Contacts of the helix formed by residues 299 - 317 (chain B) in PDB entry 6GR2
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 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 2.7 20.4 + - + +
297B ARG* 3.3 35.4 + - + +
298B GLY* 1.3 68.6 - - - +
300B TYR* 1.3 57.7 + - - +
301B ARG* 3.7 7.6 + - - +
302B ALA* 3.0 33.6 + - - +
303B PHE* 2.9 27.5 + - - +
305B ARG* 5.5 0.5 + - - -
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 5.2 2.0 - - + +
215B ASP* 2.9 39.5 + - - +
217B LYS* 5.8 1.6 - - + -
218B LEU* 3.4 40.5 - - + +
295B LEU* 4.2 21.3 - - + -
298B GLY* 2.9 36.1 + - - -
299B ASP* 1.3 70.1 - - - +
301B ARG* 1.3 57.2 + - - +
303B PHE* 3.6 6.1 - - + +
304B GLY 2.7 31.2 + - - -
339B TYR* 3.5 41.7 - - + +
355B LEU* 4.0 6.2 - - + +
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 5.2 5.7 - - + +
299B ASP* 3.3 6.6 + - - +
300B TYR* 1.3 79.7 - - - +
302B ALA* 1.3 56.6 + - - +
304B GLY* 3.5 1.0 + - - -
305B ARG* 3.0 38.3 + - - +
339B TYR* 3.7 21.8 - - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 4.2 8.5 - - + -
297B ARG* 4.8 4.5 - - - +
299B ASP* 3.0 36.1 + - + +
301B ARG* 1.3 74.0 - - - +
303B PHE* 1.3 67.4 + - - +
305B ARG* 3.1 37.0 + - - +
306B LEU* 3.1 20.6 + - + +
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.0 24.2 - - + -
41B ILE* 4.4 2.9 - - + -
53B LEU* 3.6 24.0 - - + -
291B ALA* 3.0 45.7 - - + +
294B ALA* 4.0 5.7 - - + +
295B LEU* 4.2 21.3 - - + +
299B ASP 2.9 18.0 + - - +
300B TYR* 3.6 11.0 - - + +
302B ALA* 1.3 76.3 - - - +
304B GLY* 1.3 60.9 + - - +
306B LEU* 3.3 9.9 + - - +
307B MET* 3.1 46.2 + - + +
355B LEU* 3.6 22.4 - - + -
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR 2.7 17.7 + - - -
303B PHE* 1.3 74.1 - - - +
305B ARG* 1.3 60.9 + - - +
307B MET* 3.1 20.4 + - - +
308B VAL* 3.2 18.0 + - - +
339B TYR* 3.2 33.4 - - - +
340B GLY* 3.5 5.3 - - - -
355B LEU* 5.5 0.4 - - - +
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Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 4.2 27.5 - - + +
299B ASP* 5.5 0.2 + - - -
301B ARG* 3.0 20.0 + - - +
302B ALA* 3.1 45.4 + - - +
304B GLY* 1.3 76.6 - - - +
306B LEU* 1.3 63.5 + - + +
308B VAL* 3.2 16.5 + - - +
309B GLU* 3.3 26.5 + - + +
339B TYR 3.9 1.3 + - - -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.9 16.8 - - + +
287B ARG* 3.8 19.3 - - + +
290B GLN* 3.6 30.3 - - + +
291B ALA* 3.5 37.5 - - + +
294B ALA* 5.1 2.7 - - + -
302B ALA* 3.1 19.1 + - + +
303B PHE* 3.3 6.0 + - - +
305B ARG* 1.3 74.9 - - + +
307B MET* 1.3 66.3 + - - +
309B GLU* 3.4 19.1 + - - +
310B SER* 3.0 22.5 + - - -
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Residues in contact with MET 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.1 13.0 - - + +
41B ILE* 4.6 4.7 - - + -
303B PHE* 3.1 44.1 + - + +
304B GLY* 3.1 13.8 + - - +
306B LEU* 1.3 77.4 - - - +
308B VAL* 1.3 60.5 + - - +
310B SER* 3.3 2.1 + - - -
311B HIS 3.1 16.8 + - - -
340B GLY 3.9 13.5 - - - +
341B SER* 4.1 7.6 - - - +
342B ARG* 3.3 24.6 - - + +
353B VAL* 3.6 42.8 - - + +
354B THR 4.5 0.2 - - - -
355B LEU* 3.9 24.0 - - + +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 4.8 8.5 - - + -
304B GLY 3.2 15.4 + - - +
305B ARG* 3.2 8.0 + - + +
306B LEU 3.2 0.2 - - - -
307B MET* 1.3 73.7 - - - +
309B GLU* 1.3 66.5 + - + +
311B HIS* 3.2 5.5 + - + +
312B ARG* 3.0 58.6 + - + +
329B VAL* 5.7 1.3 - - + -
333B LEU* 3.9 41.5 - - + -
339B TYR 4.8 1.1 - - - +
340B GLY* 4.0 6.3 - - - -
341B SER 3.9 9.9 - - - +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ARG* 3.6 33.3 + - - +
305B ARG* 3.3 27.9 + - + +
306B LEU* 3.7 16.1 - - - +
308B VAL* 1.3 75.5 - - + +
310B SER* 1.3 59.4 + - - +
312B ARG* 3.2 14.5 + - - +
313B SER* 2.8 31.9 + - - -
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.2 6.1 - - - -
280B HIS* 4.4 0.2 - - - -
284B GLU* 2.6 41.0 + - - -
287B ARG* 3.7 5.3 - - - +
306B LEU 3.0 14.2 + - - -
307B MET 3.4 10.1 - - - -
308B VAL 3.3 0.4 - - - -
309B GLU* 1.3 75.7 - - - +
311B HIS* 1.3 58.5 + - - +
313B SER* 3.4 1.4 + - - -
314B LEU* 2.9 33.0 + - - +
342B ARG* 3.4 24.5 + - - -
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Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B MET 3.1 6.2 + - - +
308B VAL* 3.6 9.4 - - + +
309B GLU 3.2 0.2 - - - -
310B SER* 1.3 73.1 - - - +
312B ARG* 1.3 57.6 + - + +
314B LEU* 3.1 7.4 + - - +
315B ARG* 2.7 54.6 + - - +
321B SER* 3.6 13.0 - - - -
325B LEU 4.2 3.4 - - - -
326B ASP* 3.0 30.7 + - - -
329B VAL* 3.3 41.5 - - + +
330B GLU* 5.5 1.8 + - - -
341B SER 4.2 3.1 - - - +
342B ARG* 3.5 18.8 - - + +
343B MET* 3.2 29.3 + - + +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 5.5 10.9 + - - +
308B VAL* 3.0 44.6 + - + +
309B GLU* 3.6 15.0 - - - +
311B HIS* 1.3 76.1 - - + +
313B SER* 1.3 58.0 + - - +
315B ARG* 4.1 33.6 - - - +
316B ASP* 2.8 41.4 + - - +
330B GLU* 5.8 3.2 + - - -
333B LEU* 5.7 1.2 - - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B HIS* 2.5 44.2 + - - +
287B ARG* 3.3 22.4 + - - -
309B GLU 2.8 16.8 + - - -
310B SER 3.6 1.8 - - - -
312B ARG* 1.3 72.4 - - - +
314B LEU* 1.3 60.1 + - - +
316B ASP* 5.1 0.4 - - - -
317B ASP* 2.9 35.2 + - - +
318B TYR* 3.0 8.3 + - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 3.5 21.8 - - + -
44B HIS* 3.8 7.0 - - + -
280B HIS* 3.2 29.8 - - + +
310B SER* 2.9 24.5 + - - +
311B HIS* 3.6 4.9 - - - +
313B SER* 1.3 76.3 - - - +
315B ARG* 1.3 57.8 + - - +
318B TYR* 3.6 5.5 - - + -
319B GLU 2.9 21.5 + - - -
320B VAL* 3.1 31.5 + - + +
321B SER* 3.9 2.0 + - - -
342B ARG* 3.5 28.5 - - - +
343B MET* 3.9 28.0 - - + -
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B HIS* 2.7 36.5 + - - +
312B ARG* 3.7 30.3 - - - +
314B LEU* 1.3 75.9 - - - +
316B ASP* 1.3 89.9 + - - +
319B GLU* 3.8 17.4 - - - +
321B SER* 4.0 15.3 - - - -
326B ASP* 3.5 37.8 - - - +
330B GLU* 4.8 9.9 + - - -
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ARG* 3.5 16.1 + - - -
312B ARG* 2.8 26.1 + - - +
313B SER* 5.1 0.4 - - - -
315B ARG* 1.3 115.2 + - - +
317B ASP* 1.3 69.4 + - - +
319B GLU* 3.5 11.3 - - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ARG* 3.2 36.9 + - - +
277B ARG* 2.7 33.6 + - - -
279B ARG* 2.8 53.0 + - - +
280B HIS* 4.1 9.5 + - + -
313B SER* 2.9 22.6 + - - +
316B ASP* 1.3 81.2 - - - +
318B TYR* 1.3 52.8 + - - +
319B GLU 3.4 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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