Contacts of the helix formed by residues 172 - 183 (chain B) in PDB entry 3A46
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 GLY 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 2.7 28.4 + - - +
60B LYS* 3.7 1.3 - - - -
162B MET* 3.6 8.7 - - - -
171B LEU* 1.3 75.0 - - - +
173B ASN* 1.3 66.8 + - - -
174B TYR 3.2 3.6 + - - -
175B LEU 3.2 0.9 + - - -
176B VAL* 3.1 24.4 + - - +
21F G 3.3 15.9 - - - -
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Residues in contact with ASN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 3.4 0.6 + - - -
158B VAL* 5.9 1.6 - - - +
162B MET* 3.6 22.3 - - + +
172B GLY* 1.3 71.2 - - - +
174B TYR* 1.3 61.0 + - - +
176B VAL* 4.6 1.0 - - - +
177B ALA* 3.7 18.9 + - - +
253B TYR* 4.2 6.9 - - - -
270B ILE* 5.1 0.7 - - - +
277B ARG* 3.5 29.4 - - - +
278B THR* 3.0 38.3 + - - +
279B THR* 4.7 5.7 + - - +
19F A 5.4 0.6 + - - -
20F 3DR 2.8 34.0 + - - +
21F G 2.9 9.5 + - - +
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 2.8 30.7 + - + +
5B PRO* 5.0 0.2 - - - +
6B GLU* 2.6 35.7 + - - -
173B ASN* 1.3 77.3 - - - +
175B LEU* 1.3 91.4 + - + +
177B ALA* 3.5 2.6 + - - +
178B GLU* 3.2 27.2 + - - +
213B ALA* 4.3 4.9 - - - +
219B ILE* 3.6 15.0 - - + +
221B TYR* 3.7 29.8 - + - -
248B PHE* 4.0 17.5 - + - -
250B PHE* 3.6 14.8 - + + -
253B TYR* 3.7 37.0 - - + +
20F 3DR 3.5 14.1 - - - -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 3.0 22.1 + - + +
5B PRO* 3.6 33.0 - - + -
170B GLY 4.1 4.5 - - - +
171B LEU* 3.8 28.9 - - + -
172B GLY 3.2 3.6 + - - +
174B TYR* 1.3 102.2 - - + +
176B VAL* 1.3 57.3 + - - +
178B GLU* 3.3 3.6 + - - +
179B ILE* 2.8 36.5 + - + +
209B GLU* 4.1 28.9 - - + +
210B THR* 4.5 2.5 - - + +
213B ALA* 4.2 6.5 - - + -
248B PHE* 4.2 9.4 - - + -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.6 35.0 - - + +
161B LEU* 3.8 28.9 - - + -
162B MET* 4.0 15.9 - - - -
171B LEU* 3.8 20.6 - - + -
172B GLY 3.1 16.5 + - - +
173B ASN 4.6 1.6 - - - +
175B LEU* 1.3 76.0 - - - +
177B ALA* 1.3 57.3 + - - +
179B ILE* 3.8 6.6 - - - +
180B LEU* 2.9 42.2 + - + +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN 3.7 16.0 + - - +
174B TYR* 3.5 6.2 + - - +
175B LEU 3.2 1.0 - - - -
176B VAL* 1.3 80.5 - - - +
178B GLU* 1.3 62.2 + - - +
180B LEU* 4.0 4.0 - - - +
181B TYR* 3.1 24.4 + - - +
252B VAL* 3.7 11.2 - - + +
253B TYR* 4.8 7.9 - - + -
278B THR 6.0 0.2 - - - +
279B THR* 5.0 9.2 - - + +
280B TYR* 3.5 35.3 - - + +
286B GLN* 4.9 0.7 + - - -
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR 3.2 14.6 + - - +
175B LEU 3.7 6.1 - - - +
177B ALA* 1.3 75.6 - - - +
179B ILE* 1.3 62.9 + - - +
181B TYR* 3.4 2.7 + - - +
182B ARG* 3.1 30.6 + - + +
209B GLU* 3.2 20.4 - - + +
248B PHE* 3.7 19.7 - - + -
249B ASP 3.6 6.2 - - - +
250B PHE* 3.7 9.4 - - + -
251B LEU* 2.6 37.5 + - - +
252B VAL* 2.9 13.6 + - - +
253B TYR* 2.9 33.1 + - - +
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.8 5.6 - - + -
171B LEU* 3.8 39.5 - - + -
175B LEU* 2.8 28.2 + - + +
176B VAL* 3.8 4.9 - - - +
178B GLU* 1.3 76.4 - - - +
180B LEU* 1.3 63.6 + - - +
182B ARG* 3.3 4.3 + - - +
183B ALA* 3.0 22.7 + - - +
202B LEU* 3.9 16.2 - - + -
205B TRP* 4.1 4.8 - - + +
206B ILE* 3.9 39.5 - - + +
209B GLU* 3.6 30.3 - - + -
210B THR* 5.0 0.4 - - + -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 4.0 18.8 - - + -
158B VAL* 4.0 14.4 - - + -
161B LEU* 4.1 8.5 - - + -
176B VAL* 2.9 40.5 + - + +
177B ALA* 4.0 4.3 - - - +
179B ILE* 1.3 75.5 - - - +
181B TYR* 1.3 56.6 + - - +
183B ALA* 3.6 2.1 + - - +
184B LYS 3.1 5.9 + - - -
185B ILE* 2.9 45.6 + - + +
187B PRO* 4.0 28.0 - - + -
202B LEU* 4.1 20.0 - - + -
279B THR* 5.4 0.9 - - + -
286B GLN* 3.3 16.9 + - - +
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Residues in contact with TYR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA 3.1 17.9 + - - +
178B GLU 3.6 5.4 - - - +
179B ILE 3.2 0.2 - - - -
180B LEU* 1.3 75.4 - - - +
182B ARG* 1.3 66.0 + - - +
184B LYS* 3.0 19.8 + - - +
251B LEU* 3.7 42.0 - - + -
252B VAL* 3.5 23.1 - - + -
258B ASP* 2.8 38.3 + - + +
259B PRO* 3.6 6.7 - - + +
260B ASN* 4.0 8.7 + - - -
282B ALA* 3.8 14.8 - - + -
285B ILE* 3.8 27.5 - - + +
286B GLN* 3.5 22.6 - - - +
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Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 3.1 19.4 + - - +
179B ILE 3.8 3.6 - - - +
181B TYR* 1.3 81.2 - - - +
183B ALA* 1.3 59.9 + - - +
184B LYS* 3.1 15.8 + - - +
205B TRP* 3.5 55.6 + - + -
208B TYR* 3.8 15.7 + - - -
209B GLU* 3.1 30.6 + - + +
212B LEU* 4.0 6.5 - - - +
245B GLU* 3.2 32.3 + - - +
248B PHE* 5.8 0.4 - - - -
249B ASP 5.2 3.0 + - - +
251B LEU* 3.4 38.8 - - + +
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE 3.0 17.1 + - - +
180B LEU 4.2 1.8 - - - +
182B ARG* 1.3 74.7 - - - +
184B LYS* 1.3 70.2 + - - +
185B ILE* 3.4 25.3 + - + +
201B ASN* 3.2 22.1 + - - +
202B LEU* 4.3 15.5 - - + -
205B TRP* 3.6 21.1 - - + -
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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
------------------------------------------------------------
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