Contacts of the helix formed by residues 233 - 246 (chain A) in PDB entry 1MAQ
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 ILE 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.4 28.5 - - + +
226A GLN* 3.0 44.4 + - + +
227A GLY* 4.1 16.6 - - - -
231A GLY 4.4 0.2 + - - -
232A ASP* 1.3 73.2 + - - +
234A ASN* 1.3 85.2 + - - +
236A ASP 3.7 0.2 + - - -
237A ALA* 3.4 10.0 + - - +
316A ARG* 4.6 13.0 - - - +
319A TRP* 4.6 13.5 - - + -
320A LEU* 3.8 37.5 - - + +
323A VAL* 5.1 6.5 - - + -
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Residues in contact with ASN 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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89A GLY* 5.4 2.6 - - - -
232A ASP* 3.0 9.2 + - - +
233A ILE* 1.3 93.5 - - - +
235A ARG* 1.3 62.5 + - - +
237A ALA* 3.3 12.0 + - - +
238A TRP* 3.6 10.2 + - - +
241A ARG* 3.3 36.8 + - - +
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Residues in contact with ARG 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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202A GLN* 3.4 31.2 + - - +
230A SER* 3.1 34.1 - - - +
232A ASP* 3.3 17.9 + - + +
234A ASN* 1.3 80.8 - - - +
236A ASP* 1.3 61.0 + - - +
238A TRP* 3.2 28.3 + - - +
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Residues in contact with ASP 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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190A ALA* 4.2 7.3 - - - +
191A CYS* 3.6 29.9 - - - +
223A MET* 4.6 3.5 - - - +
225A TYR 3.9 0.3 - - - +
226A GLN* 4.4 4.0 - - + -
227A GLY* 2.9 32.4 + - - +
228A PHE 3.1 1.6 + - - -
229A ALA* 2.9 35.0 + - - +
230A SER* 2.9 28.6 + - - -
232A ASP 3.2 14.6 + - - +
233A ILE 4.1 3.8 - - - +
234A ASN 3.4 0.4 - - - -
235A ARG* 1.3 76.7 - - - +
237A ALA* 1.3 57.2 + - - +
238A TRP 3.3 1.4 + - - -
239A ALA 5.2 1.0 + - - -
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Residues in contact with ALA 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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87A ALA 4.0 6.7 - - - +
190A ALA* 6.0 0.2 - - - -
223A MET* 4.5 11.2 - - - -
226A GLN* 3.5 28.3 - - - +
233A ILE 3.4 5.1 + - - +
234A ASN 3.3 5.5 + - - +
235A ARG 3.1 1.2 - - - -
236A ASP* 1.3 79.9 - - - +
238A TRP* 1.3 61.4 + - - +
239A ALA 3.6 1.3 - - - -
240A LEU* 3.7 7.5 + - + +
241A ARG* 3.1 43.5 + - - +
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Residues in contact with TRP 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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202A GLN* 3.6 69.8 + - + +
205A TRP* 3.7 19.5 - + + -
206A LYS* 3.5 30.1 - - + -
234A ASN 3.6 5.6 + - - +
235A ARG* 3.2 24.8 + - - +
236A ASP 3.3 1.6 - - - -
237A ALA* 1.3 79.0 - - - +
239A ALA* 1.3 75.8 + - + +
241A ARG* 3.2 8.2 + - + +
242A HIS* 2.8 58.1 + + + +
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Residues in contact with ALA 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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190A ALA 4.5 7.2 - - - +
205A TRP* 3.3 58.8 - - + +
221A PHE* 4.6 2.0 - - + -
236A ASP 5.2 0.8 + - - -
237A ALA 3.6 0.4 - - - -
238A TRP* 1.3 87.9 - - - +
240A LEU* 1.3 63.8 + - - +
242A HIS* 3.0 2.5 + - - +
243A PHE* 2.9 31.1 + - - -
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Residues in contact with LEU 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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87A ALA* 3.8 39.5 - - + +
88A LEU* 4.8 4.9 - - + -
190A ALA* 5.0 7.7 - - + +
221A PHE* 3.7 46.2 - - + -
223A MET* 4.2 14.4 - - + -
237A ALA* 3.7 11.8 + - - +
238A TRP 3.3 0.2 - - - -
239A ALA* 1.3 78.0 - - - +
241A ARG* 1.3 63.9 + - - +
243A PHE* 3.4 3.8 + - - +
244A ILE* 3.4 30.0 + - + +
250A VAL* 3.9 17.3 - - + -
252A LEU* 4.2 14.4 - - + -
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Residues in contact with ARG 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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85A GLU 4.4 0.4 + - - -
86A LEU 3.1 26.9 + - - -
87A ALA 2.8 20.2 + - - +
88A LEU* 3.1 24.3 + - + +
89A GLY* 3.4 18.6 - - - +
91A ASN* 5.7 1.2 - - - +
226A GLN* 4.3 1.0 - - - +
234A ASN* 3.3 41.6 + - - +
237A ALA* 3.1 25.3 - - - +
238A TRP* 3.2 9.0 + - + +
240A LEU* 1.3 75.5 - - + +
242A HIS* 1.3 65.2 + - - +
244A ILE* 3.4 8.7 + - - +
245A GLU* 3.1 26.4 + - - +
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Residues in contact with HIS 242 (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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205A TRP 4.6 2.0 + - - -
206A LYS* 3.6 44.9 + - + +
209A ALA* 4.0 13.4 - - + +
238A TRP* 2.8 47.1 + + + +
239A ALA 3.0 8.3 + - - +
241A ARG* 1.3 78.5 - - - +
243A PHE* 1.3 65.1 + - - +
245A GLU* 3.4 23.8 + - - +
246A GLN* 3.1 54.7 + - + +
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Residues in contact with PHE 243 (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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188A LEU* 4.1 17.9 - - + -
205A TRP* 3.5 50.3 - + + -
208A LEU* 4.3 4.9 - - + -
209A ALA* 3.9 27.1 - - + -
212A VAL* 4.3 14.1 - - + -
219A ALA* 4.6 2.2 - - + -
221A PHE* 3.9 15.5 - + + -
239A ALA* 2.9 29.6 + - + -
240A LEU 3.6 7.6 - - - +
241A ARG 3.3 0.2 - - - -
242A HIS* 1.3 79.1 - - - +
244A ILE* 1.3 60.0 + - - +
246A GLN* 3.1 9.6 + - - +
248A ILE* 3.0 59.5 + - + +
250A VAL* 4.3 9.2 - - + -
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Residues in contact with ILE 244 (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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88A LEU* 3.5 31.6 - - + -
92A SER* 5.5 2.0 - - - +
94A ALA* 4.1 22.9 - - + -
99A ARG* 4.7 10.8 + - - +
240A LEU* 3.4 27.5 + - + +
241A ARG* 3.8 9.4 - - - +
242A HIS 3.3 0.2 - - - -
243A PHE* 1.3 75.0 - - - +
245A GLU* 1.3 57.5 + - - +
246A GLN 3.2 0.2 - - - -
247A GLY* 3.2 17.2 + - - -
248A ILE 3.4 17.7 + - - +
249A ASP* 5.2 1.0 - - - +
250A VAL* 4.4 11.2 - - + -
273A ILE* 4.0 24.2 - - + -
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Residues in contact with GLU 245 (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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241A ARG 3.1 16.8 + - - +
242A HIS* 3.8 24.2 - - - +
244A ILE* 1.3 73.6 - - + +
246A GLN* 1.3 67.8 + - - +
247A GLY 3.2 5.2 - - - -
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Residues in contact with GLN 246 (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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209A ALA* 4.5 9.0 - - + +
210A SER* 6.1 1.0 - - - +
213A LYS* 3.3 25.3 + - + -
242A HIS* 3.1 45.4 + - + +
243A PHE 3.1 11.4 + - - +
245A GLU* 1.3 88.9 - - - +
247A GLY* 1.3 58.4 + - - +
248A ILE* 4.3 12.6 - - + -
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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