Contacts of the helix formed by residues 172 - 183 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLU* 2.8 27.2 + - - -
60A LYS* 3.7 2.0 - - - -
162A MET* 3.4 10.1 - - - -
170A GLY 3.7 0.4 + - - -
171A LEU* 1.3 73.4 - - - +
173A ASN* 1.3 65.1 - - - -
174A TYR 3.3 0.3 + - - -
175A LEU* 3.3 0.9 + - - +
176A VAL* 3.1 24.8 + - - +
21D G 3.2 16.8 - - - -
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.4 0.2 + - - -
158A VAL* 6.0 1.0 - - - +
162A MET* 3.5 20.4 - - + +
172A GLY* 1.3 72.1 - - - +
174A TYR* 1.3 62.3 + - - +
176A VAL* 4.6 0.7 - - - +
177A ALA* 3.6 19.4 + - - +
253A TYR* 3.9 10.1 - - - -
270A ILE* 5.7 0.9 - - - +
277A ARG* 3.6 30.3 - - - +
278A THR* 3.0 37.1 + - - +
279A THR* 4.8 4.5 + - - -
280A TYR* 5.2 0.2 - - - -
19D A 5.5 0.4 + - - -
20D 3DR 2.8 32.0 + - - +
21D G 2.9 10.5 + - - +
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 2.8 37.2 + - + +
5A PRO* 5.1 0.3 - - - +
6A GLU* 2.5 31.8 + - - -
173A ASN* 1.3 73.9 - - - +
175A LEU* 1.3 89.6 + - + +
177A ALA* 3.5 2.9 + - - +
178A GLU* 3.2 27.4 + - - +
213A ALA* 4.3 5.5 - - - +
219A ILE* 3.6 14.5 - - + +
221A TYR* 3.6 28.7 - + - -
248A PHE* 4.0 17.0 - + - -
250A PHE* 3.5 19.3 - + + -
253A TYR* 3.7 33.4 - - + -
20D 3DR 3.2 14.3 - - - +
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Residues in contact with LEU 175 (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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3A GLU* 3.0 29.0 + - + +
5A PRO* 3.6 32.3 - - + -
170A GLY 4.0 7.4 - - - +
171A LEU* 4.1 19.1 - - + -
172A GLY 3.9 3.8 - - - +
174A TYR* 1.3 103.0 - - + +
176A VAL* 1.3 57.4 + - - +
178A GLU* 3.4 2.7 + - - +
179A ILE* 2.9 37.7 + - + +
209A GLU* 4.1 28.9 - - + +
210A THR* 4.6 2.2 - - + +
213A ALA* 4.1 7.9 - - + -
248A PHE* 4.2 8.7 - - + -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.5 29.6 - - + -
161A LEU* 3.8 28.9 - - + +
162A MET* 3.7 18.2 - - - -
171A LEU* 3.8 23.8 - - + -
172A GLY 3.1 16.9 + - - +
173A ASN 4.6 1.1 - - - +
175A LEU* 1.3 76.9 - - - +
177A ALA* 1.3 63.0 + - - +
179A ILE* 3.8 5.7 - - - +
180A LEU* 3.0 36.8 + - + +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 5.7 0.2 - - - +
173A ASN 3.6 16.9 + - - +
174A TYR 3.5 4.9 + - - +
175A LEU 3.3 0.4 - - - -
176A VAL* 1.3 79.8 - - - +
178A GLU* 1.3 62.3 - - - +
180A LEU* 3.6 5.7 + - - +
181A TYR* 3.2 23.6 + - - +
252A VAL* 3.6 11.1 - - + +
253A TYR* 4.6 8.7 - - + -
278A THR 6.0 0.2 - - - +
279A THR* 5.1 7.4 - - + -
280A TYR* 3.5 36.4 - - + +
286A GLN* 4.6 0.7 + - - -
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Residues in contact with GLU 178 (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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174A TYR 3.2 15.8 + - - +
175A LEU* 3.8 4.0 - - - +
177A ALA* 1.3 76.2 - - - +
179A ILE* 1.3 63.0 + - - +
181A TYR* 3.5 2.5 + - - +
182A ARG* 3.0 32.0 + - - +
209A GLU* 3.5 17.8 - - - +
248A PHE* 3.9 17.5 - - + -
249A ASP 3.6 6.4 - - - +
250A PHE* 3.7 12.5 - - + -
251A LEU* 2.8 36.3 + - - +
252A VAL* 2.8 28.4 + - - +
253A TYR* 2.8 18.7 + - + +
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Residues in contact with ILE 179 (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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161A LEU* 4.9 4.7 - - + -
171A LEU* 4.0 30.1 - - + -
175A LEU* 2.9 24.8 + - + +
176A VAL* 3.8 4.9 - - - +
178A GLU* 1.3 76.2 - - - +
180A LEU* 1.3 57.5 + - - +
182A ARG* 3.4 3.8 + - - +
183A ALA* 2.9 27.2 + - - +
202A LEU* 3.7 25.8 - - + -
205A TRP* 3.9 5.6 - - + +
206A ILE* 3.8 37.2 - - + +
209A GLU* 3.5 31.0 - - + -
210A THR* 4.9 0.9 - - + -
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Residues in contact with LEU 180 (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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157A ILE* 3.9 22.0 - - + -
158A VAL* 3.9 23.6 - - + -
161A LEU* 4.0 18.4 - - + -
176A VAL* 3.0 39.4 + - + +
177A ALA* 4.2 3.8 - - - +
179A ILE* 1.3 73.7 - - - +
181A TYR* 1.3 61.0 + - - +
183A ALA* 3.6 2.2 - - - -
184A LYS 2.8 6.2 + - - -
185A ILE* 2.8 42.7 + - + +
187A PRO* 4.0 19.1 - - + -
202A LEU* 4.1 12.1 - - + -
279A THR* 5.5 0.4 - - + -
286A GLN* 3.3 15.2 + - - +
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Residues in contact with TYR 181 (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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177A ALA 3.2 17.8 + - - +
178A GLU 3.7 4.0 - - - +
179A ILE 3.3 0.2 - - - -
180A LEU* 1.3 73.8 - - - +
182A ARG* 1.3 69.3 + - - +
184A LYS* 3.0 20.3 + - - +
251A LEU* 3.8 43.7 - - + -
252A VAL* 4.0 13.9 - - + -
258A ASP* 2.8 45.7 + - + +
259A PRO* 3.7 5.8 - - + +
260A ASN* 4.2 8.7 + - - -
282A ALA* 3.9 9.0 - - + -
285A ILE* 3.9 27.7 - - + +
286A GLN* 3.3 24.4 - - - +
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Residues in contact with ARG 182 (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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178A GLU* 3.0 24.7 + - - +
179A ILE 3.6 4.0 - - - +
181A TYR* 1.3 79.1 - - - +
183A ALA* 1.3 61.7 + - - +
184A LYS* 3.1 14.9 + - - +
205A TRP* 3.4 54.7 + - + -
208A TYR* 4.0 13.4 + - - -
209A GLU* 3.3 29.0 + - + +
212A LEU* 4.3 6.1 - - - +
245A GLU* 3.0 31.3 + - - +
249A ASP* 5.1 4.9 + - - +
251A LEU* 3.3 37.8 - - + +
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Residues in contact with ALA 183 (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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179A ILE 2.9 17.7 + - - +
180A LEU* 4.0 2.2 - - - +
182A ARG* 1.3 75.6 - - - +
184A LYS* 1.3 71.4 + - - +
185A ILE* 3.4 26.6 - - + +
201A ASN* 3.3 25.4 + - - +
202A LEU* 4.3 13.7 - - + -
205A TRP* 3.6 16.8 - - + -
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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