Contacts of the helix formed by residues 259 - 273 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B ARG* 2.7 41.3 + - - -
176B LEU* 3.4 26.2 - - + +
177B LYS* 4.5 7.1 + - - +
77C LYS* 2.8 20.2 + - - +
124C ASP* 3.3 7.2 - - - -
257C ASP* 3.1 11.7 + - - +
258C PRO* 1.3 83.1 - - - +
260C TYR* 1.3 66.0 + - - +
261C GLY 3.2 2.7 - - - -
262C ILE* 3.0 11.9 + - + -
263C ARG* 2.9 21.2 + - - +
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Residues in contact with TYR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASP* 4.7 1.1 - - + -
125C THR* 3.5 29.2 - - + -
207C ASP* 2.5 31.2 + - - -
208C GLY* 4.1 17.7 - - - -
245C LEU* 4.3 9.2 - - + +
253C LEU* 4.1 28.0 - - + -
257C ASP* 2.9 31.7 + - + +
258C PRO 3.2 1.8 + - - -
259C ASP* 1.3 76.6 - - - +
261C GLY* 1.3 62.7 + - - +
263C ARG* 3.3 3.3 + - - +
264C ASP* 2.8 50.9 + - + +
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Residues in contact with GLY 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ASP* 2.9 18.7 + - - +
208C GLY* 5.1 7.2 - - - -
209C HIS* 3.9 23.6 + - - -
260C TYR* 1.3 88.0 - - - +
262C ILE* 1.3 62.2 + - - +
264C ASP* 3.9 4.3 - - - +
265C LEU* 3.2 22.9 + - - +
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B THR 3.4 25.6 - - - +
175B HIS* 4.3 19.1 - - + +
176B LEU* 3.7 9.0 - - + -
77C LYS* 3.4 33.4 - - - +
78C GLY 4.1 10.1 - - - +
79C ALA* 3.9 27.5 - - + +
124C ASP* 3.3 5.4 + - - +
209C HIS* 5.8 0.2 - - - +
259C ASP* 3.0 22.2 + - + +
261C GLY* 1.3 76.0 - - - +
263C ARG* 1.3 67.5 + - - +
265C LEU* 3.3 2.4 + - - +
266C PHE* 3.0 25.1 + - + +
325C TYR* 5.5 3.6 - - + -
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Residues in contact with ARG 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 3.8 42.1 - - + +
177B LYS* 5.1 8.1 + - - +
6C ASP* 3.9 15.5 + - - +
8C ALA* 4.6 2.5 - - + +
9C SER* 4.4 10.7 + - - -
257C ASP* 2.6 39.0 + - - +
259C ASP* 2.9 13.5 + - - +
260C TYR* 3.7 4.0 - - - +
262C ILE* 1.3 75.9 - - - +
264C ASP* 1.3 64.1 + - - +
266C PHE* 3.2 3.5 + - - +
267C ASN* 3.0 48.4 + - - +
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Residues in contact with ASP 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ASP 5.5 1.1 - - - +
208C GLY* 4.3 16.4 - - - -
209C HIS 4.6 1.6 + - - -
210C ARG* 2.8 39.6 + - - +
260C TYR* 2.8 45.4 + - + +
261C GLY* 3.9 6.0 - - - +
263C ARG* 1.3 72.9 - - - +
265C LEU* 1.3 64.3 + - - +
267C ASN* 3.7 5.7 + - - +
268C ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA* 4.3 12.8 - - + -
80C GLY 4.0 20.6 - - - +
81C ALA* 4.1 5.6 - - + -
113C PHE* 4.0 35.2 - - + -
209C HIS* 4.8 6.1 - - + -
210C ARG* 4.0 28.0 - - + +
261C GLY 3.2 15.1 + - - +
262C ILE 3.7 2.2 - - - +
264C ASP* 1.3 81.0 + - - +
266C PHE* 1.3 70.2 + - - +
268C ALA* 3.1 12.8 + - - +
269C ILE* 3.2 25.3 + - + +
275C PRO* 4.3 11.0 - - + -
318C LEU* 4.8 4.0 - - + -
321C ASN* 5.6 0.4 - - - +
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLN* 3.9 32.8 - - + -
174B THR* 3.5 38.1 - - + -
176B LEU* 5.5 1.1 - - + -
7C PRO* 4.7 3.8 - - + -
8C ALA* 4.0 25.1 - - + -
11C GLN* 5.7 1.3 - - + -
262C ILE* 3.0 17.6 + - + +
263C ARG* 3.6 7.0 - - - +
265C LEU* 1.3 81.1 - - - +
267C ASN* 1.3 59.6 + - - +
269C ILE 3.3 0.5 + - - -
270C ALA* 2.9 35.5 + - + -
321C ASN* 2.9 48.3 - - + +
322C PRO* 4.4 7.0 - - + -
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Residues in contact with ASN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASP* 3.5 19.7 + - - +
7C PRO* 3.5 10.7 - - + +
8C ALA* 3.1 31.5 + - - +
263C ARG* 3.0 42.0 + - - +
264C ASP* 4.1 5.6 - - - +
266C PHE* 1.3 75.8 - - - +
268C ALA* 1.3 68.8 + - - +
270C ALA* 3.0 6.7 + - - +
271C THR* 2.9 29.6 + - + +
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ARG* 3.6 31.9 - - - +
264C ASP 3.2 12.3 + - - +
265C LEU 3.1 9.5 + - - +
267C ASN* 1.3 77.1 - - - +
269C ILE* 1.3 62.9 + - - +
271C THR* 2.9 20.6 + - - -
273C LYS* 2.9 39.5 + - + +
275C PRO* 4.8 1.8 - - + -
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.6 27.1 - - + -
265C LEU* 3.2 18.3 + - + +
266C PHE 3.6 0.4 - - - +
268C ALA* 1.3 79.3 - - - +
270C ALA* 1.3 63.2 + - - +
271C THR 3.1 1.0 + - - -
272C GLY 3.1 10.7 + - - -
274C TYR* 3.1 25.2 + - + +
275C PRO* 4.1 9.4 - - + -
318C LEU* 3.7 22.7 - - + +
319C ASN 3.9 4.9 - - - -
320C ARG* 3.6 25.4 - - - +
321C ASN* 2.9 44.0 - - - +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO* 3.5 31.6 - - + +
266C PHE* 2.9 25.1 + - + +
267C ASN* 3.0 6.9 + - - +
269C ILE* 1.3 75.7 - - - +
271C THR* 1.3 59.7 + - - +
272C GLY 3.5 1.1 + - - -
321C ASN* 4.0 7.9 - - - +
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO* 4.0 21.1 - - + -
267C ASN* 2.9 19.7 + - + +
268C ALA* 2.9 11.1 + - - -
270C ALA* 1.3 81.6 - - - +
272C GLY* 1.3 62.0 + - - +
273C LYS* 3.1 30.3 + - - +
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Residues in contact with GLY 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ILE 3.1 6.3 + - - -
270C ALA 3.5 1.6 + - - -
271C THR* 1.3 77.4 - - - +
273C LYS* 1.3 58.7 + - - +
274C TYR* 3.3 39.9 + - - -
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Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ARG* 5.1 5.8 + - - +
240C GLN* 6.1 0.3 - - - +
268C ALA* 2.9 33.3 + - + +
271C THR* 3.6 26.8 + - - +
272C GLY* 1.3 77.2 - - - +
274C TYR* 1.3 64.1 + - - +
275C PRO* 3.1 11.7 - - - +
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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