Contacts of the helix formed by residues 186 - 195 (chain A) in PDB entry 2AW9
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 ARG 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASN 3.5 15.8 + - - -
183A TYR* 2.9 41.2 + - + +
184A GLN* 3.1 25.2 + - - +
185A ASN* 1.3 90.4 + - - +
187A ARG* 1.3 65.2 + - - +
188A PRO* 3.3 7.2 - - + -
189A ASP* 3.2 45.0 + - - +
190A TYR 3.2 9.2 + - - -
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Residues in contact with ARG 187 (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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126A ALA 2.7 33.3 + - - -
127A LYS* 3.4 14.0 + - + +
129A ARG 2.7 25.2 + - - -
131A GLY* 3.4 20.0 + - - +
174A VAL* 3.3 30.8 + - - +
176A GLU* 5.3 4.0 + - - +
179A TYR* 2.9 44.3 + - + +
185A ASN 2.7 12.2 + - - +
186A ARG* 1.3 71.7 - - - +
188A PRO* 1.3 64.3 - - + +
190A TYR* 3.0 11.5 + - + +
191A LEU* 2.8 44.6 + - + +
175B TRP* 5.9 2.8 - - - -
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Residues in contact with PRO 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 4.8 4.8 - - - +
127A LYS* 3.9 32.1 - - + +
185A ASN 4.6 1.1 - - - +
186A ARG* 3.4 8.3 - - + -
187A ARG* 1.3 92.4 - - + +
189A ASP* 1.3 67.3 + - - +
191A LEU* 3.3 12.2 + - + +
192A ALA* 3.0 24.7 + - - +
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Residues in contact with ASP 189 (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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183A TYR* 3.8 20.6 - - + -
186A ARG* 3.2 42.3 + - - +
188A PRO* 1.3 78.7 - - - +
190A TYR* 1.3 66.0 + - - +
192A ALA* 3.5 6.3 + - - +
193A ALA* 3.1 23.0 + - - +
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Residues in contact with TYR 190 (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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18A HIS 5.3 0.4 - - - -
19A ILE* 4.7 20.3 - - + +
84A PHE* 3.9 15.1 - - - -
172A VAL* 3.7 21.0 - - + +
173A ASP 3.0 28.9 + - - -
174A VAL* 4.4 3.8 - - + -
178A ALA* 3.7 25.5 + - + +
179A TYR* 3.6 34.5 - + + -
183A TYR* 3.7 31.7 - + + -
186A ARG 3.2 9.7 + - - +
187A ARG* 3.0 12.5 + - + +
189A ASP* 1.3 75.4 - - - +
191A LEU* 1.3 69.8 + - + +
193A ALA* 3.1 15.0 + - + +
194A PHE* 3.1 17.8 + + + +
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Residues in contact with LEU 191 (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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122A PHE* 5.5 3.4 - - + -
123A GLU* 3.9 21.5 - - + +
126A ALA* 3.6 34.3 - - + -
127A LYS* 3.7 28.7 - - + +
172A VAL* 4.1 26.7 - - + -
174A VAL* 4.2 7.0 - - + -
187A ARG* 2.8 32.3 + - + +
188A PRO* 3.6 8.1 - - + +
190A TYR* 1.3 77.1 - - + +
192A ALA* 1.3 61.7 + - - +
194A PHE* 3.3 19.4 - - + +
195A TRP* 3.5 16.5 + - - -
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Residues in contact with ALA 192 (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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123A GLU* 4.3 10.5 + - - +
188A PRO 3.0 16.5 + - - +
189A ASP* 3.7 7.4 - - - +
191A LEU* 1.3 76.2 - - - +
193A ALA* 1.3 61.5 + - - +
194A PHE 3.4 0.5 + - - -
195A TRP* 3.5 25.6 + - - +
196A ASN* 4.1 5.8 + - - -
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Residues in contact with ALA 193 (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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18A HIS* 3.9 25.6 - - + +
19A ILE* 6.4 0.2 - - + -
183A TYR* 3.2 27.4 - - + +
189A ASP 3.1 9.1 + - - +
190A TYR* 3.1 8.9 + - + +
192A ALA* 1.3 74.5 - - - +
194A PHE* 1.3 65.8 + - - +
196A ASN* 3.0 31.9 + - - +
197A VAL 3.9 0.5 + - - -
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Residues in contact with PHE 194 (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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19A ILE* 5.2 5.4 - - + -
84A PHE* 3.8 11.7 - + - -
87A ILE* 4.0 12.8 - - + -
88A MET* 3.8 27.4 - - + -
122A PHE* 4.4 14.6 - + - -
170A LEU* 4.2 9.6 - - + -
171A GLY 3.7 19.5 - - - -
172A VAL* 3.9 28.0 - - + -
190A TYR* 3.1 19.5 + + + +
191A LEU* 3.3 18.2 - - + +
192A ALA 3.2 0.4 - - - -
193A ALA* 1.3 76.7 - - - +
195A TRP* 1.3 63.1 + + - +
197A VAL* 2.8 34.9 + - + +
198A VAL* 3.2 30.2 + - + +
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Residues in contact with TRP 195 (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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98A ASN* 2.9 33.5 + - - +
115A PHE* 4.6 2.5 - + + -
118A PHE* 3.7 31.4 - + - -
119A LYS* 3.7 54.0 - - + +
122A PHE* 3.4 37.0 - + + -
123A GLU* 2.9 28.7 + - + -
170A LEU* 4.5 7.2 - - + -
191A LEU 3.5 14.5 + - - -
192A ALA* 3.5 21.5 - - - +
193A ALA 3.2 0.6 - - - -
194A PHE* 1.3 80.5 - + - +
196A ASN* 1.3 57.3 + - - +
197A VAL 3.5 0.2 + - - -
198A VAL* 3.8 10.4 + - + +
200A TRP* 3.9 26.0 + + - -
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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