Contacts of the helix formed by residues 239 - 254 (chain B) in PDB entry 3Q72
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 ASN 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B ILE* 3.9 21.1 - - + +
231B GLU* 2.7 28.5 + - - +
232B THR* 3.6 5.4 - - + +
237B HIS 3.9 1.8 + - - -
238B HIS* 1.3 101.2 + - - +
240B VAL* 1.3 57.8 + - - +
241B GLN 3.4 2.2 - - - -
242B ALA* 3.9 16.1 - - - +
243B LEU* 2.9 30.0 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.6 44.0 - - + +
110B ILE* 4.2 17.7 - - + -
111B PHE* 4.1 14.4 - - + +
232B THR* 4.7 2.9 - - - -
234B ALA* 4.6 3.4 - - - -
237B HIS* 3.8 32.1 + - - +
238B HIS 3.1 5.1 - - - +
239B ASN* 1.3 74.7 - - - +
241B GLN* 1.3 65.5 + - - +
243B LEU* 3.3 9.7 - - - +
244B PHE* 3.0 36.6 - - + -
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.8 7.9 - - - -
129B ARG* 2.7 44.0 + - - +
131B ILE* 3.3 24.2 - - - +
237B HIS 5.6 0.4 + - - -
239B ASN* 4.5 0.2 - - - +
240B VAL* 1.3 75.7 - - - +
242B ALA* 1.3 58.0 + - - +
244B PHE* 3.0 3.6 + - - +
245B GLU* 2.7 67.6 + - - +
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Residues in contact with ALA 242 (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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228B LYS* 4.9 2.6 + - - -
230B ILE* 3.8 17.3 - - + +
239B ASN* 3.6 23.1 + - - +
240B VAL 3.4 0.2 - - - -
241B GLN* 1.3 77.8 - - - +
243B LEU* 1.3 57.3 + - - +
245B GLU* 3.9 10.1 - - - +
246B GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 243 (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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107B LEU* 4.4 17.5 - - + -
166B VAL* 4.3 10.5 - - + -
199B ILE* 3.7 17.7 - - + +
201B VAL* 3.6 33.0 - - + -
228B LYS* 5.5 1.2 + - - +
230B ILE* 3.9 11.9 - - + +
232B THR* 4.3 15.7 - - + -
239B ASN 2.9 20.0 + - - +
240B VAL 3.3 3.8 - - - +
241B GLN 3.1 0.2 - - - -
242B ALA* 1.3 77.8 - - - +
244B PHE* 1.3 88.9 + - + +
246B GLY* 3.3 2.3 + - - -
247B VAL* 3.1 29.9 + - + +
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 4.4 9.6 - - + -
96B LEU* 4.3 17.7 - - + -
107B LEU* 4.0 13.2 - - + -
108B ALA* 4.7 1.1 - - - -
111B PHE* 3.4 52.7 - + + -
131B ILE* 4.2 2.7 - - - -
140B LEU* 3.7 20.0 - - + +
142B VAL* 3.8 30.5 - - + -
166B VAL* 4.9 2.0 - - + -
240B VAL* 3.0 29.1 + - + -
241B GLN 3.0 3.7 + - - +
243B LEU* 1.3 100.5 - - + +
245B GLU* 1.3 65.0 + - - +
247B VAL* 3.3 10.4 + - + +
248B VAL* 3.3 25.1 + - - +
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Residues in contact with GLU 245 (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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131B ILE* 3.8 9.8 - - + +
132B VAL 4.3 4.9 - - - +
133B VAL* 3.6 29.9 - - + +
134B ASP* 3.8 18.2 - - - +
241B GLN* 2.7 51.4 + - - +
242B ALA* 3.9 7.7 - - - +
244B PHE* 1.3 71.9 - - - +
246B GLY* 1.3 62.1 + - - +
248B VAL* 3.2 6.4 + - - +
249B ARG* 3.2 30.3 + - - +
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Residues in contact with GLY 246 (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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199B ILE* 4.8 6.0 - - - +
228B LYS* 4.2 16.8 - - - +
242B ALA 2.9 15.2 + - - -
243B LEU 3.6 5.2 - - - -
244B PHE 3.2 0.2 - - - -
245B GLU* 1.3 74.3 - - - +
247B VAL* 1.3 57.8 + - - +
249B ARG* 3.3 12.3 + - - +
250B GLN* 2.9 35.6 + - - +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.8 22.4 - - + -
140B LEU* 4.7 3.8 - - + -
164B ALA* 3.6 26.9 - - + +
166B VAL* 3.8 21.3 - - + -
199B ILE* 3.8 24.7 - - + -
243B LEU* 3.1 17.9 + - + +
244B PHE* 3.4 17.7 - - + +
245B GLU 3.3 0.2 - - - -
246B GLY* 1.3 75.4 - - - +
248B VAL* 1.3 59.9 + - - +
250B GLN* 3.9 1.4 - - - +
251B ILE* 3.0 28.9 + - + +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 4.4 7.2 - - + -
131B ILE* 4.0 15.7 - - + -
133B VAL* 3.9 11.9 - - + -
138B ALA* 3.8 21.5 - - + -
140B LEU* 4.1 17.9 - - + -
244B PHE 3.3 13.9 + - - +
245B GLU 3.2 8.0 + - - +
246B GLY 3.2 0.4 - - - -
247B VAL* 1.3 78.4 - - - +
249B ARG* 1.3 58.6 + - - +
251B ILE* 3.3 6.7 + - - +
252B ARG* 3.1 64.9 + - - +
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Residues in contact with ARG 249 (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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133B VAL* 3.4 24.7 - - + +
134B ASP* 6.2 1.2 - - - -
245B GLU* 3.2 22.3 + - - -
246B GLY* 3.8 9.9 - - - +
248B VAL* 1.3 74.9 - - - +
250B GLN* 1.3 64.7 + - - +
252B ARG* 3.5 9.7 + - - +
253B LEU* 2.9 27.4 + - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PRO* 3.7 29.3 - - + +
198B ILE 5.2 2.7 - - - +
199B ILE* 4.3 13.7 - - + -
228B LYS* 4.1 30.0 - - + +
246B GLY* 2.9 18.5 + - - +
247B VAL 3.9 3.6 - - - +
249B ARG* 1.3 79.5 - - - +
251B ILE* 1.3 64.5 + - - +
253B LEU* 3.0 43.9 + - - +
254B ARG* 3.0 12.0 + - - +
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Residues in contact with ILE 251 (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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92B TYR* 3.8 55.6 - - + +
93B LYS 5.3 0.2 - - - +
94B VAL* 5.3 0.4 - - + -
163B ASP* 3.5 34.3 - - + +
164B ALA* 3.9 10.3 - - + -
197B PRO* 3.7 13.5 - - + -
247B VAL* 3.0 24.3 + - + +
248B VAL 3.3 4.2 + - - +
250B GLN* 1.3 78.2 - - - +
252B ARG* 1.3 58.5 + - - +
254B ARG* 3.8 4.5 + - - +
255B ARG* 2.9 44.7 + - - +
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Residues in contact with ARG 252 (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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1B CA 3.1 14.0 - - - -
90B SER* 5.0 2.6 + - - -
92B TYR* 4.2 16.5 + - - +
133B VAL* 2.5 29.7 + - - +
136B GLU* 3.1 47.2 + - - +
137B GLU 3.7 5.5 + - - -
138B ALA* 3.5 14.3 - - - +
248B VAL* 3.1 39.6 + - - +
249B ARG* 3.9 7.8 - - - +
251B ILE* 1.3 75.9 - - - +
253B LEU* 1.3 60.7 + - - +
255B ARG* 2.8 24.6 + - - +
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Residues in contact with LEU 253 (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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249B ARG 2.9 18.7 + - - +
250B GLN* 3.0 30.3 + - - +
252B ARG* 1.3 73.7 - - - +
254B ARG* 1.3 56.8 + - - +
255B ARG 2.8 17.6 + - - +
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Residues in contact with ARG 254 (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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194B ASP 5.2 6.2 + - - +
195B ASP* 4.3 39.6 + - - +
196B VAL 5.9 0.2 - - - -
197B PRO* 4.6 14.6 - - + -
250B GLN 3.0 13.7 + - - +
251B ILE 4.4 1.8 - - - +
253B LEU* 1.3 73.5 - - - +
255B ARG* 1.3 78.5 + - - +
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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