - - - +
306B ALA* 1.3 65.0 + - - +
308B GLU* 2.6 33.5 + - - +
309B LEU* 3.1 34.2 + - + +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.2 10.1 - - + -
202B VAL* 4.3 20.4 - - + -
204B LEU* 5.0 0.8 - - - +
302B MET 3.0 19.0 + - - +
303B THR 3.4 5.8 - - - +
305B LYS* 1.3 76.6 - - - +
307B ILE* 1.3 58.7 + - - +
309B LEU* 3.9 2.6 - - - -
310B LEU* 2.9 39.2 + - + +
319B LEU* 4.0 26.9 - - + -
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.7 25.6 - - + -
303B THR* 3.0 26.7 + - + +
304B ASP* 3.6 11.4 - - - +
305B LYS 3.2 0.4 - - - -
306B ALA* 1.3 75.0 - - - +
308B GLU* 1.3 54.8 + - - +
310B LEU* 4.6 3.4 - - - +
311B SER* 2.7 41.8 + - - -
317B PHE* 4.6 6.3 - - + -
319B LEU* 4.0 13.9 - - + -
351B ARG* 4.5 3.4 - - + +
352B ALA* 4.3 7.6 - - - +
355B PHE* 3.4 51.8 - - + -
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B THR* 5.6 2.1 - - - -
304B ASP* 3.2 14.0 + - - +
305B LYS* 2.6 47.7 + - - +
307B ILE* 1.3 77.4 - - - +
309B LEU* 1.3 64.7 + - + +
311B SER* 3.1 17.1 + - - -
312B LYS* 3.8 23.6 - - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.1 9.4 - - + -
204B LEU* 6.3 0.2 - - + -
246B VAL* 3.9 17.7 - - + +
247B THR 3.7 9.4 - - - +
248B GLU* 3.6 34.9 - - - +
249B ALA* 3.8 31.1 + - + +
255B LEU* 3.6 31.9 - - + -
305B LYS* 3.1 28.7 + - + +
306B ALA 4.1 2.7 - - - +
308B GLU* 1.3 82.1 - - + +
310B LEU* 1.3 59.6 + - - +
312B LYS* 4.0 18.1 + - - +
313B ASN 5.0 0.7 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 3.6 21.4 - - + +
143B THR 3.6 21.8 - - - +
144B GLY* 3.8 23.3 - - - +
201B ASP* 3.9 5.8 - - + -
202B VAL* 3.8 17.7 - - + -
249B ALA 5.6 0.7 - - - +
306B ALA* 2.9 31.2 + - + +
307B ILE 4.3 0.7 - - - +
309B LEU* 1.3 74.6 - - - +
311B SER* 1.3 59.1 + - - +
312B LYS 3.0 10.9 + - - -
313B ASN* 3.2 21.7 + - - +
317B PHE* 3.6 38.7 - - + -
319B LEU* 4.0 13.5 - - + -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 5.4 4.9 + - - -
44B ASN* 6.0 0.4 - - - +
307B ILE* 2.7 23.7 + - - +
308B GLU* 3.1 13.3 + - - -
310B LEU* 1.3 76.1 - - - +
312B LYS* 1.3 60.7 + - - +
313B ASN 3.2 6.5 + - - +
314B GLU* 5.1 3.8 - - - +
317B PHE* 3.8 13.4 - - - -
355B PHE* 4.2 23.0 - - - -
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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