Contacts of the helix formed by residues 270 - 274 (chain A) in PDB entry 1QWN
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 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 6.1 0.2 - - - -
268A SER* 3.0 17.2 + - - +
269A TYR* 1.3 83.4 - - - +
271A ILE* 1.3 64.1 + - - +
272A PRO* 3.6 12.4 - - + +
273A HIS* 2.8 41.1 + - - -
274A THR* 2.8 14.6 + - - -
289A ARG* 4.3 6.6 + - - -
299A TRP* 5.6 0.9 - - - -
339A GLY 3.6 7.6 - - - -
340A ASP* 3.4 28.4 - - - +
2004A TRS 4.7 8.3 + - - +
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Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASP* 1.3 72.8 - - - +
272A PRO* 1.3 72.9 - - + +
273A HIS 3.0 1.6 + - - -
274A THR* 3.1 17.0 + - - +
275A CYS* 3.6 6.3 + - + -
282A CYS* 3.5 18.2 - - + +
285A PHE* 3.9 13.5 - - + +
286A ASP* 3.4 44.6 + - + +
337A PRO 5.7 0.2 - - - +
338A LEU* 3.8 28.5 - - + -
339A GLY* 3.5 30.6 + - - +
340A ASP* 4.8 1.2 + - - +
343A ARG* 3.9 7.9 - - - +
344A PHE* 6.1 0.4 - - + -
353A GLN* 3.8 11.4 - - - +
357A TYR* 4.7 1.8 - - - +
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Residues in contact with PRO 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASP* 3.5 12.6 - - - +
271A ILE* 1.3 94.3 - - + +
273A HIS* 1.3 62.9 + - - +
274A THR 3.5 0.2 - - - -
276A GLY 4.3 1.4 - - - +
279A PRO* 3.2 28.4 - - + +
282A CYS* 3.2 20.5 - - + +
283A CYS* 3.8 17.0 - - + +
289A ARG* 3.6 26.7 - - - +
299A TRP* 3.6 37.5 - - + -
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Residues in contact with HIS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A MET* 5.7 0.2 - - - +
265A PRO* 5.8 0.3 - - - +
266A PHE* 3.3 32.6 - + + +
267A TYR* 3.7 30.0 - + + -
268A SER* 3.4 33.2 - - - +
270A ASP* 2.8 30.2 + - - +
272A PRO* 1.3 75.1 - - + +
274A THR* 1.3 63.9 + - - +
275A CYS 3.9 0.4 - - - -
276A GLY 4.5 3.1 - - - -
279A PRO* 3.8 15.2 - - + +
299A TRP* 3.9 26.5 - + - -
2002A MPD 2.8 33.9 + - + -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A MET* 3.8 18.2 - - + -
266A PHE* 4.8 0.4 - - - -
269A TYR* 3.5 26.3 + - - +
270A ASP 2.8 22.7 + - - +
271A ILE* 3.1 12.7 + - - +
273A HIS* 1.3 83.9 - - - +
275A CYS* 1.3 62.7 + - - +
276A GLY 3.4 1.8 - - - -
325A LYS* 2.8 29.6 + - - +
336A ILE* 3.6 10.9 - - - +
337A PRO* 3.2 34.8 + - + -
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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
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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