Contacts of the helix formed by residues 231 - 241 (chain A) in PDB entry 3Q2H
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLY 4.3 4.3 - - - +
229A SER 4.2 1.2 + - - -
230A TYR* 1.3 75.1 - - - +
232A ALA* 1.3 58.9 + - - +
233A ASN* 3.1 16.2 + - - -
234A ARG* 2.8 30.0 + - - +
235A GLN* 2.9 13.3 + - - +
280A THR* 4.4 5.4 - - + -
281A SER* 5.6 9.2 - - - +
602A CD 2.2 30.7 - - - -
28B HIS* 2.9 20.6 - - + -
222B PRO* 5.6 0.5 - - - +
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Residues in contact with ALA 232 (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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231A ASP* 1.3 76.0 - - - +
233A ASN* 1.3 58.3 + - - +
235A GLN* 3.4 9.8 + - - +
236A CYS* 3.0 32.4 + - - -
246A HIS* 3.6 36.6 - - + +
257A LEU* 3.9 4.1 - - + +
276A TRP* 4.3 11.4 - - + -
280A THR* 3.7 20.5 - - + +
281A SER 5.4 0.9 - - - +
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Residues in contact with ASN 233 (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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231A ASP* 3.1 13.4 + - - +
232A ALA* 1.3 74.8 - - - +
234A ARG* 1.3 66.6 + - + +
236A CYS* 3.4 2.8 + - - +
237A GLN* 3.0 33.9 + - + +
244A SER 4.1 1.1 - - - +
245A LYS* 3.3 19.0 - - + +
246A HIS* 2.9 36.5 + - - +
602A CD 4.3 10.7 - - - -
220B GLN* 5.2 7.9 + - - -
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Residues in contact with ARG 234 (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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22A HIS* 5.7 1.2 + - - -
25A GLY* 6.2 1.6 - - - -
229A SER 5.1 1.7 + - - +
230A TYR* 4.1 20.4 - - + -
231A ASP* 2.8 33.5 + - - +
233A ASN* 1.3 74.3 - - - +
235A GLN* 1.3 65.0 + - - +
237A GLN* 3.1 32.1 + - - +
238A PHE* 2.9 64.5 + - + -
602A CD 4.3 2.7 - - - -
24B SER* 3.3 23.8 + - - -
25B GLY* 3.6 21.3 - - - -
28B HIS* 3.7 31.0 - - + +
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Residues in contact with GLN 235 (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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140A GLY* 5.3 0.3 - - - -
141A LEU* 4.2 17.0 + - + +
230A TYR* 3.2 21.3 + - + +
231A ASP 2.9 12.9 + - - +
232A ALA* 3.6 11.4 - - - +
233A ASN 3.4 0.2 - - - -
234A ARG* 1.3 74.5 - - - +
236A CYS* 1.3 61.8 + - - +
238A PHE* 3.2 21.8 + - - +
239A THR* 3.3 16.6 + - - -
257A LEU* 3.7 21.3 - - + +
275A PRO 4.6 0.5 - - - +
276A TRP* 3.6 8.7 - - - -
277A ALA* 2.8 34.1 + - - +
280A THR* 2.5 38.3 + - - +
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Residues in contact with CYS 236 (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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232A ALA 3.0 15.1 + - - +
233A ASN 3.6 5.2 - - - +
234A ARG 3.2 0.2 - - - -
235A GLN* 1.3 75.3 - - - +
237A GLN* 1.3 52.6 + - - +
239A THR* 3.2 1.3 + - - -
240A PHE* 2.8 40.6 + - - +
244A SER* 3.8 4.5 - - - +
245A LYS* 3.5 17.5 - - - +
246A HIS* 3.7 4.0 - - - -
257A LEU* 3.4 19.3 - - - -
258A TRP 3.5 3.1 - - - -
259A CYS* 2.1 56.5 - - + -
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Residues in contact with GLN 237 (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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21A PHE* 3.4 10.9 - - - -
233A ASN* 3.0 19.7 + - + +
234A ARG* 3.3 36.3 + - - +
236A CYS* 1.3 74.9 - - - +
238A PHE* 1.3 61.5 + - - +
241A GLY* 2.9 35.6 + - - +
242A GLU* 2.7 33.5 + - - +
244A SER 3.1 22.0 - - - +
24B SER* 3.3 23.4 + - - +
27B LYS* 3.1 22.5 - - - +
28B HIS 5.6 0.2 + - - -
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Residues in contact with PHE 238 (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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21A PHE* 4.4 5.6 - + - -
22A HIS* 3.8 19.3 - + - -
29A TYR* 3.7 35.2 - + - +
106A ARG* 2.9 32.7 + - - +
139A ASP 3.6 1.0 - - - -
140A GLY* 3.5 23.1 + - - -
141A LEU* 4.3 10.5 - - + -
230A TYR* 3.4 50.0 - + + -
234A ARG* 2.9 55.4 + - - -
235A GLN* 3.2 11.6 + - - +
237A GLN* 1.3 76.6 - - - +
239A THR* 1.3 57.6 + - - +
24B SER* 4.3 1.3 - - - -
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Residues in contact with THR 239 (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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106A ARG* 4.4 5.1 + - - -
139A ASP* 3.1 25.0 + - + +
140A GLY* 3.9 5.0 - - - -
142A GLN* 4.2 6.6 + - - +
235A GLN 3.3 10.4 + - - -
236A CYS* 3.2 3.9 + - - -
237A GLN 3.1 0.2 - - - -
238A PHE* 1.3 81.8 - - - +
240A PHE* 1.3 82.0 + - + +
241A GLY 3.6 1.2 + - - -
257A LEU* 5.3 5.2 - - - +
259A CYS* 5.5 0.2 - - - -
272A LYS* 3.5 40.1 + - + +
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Residues in contact with PHE 240 (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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236A CYS 2.8 13.0 + - - -
239A THR* 1.3 91.7 - - + +
241A GLY* 1.3 60.5 + - - +
243A ASP* 5.3 1.0 + - - +
244A SER* 3.6 16.8 + - - +
257A LEU 5.3 0.4 - - - -
259A CYS* 3.3 43.5 - - + -
270A GLN* 3.2 50.8 + - + +
271A THR* 4.0 25.4 - - - -
272A LYS* 3.5 23.8 - - + -
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Residues in contact with GLY 241 (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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21A PHE* 4.2 13.2 - - - -
106A ARG* 4.8 3.3 - - - +
237A GLN* 2.9 21.0 + - - -
239A THR 3.6 2.2 + - - -
240A PHE* 1.3 78.2 - - - +
242A GLU* 1.3 66.3 + - - -
243A ASP* 3.2 3.1 - - - -
244A SER* 3.0 17.2 + - - -
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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