Contacts of the helix formed by residues 259 - 273 (chain B) in PDB entry 1QQW
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 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LYS* 2.6 27.2 + - - -
124B ASP* 3.5 7.9 - - - -
257B ASP* 3.0 11.1 + - - +
258B PRO* 1.3 82.8 - - - +
260B TYR* 1.3 63.1 + - - +
261B GLY 3.4 2.2 - - - -
262B ILE* 3.2 7.8 + - + +
263B ARG* 3.0 23.9 + - - +
170C ARG* 2.7 33.7 + - - -
175C HIS 4.5 0.7 - - - +
176C LEU* 3.3 28.6 - - + +
177C LYS* 4.7 10.0 + - - +
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Residues in contact with TYR 260 (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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125B THR* 3.4 30.7 - - + -
207B ASP* 2.7 30.2 + - - -
208B GLY* 4.3 12.8 - - - -
245B LEU* 4.3 8.6 - - + +
253B LEU* 4.2 30.1 - - + -
257B ASP* 2.9 36.8 + - + +
258B PRO 3.3 2.6 + - - -
259B ASP* 1.3 76.5 - - - +
261B GLY* 1.3 67.5 + - - +
262B ILE 3.2 0.3 + - - -
263B ARG* 3.3 1.8 + - + +
264B ASP* 2.9 41.2 + - + +
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Residues in contact with GLY 261 (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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124B ASP* 3.1 16.2 + - - +
208B GLY* 5.1 7.0 - - - -
209B HIS* 3.4 33.1 - - - -
260B TYR* 1.3 85.7 - - - +
262B ILE* 1.3 64.0 + - - +
264B ASP* 3.7 5.5 + - - +
265B LEU* 3.3 15.6 + - - +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 3.9 18.4 - - + +
78B GLY 4.1 8.5 - - - +
79B ALA* 4.0 25.6 - - + -
124B ASP* 3.2 6.5 + - - +
209B HIS* 4.4 0.4 + - - +
259B ASP* 3.2 35.6 + - + +
260B TYR 3.2 0.4 - - - -
261B GLY* 1.3 79.4 - - - +
263B ARG* 1.3 66.3 + - - +
265B LEU* 3.3 3.1 + - - +
266B PHE* 3.1 22.5 + - + +
325B TYR* 5.6 2.5 - - + -
174C THR 3.4 17.7 - - - +
175C HIS* 4.2 20.4 - - + -
176C LEU* 3.2 19.7 - - + -
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Residues in contact with ARG 263 (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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6B ASP* 4.1 14.4 + - - +
8B ALA* 4.4 1.8 - - + +
9B SER* 5.0 5.7 + - - -
257B ASP* 3.0 36.0 + - - +
259B ASP* 3.0 11.1 + - - +
260B TYR* 3.8 3.4 - - + +
262B ILE* 1.3 79.5 - - - +
264B ASP* 1.3 65.0 + - - +
266B PHE* 3.2 5.0 + - - +
267B ASN* 2.9 50.4 + - - +
176C LEU* 3.3 44.0 - - + +
177C LYS 5.4 4.4 + - - +
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASP 4.8 1.9 - - - +
208B GLY* 4.1 19.0 - - - -
209B HIS 4.4 3.6 + - - -
210B ARG* 2.7 41.4 + - - +
211B HIS* 5.9 0.3 - - - -
260B TYR* 2.9 40.6 + - + +
261B GLY* 3.8 6.5 - - - +
263B ARG* 1.3 72.5 - - - +
265B LEU* 1.3 63.7 + - - +
267B ASN* 4.0 4.3 - - - +
268B ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 265 (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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79B ALA* 4.1 15.3 - - + -
80B GLY 4.0 20.4 - - - +
81B ALA* 4.2 6.5 - - + -
113B PHE* 3.8 36.3 - - + -
209B HIS* 4.5 6.5 - - + -
210B ARG* 4.4 10.8 - - + +
261B GLY 3.3 14.7 + - - +
262B ILE 3.6 2.7 - - - +
264B ASP* 1.3 84.3 + - - +
266B PHE* 1.3 65.0 + - - +
268B ALA* 3.3 4.6 + - - +
269B ILE* 3.2 31.6 + - + +
275B PRO* 4.3 23.3 - - + -
318B LEU* 4.6 4.3 - - + -
321B ASN* 4.9 1.1 - - - +
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Residues in contact with PHE 266 (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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7B PRO* 4.7 3.8 - - + -
8B ALA* 4.0 24.5 - - + -
11B GLN* 5.5 0.9 - - + -
262B ILE* 3.1 13.1 + - + +
263B ARG* 3.6 9.9 - - - +
265B LEU* 1.3 79.1 - - - +
267B ASN* 1.3 59.7 + - - +
269B ILE 3.3 1.6 + - - -
270B ALA* 2.9 34.5 + - + +
321B ASN* 3.0 51.2 - - + +
322B PRO* 4.4 6.3 - - + -
173C GLN* 3.8 43.5 - - + -
174C THR* 3.8 27.1 - - + -
176C LEU* 5.8 0.4 - - + -
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Residues in contact with ASN 267 (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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6B ASP* 3.3 19.7 + - - +
7B PRO* 3.0 18.0 - - + +
8B ALA* 2.9 32.0 + - - +
263B ARG* 2.9 45.0 + - - +
264B ASP* 4.0 3.5 - - - +
266B PHE* 1.3 74.2 - - - +
268B ALA* 1.3 63.8 + - - +
270B ALA* 3.4 0.4 + - - -
271B THR* 2.8 33.2 + - + +
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Residues in contact with ALA 268 (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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210B ARG* 3.7 36.3 - - - +
264B ASP 3.0 19.1 + - - +
265B LEU 3.5 5.2 - - - +
266B PHE 3.2 0.2 - - - -
267B ASN* 1.3 76.9 - - - +
269B ILE* 1.3 59.4 + - - +
271B THR* 3.0 12.8 + - - -
273B LYS* 2.9 42.8 + - + +
275B PRO* 5.0 0.9 - - + -
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Residues in contact with ILE 269 (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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81B ALA* 3.8 23.8 - - + -
265B LEU* 3.2 14.4 + - + +
266B PHE 3.7 0.4 - - - +
268B ALA* 1.3 75.0 - - - +
270B ALA* 1.3 62.0 + - - +
271B THR 3.0 5.7 + - - -
272B GLY 3.2 10.6 + - - -
273B LYS 4.8 0.2 - - - +
274B TYR* 3.7 17.7 - - + +
275B PRO* 3.9 10.8 - - + -
318B LEU* 3.8 28.0 - - + +
319B ASN* 4.0 5.4 - - - -
320B ARG* 3.8 18.4 - - - +
321B ASN* 3.2 48.5 - - - +
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Residues in contact with ALA 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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7B PRO* 3.6 33.5 - - + +
266B PHE* 2.9 25.6 + - + +
267B ASN* 3.8 0.7 - - - +
269B ILE* 1.3 76.4 - - - +
271B THR* 1.3 60.5 + - - +
272B GLY 3.6 1.4 + - - -
321B ASN* 4.2 7.0 - - - +
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Residues in contact with THR 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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7B PRO* 3.8 21.5 - - + -
267B ASN* 2.8 22.6 + - + +
268B ALA* 3.0 8.7 + - - -
269B ILE 3.0 1.0 - - - -
270B ALA* 1.3 83.2 - - - +
272B GLY* 1.3 55.5 + - - +
273B LYS* 2.9 35.2 + - - -
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Residues in contact with GLY 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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269B ILE 3.2 7.4 + - - -
270B ALA 3.6 1.8 + - - -
271B THR* 1.3 74.6 - - - +
273B LYS* 1.3 58.1 + - - +
274B TYR* 3.2 39.4 + - - -
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Residues in contact with LYS 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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210B ARG* 4.8 9.2 + - - +
240B GLN* 6.1 0.2 - - - +
268B ALA* 2.9 33.6 + - + +
271B THR* 2.9 28.8 + - - +
272B GLY* 1.3 76.8 - - - +
274B TYR* 1.3 65.7 + - - +
275B PRO* 3.2 9.1 - - - +
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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