Contacts of the helix formed by residues 295 - 309 (chain B) in PDB entry 2QQ6
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 GLY 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B SER* 3.5 6.0 + - - -
93B GLU* 3.3 16.6 - - - -
290B VAL* 3.3 21.1 + - - -
293B CYS* 4.0 0.4 - - - -
294B GLY* 1.3 81.0 - - - +
296B LEU* 1.3 56.2 + - - -
297B ALA 3.3 2.5 - - - -
298B GLU* 3.2 1.6 + - - +
299B ALA* 2.8 35.3 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLU* 2.8 19.2 + - - +
94B THR* 3.6 34.8 - - + +
97B TRP* 4.1 20.6 - - + -
108B VAL* 3.9 29.4 - - + -
112B LEU* 4.1 11.7 - - + -
290B VAL* 3.8 15.9 - - + -
295B GLY* 1.3 70.7 - - - -
297B ALA* 1.3 51.4 + - - +
299B ALA* 3.2 3.2 + - - +
300B LYS* 2.7 35.9 + - - +
326B ALA* 4.2 17.9 - - + +
330B VAL* 3.5 26.7 - - + +
375B LEU* 5.5 1.6 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLU* 4.5 27.6 - - + +
68B TYR* 6.1 3.6 - - + -
93B GLU* 3.1 16.5 + - - +
97B TRP* 3.7 18.4 - - + +
112B LEU* 4.9 5.6 - - + +
296B LEU* 1.3 78.2 - - - +
298B GLU* 1.3 63.6 + - - +
300B LYS* 2.9 18.5 + - - +
301B ARG* 3.0 17.5 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.6 20.2 + - + -
72B ARG* 5.2 0.7 - - - -
93B GLU* 4.1 0.8 + - - -
270B THR* 3.1 34.0 - - - +
271B ARG* 2.8 47.9 + - - +
293B CYS* 4.3 2.9 - - - +
294B GLY* 3.8 24.7 - - - +
295B GLY 3.2 9.2 + - - +
297B ALA* 1.3 78.3 - - - +
299B ALA* 1.3 64.6 + - - +
301B ARG* 3.0 10.0 + - - +
302B ILE* 2.9 33.2 + - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PRO* 5.2 2.7 - - + -
290B VAL* 3.6 28.3 - - + -
293B CYS* 4.2 9.1 - - - -
295B GLY 2.8 20.4 + - - +
296B LEU* 3.5 4.7 - - - +
298B GLU* 1.3 73.6 - - - +
300B LYS* 1.3 61.9 + - - +
302B ILE* 3.4 13.5 + - - +
303B ALA* 3.1 20.8 + - - +
313B PHE* 3.8 13.3 - - + -
330B VAL* 4.4 8.1 - - + -
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.0 45.2 + - + +
113B GLY* 5.1 1.9 - - - -
296B LEU 2.7 16.9 + - - +
297B ALA* 2.9 10.3 + - - +
299B ALA* 1.3 70.9 - - - +
301B ARG* 1.3 67.6 + - - +
303B ALA* 3.1 6.8 + - - +
304B ASN* 2.9 46.0 + - - +
330B VAL* 4.2 13.7 - - + +
333B ALA* 4.0 18.8 - - + -
334B VAL* 4.2 10.1 - - + -
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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
----------------------------------------------------------
65B GLU* 4.5 17.9 + - - +
69B GLU* 6.1 0.2 - - - -
271B ARG* 3.1 56.3 - - + +
297B ALA 3.0 14.1 + - - +
298B GLU* 3.0 15.5 + - - +
300B LYS* 1.3 74.9 - - - +
302B ILE* 1.3 63.6 + - - +
304B ASN* 2.9 14.3 + - - +
305B LEU* 2.9 28.9 + - + +
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR 4.5 3.6 - - - -
271B ARG* 4.4 14.4 - - - +
274B PHE* 3.4 57.0 - - + -
278B PHE* 3.8 4.1 - - + -
286B VAL* 4.7 4.7 - - + -
288B PRO* 3.8 28.0 - - + -
293B CYS* 4.3 10.5 - - + -
298B GLU* 2.9 30.0 + - + +
299B ALA* 3.5 8.7 - - - +
300B LYS 3.2 0.2 - - - -
301B ARG* 1.3 75.4 - - - +
303B ALA* 1.3 61.6 + - - +
305B LEU* 3.3 12.9 + - - +
306B ALA* 3.3 18.4 + - - +
313B PHE* 4.5 2.9 - - + -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA 3.1 11.4 + - - +
300B LYS* 3.4 8.5 - - - +
302B ILE* 1.3 76.0 - - - +
304B ASN* 1.3 57.3 + - - +
306B ALA* 3.3 3.9 + - - +
307B GLU* 2.9 15.4 + - - +
313B PHE* 3.7 37.2 - - + -
334B VAL* 3.9 22.2 - - + -
336B ASN* 2.8 25.6 - - - +
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Residues in contact with ASN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LYS* 2.9 49.7 + - - +
301B ARG* 2.9 14.8 + - - +
303B ALA* 1.3 75.4 - - - +
305B LEU* 1.3 65.1 + - + +
307B GLU* 3.3 12.5 + - - +
308B LEU* 3.2 24.2 + - - +
334B VAL* 4.7 8.0 - - - +
336B ASN* 5.6 0.9 + - - -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 4.1 29.8 - - + +
274B PHE* 4.7 3.8 - - + -
275B ARG* 4.2 21.8 - - + +
278B PHE* 3.8 17.9 - - + +
301B ARG* 2.9 17.6 + - + +
302B ILE* 3.5 10.5 - - - +
303B ALA 3.3 0.2 - - - -
304B ASN* 1.3 75.4 - - + +
306B ALA* 1.3 58.4 + - - +
308B LEU* 3.0 43.8 - - + +
309B ASP* 3.8 6.4 + - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 3.5 33.6 - - + -
286B VAL* 3.8 10.8 - - + -
302B ILE 3.3 5.2 + - - +
303B ALA* 3.3 10.5 + - - +
304B ASN 3.2 0.4 - - - -
305B LEU* 1.3 75.2 - - - +
307B GLU* 1.3 65.5 + - - +
308B LEU 3.1 2.0 - - - -
309B ASP* 2.8 15.1 + - - +
311B ILE* 3.0 36.5 + - + +
312B PRO 5.1 0.9 - - - +
313B PHE* 5.7 1.3 - - + -
336B ASN* 4.1 1.3 - - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 2.9 13.7 + - - +
304B ASN* 3.3 18.8 - - - +
306B ALA* 1.3 74.8 - - - +
308B LEU* 1.3 75.3 + - - +
310B TYR* 2.8 32.9 + - - +
311B ILE 4.7 2.0 - - - +
335B SER* 4.0 22.0 + - - +
336B ASN* 3.5 18.8 + - + +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASN 3.5 10.5 - - - +
305B LEU* 3.0 36.3 - - + +
306B ALA 3.1 0.2 - - - -
307B GLU* 1.3 89.8 + - - +
309B ASP* 1.3 62.5 + - - +
310B TYR* 3.6 13.4 + - - -
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Residues in contact with ASP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.5 22.8 - - + +
281B ARG* 6.0 2.4 - - - +
305B LEU 4.5 5.2 - - - +
306B ALA* 2.8 11.0 + - - +
308B LEU* 1.3 81.9 - - - +
310B TYR* 1.3 74.7 + - - +
311B ILE* 3.2 21.8 + - + +
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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
------------------------------------------------------------
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