Contacts of the helix formed by residues 269 - 281 (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 TYR 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY* 3.2 27.9 + - - -
81A GLN* 3.6 17.6 + - + -
82B ALA* 3.8 18.8 - - + -
83B GLY* 3.3 39.6 - - - -
86B ILE* 3.7 9.2 - - + -
87B THR* 3.8 6.4 + - - -
267B ASN 3.6 19.7 - - - -
268B VAL* 1.3 78.1 - - - +
270B THR* 1.3 68.3 + - + +
273B ASP* 2.4 33.2 + - - +
274B PHE* 4.5 0.7 - - - -
292B LYS* 3.3 52.4 - - + -
293B CYS* 3.9 10.5 - - - +
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Residues in contact with THR 270 (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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68B TYR* 4.3 3.8 - - - +
72B ARG* 4.9 8.5 - - - -
80B GLY 5.3 0.2 - - - +
81B GLN 4.1 16.8 + - - +
86B ILE* 4.2 22.0 - - + -
269B TYR* 1.3 95.7 + - + +
271B ARG* 1.3 66.4 + - - +
272B PHE* 3.8 17.2 + - + +
273B ASP* 2.8 24.3 + - - -
274B PHE* 3.2 16.3 + - - -
293B CYS* 3.4 12.9 + - - +
298B GLU* 3.1 21.5 - - - +
302B ILE* 4.5 1.8 - - - -
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Residues in contact with ARG 271 (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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68B TYR* 4.4 3.2 - - - -
69B GLU* 2.8 18.0 + - - -
72B ARG* 2.6 34.2 - - - +
73B ARG* 5.4 2.0 - - - +
270B THR* 1.3 71.6 - - - +
272B PHE* 1.3 90.3 + - + +
274B PHE* 3.2 4.5 + - - +
275B ARG* 3.0 24.4 + - - +
298B GLU* 2.8 45.8 + - - +
301B ARG* 3.1 62.1 - - + +
302B ILE* 4.4 11.4 - - + -
305B LEU* 4.1 13.2 - - + +
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Residues in contact with PHE 272 (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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244A PRO* 6.1 0.7 - - + -
246A GLU* 3.3 61.8 - - + +
247A ASN* 4.5 14.8 - - + +
72B ARG* 3.9 16.8 - - - -
270B THR* 3.1 15.7 - - + +
271B ARG* 1.3 116.6 - - + +
273B ASP* 1.3 62.0 + - - +
275B ARG* 3.5 21.6 + - - +
276B GLU* 3.8 12.1 + - - +
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Residues in contact with ASP 273 (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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246A GLU 5.1 4.3 - - - +
81B GLN 4.3 8.0 - - - +
82B ALA* 4.7 4.9 - - - +
248B LEU* 4.8 3.6 - - - +
268B VAL* 3.3 19.8 - - + +
269B TYR 2.4 29.9 + - - +
270B THR* 2.8 12.1 + - - -
272B PHE* 1.3 78.4 - - - +
274B PHE* 1.3 65.7 + - - +
275B ARG 3.1 1.6 - - - -
276B GLU* 3.4 10.6 + - - +
277B LEU* 3.2 17.7 + - - +
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Residues in contact with PHE 274 (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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265B GLY* 3.3 7.6 - - - -
268B VAL* 3.0 48.9 - - + -
269B TYR* 4.4 1.6 - - - -
270B THR 3.2 11.6 + - - +
271B ARG* 3.2 6.8 + - - +
273B ASP* 1.3 75.5 - - - +
275B ARG* 1.3 60.1 + - - +
277B LEU* 3.1 13.7 + - + +
278B PHE* 2.9 48.6 + + + -
286B VAL* 3.3 35.0 - - + -
288B PRO* 3.2 27.4 - - + -
293B CYS* 5.0 0.2 - - + -
302B ILE* 3.4 40.8 - - + -
305B LEU* 4.8 2.7 - - + -
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Residues in contact with ARG 275 (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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247A ASN* 3.1 36.4 + - - +
249A ASP* 3.2 31.7 + - - +
271B ARG 3.0 12.4 + - - +
272B PHE* 3.5 17.5 + - - +
273B ASP 3.1 0.2 - - - -
274B PHE* 1.3 78.0 - - - +
276B GLU* 1.3 69.1 + - - +
278B PHE* 3.3 4.3 + - - +
279B ALA* 2.7 39.2 + - + +
305B LEU* 4.2 15.7 - - + +
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Residues in contact with GLU 276 (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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246A GLU 6.0 1.3 - - - +
247A ASN* 4.5 3.3 - - - +
248A LEU* 5.0 3.8 + - - +
249A ASP* 3.2 23.6 + - - +
280A LYS* 3.5 25.6 + - - -
248B LEU* 4.8 4.7 - - + -
272B PHE 3.8 13.0 + - - +
273B ASP* 3.4 11.2 + - - +
275B ARG* 1.3 89.2 + - - +
277B LEU* 1.3 67.5 + - - +
279B ALA* 3.1 8.9 + - - +
280B LYS* 2.9 50.9 + - + +
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Residues in contact with LEU 277 (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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248B LEU* 3.1 40.8 - - + +
251B LEU* 4.6 4.7 - - + -
264B ALA* 4.8 5.4 - - + +
265B GLY* 5.1 1.1 - - - +
268B VAL* 4.8 10.1 - - + -
273B ASP 3.2 7.7 + - - +
274B PHE* 3.1 40.4 + - + +
276B GLU* 1.3 82.0 - - - +
278B PHE* 1.3 65.7 + - + +
280B LYS* 3.0 11.5 + - - +
281B ARG 3.3 7.1 + - - -
282B ALA* 3.7 17.7 + - + +
283B VAL* 4.0 36.1 - - + -
286B VAL* 4.2 9.4 - - + -
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Residues in contact with PHE 278 (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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274B PHE* 2.9 41.3 + + + +
275B ARG* 3.9 3.4 - - - +
277B LEU* 1.3 76.7 - - + +
279B ALA* 1.3 63.2 + - - +
281B ARG* 3.0 18.9 + - - +
282B ALA 5.3 0.7 - - - +
283B VAL* 4.1 16.2 - - + -
286B VAL* 3.3 43.1 - - + -
302B ILE 3.8 7.4 - - - -
305B LEU* 3.8 35.4 - - + +
306B ALA* 3.5 26.7 - - + -
309B ASP* 4.5 21.1 - - + +
311B ILE* 4.4 11.4 - - + -
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Residues in contact with ALA 279 (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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275B ARG* 2.7 22.3 + - + +
276B GLU* 3.2 23.1 - - - +
277B LEU 3.0 0.2 - - - -
278B PHE* 1.3 78.3 - - - +
280B LYS* 1.3 61.2 + - + +
281B ARG* 3.2 10.6 + - - +
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Residues in contact with LYS 280 (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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276A GLU* 5.9 3.8 - - - -
280A LYS* 5.2 7.1 - - - +
248B LEU* 4.4 18.4 - - + +
249B ASP* 2.8 39.6 + - - +
252B ALA* 4.0 19.7 - - + +
256B ARG* 5.0 2.4 + - - -
276B GLU* 2.9 50.5 + - - +
277B LEU* 3.0 6.0 + - - +
279B ALA* 1.3 75.4 - - + +
281B ARG* 1.3 80.3 + - - +
282B ALA* 3.4 6.5 + - + +
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Residues in contact with ARG 281 (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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252B ALA* 4.6 3.8 - - - +
255B ARG* 3.6 24.2 + - - +
256B ARG* 4.4 28.1 + - - +
277B LEU 3.3 0.8 + - - -
278B PHE* 3.0 17.9 + - - +
279B ALA 3.8 10.0 + - - +
280B LYS* 1.3 81.1 + - - +
282B ALA* 1.3 60.9 + - - +
283B VAL 3.6 3.6 - - - -
309B ASP* 6.0 2.7 - - - +
311B ILE* 6.3 2.0 - - - -
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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