Contacts of the helix formed by residues 184 - 192 (chain A) in PDB entry 2AF0
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A LEU* 2.8 38.5 + - + +
181A MET 3.3 1.4 + - - -
183A ASN* 1.3 80.5 - - + +
185A SER* 1.3 66.3 + - - +
186A TYR 3.3 1.6 + - - -
187A PRO* 3.4 11.4 - - - +
188A ARG* 3.1 42.0 + - - +
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Residues in contact with SER 185 (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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97A PHE* 3.8 6.3 - - - -
100A PHE* 3.6 3.3 - - - -
101A LEU* 3.6 27.6 - - - +
106A CYS* 5.5 2.2 - - - -
180A LEU* 4.6 5.1 - - - +
181A MET* 3.1 34.5 + - - +
184A ASN* 1.3 79.1 - - - +
186A TYR* 1.3 51.2 + - - +
188A ARG* 3.2 23.4 + - - +
189A PHE* 2.7 34.7 + - - +
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Residues in contact with TYR 186 (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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80A TRP 2.6 29.6 + - - -
81A SER* 3.2 17.1 + - - -
83A ALA* 3.3 10.7 + - - -
84A PHE* 3.4 50.7 - + + -
87A LEU* 3.4 23.8 - - + -
97A PHE* 4.0 8.0 - - - -
181A MET 2.9 14.3 + - - +
182A GLU* 3.7 10.3 - - + +
185A SER* 1.3 74.3 + - - +
187A PRO* 1.4 78.3 - - + +
189A PHE* 3.0 5.5 + - - +
190A LEU* 2.9 47.3 + - + +
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Residues in contact with PRO 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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182A GLU 3.3 16.2 - - - +
183A ASN* 3.8 17.0 - - - +
184A ASN 3.4 11.2 - - - +
186A TYR* 1.4 97.7 - - + +
188A ARG* 1.3 59.2 + - - +
190A LEU* 3.4 12.6 + - + +
191A GLU* 2.9 37.2 + - - +
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Residues in contact with ARG 188 (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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100A PHE* 3.7 12.0 - - + -
104A GLU* 3.1 39.1 + - - -
106A CYS* 4.8 8.5 - - - -
184A ASN* 3.1 31.9 + - - +
185A SER* 3.2 28.0 + - - +
186A TYR 3.1 0.4 - - - -
187A PRO* 1.3 74.8 - - - +
189A PHE* 1.3 66.8 + - - +
191A GLU* 3.2 11.8 + - + +
192A SER* 3.2 18.2 + - - -
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Residues in contact with PHE 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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80A TRP* 4.3 1.3 - + - -
87A LEU* 3.8 32.3 - - + -
96A ALA* 3.8 40.6 - - + -
97A PHE* 3.8 13.2 - + + -
100A PHE* 3.6 35.1 - + + -
185A SER 2.7 15.0 + - - +
186A TYR* 3.1 12.3 - - - +
188A ARG* 1.3 76.1 - - - +
190A LEU* 1.3 73.8 + - + +
192A SER* 2.6 27.7 + - - -
194A PHE* 4.3 11.4 - + - -
195A TYR* 3.3 41.8 - + + +
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Residues in contact with LEU 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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80A TRP 4.1 5.6 - - - +
81A SER* 3.9 20.4 - - - +
186A TYR* 2.9 56.2 + - + +
187A PRO* 3.7 12.1 - - + +
188A ARG 3.2 0.2 - - - -
189A PHE* 1.3 90.8 - - + +
191A GLU* 1.3 61.0 + - + +
195A TYR* 3.3 37.1 - - + -
196A GLN* 3.2 20.1 - - - +
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Residues in contact with GLU 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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187A PRO* 2.9 27.9 + - - +
188A ARG* 3.2 12.9 + - + +
189A PHE 3.2 0.8 - - - -
190A LEU* 1.3 78.6 - - + +
192A SER* 1.3 63.8 + - - +
193A GLU* 3.7 0.9 + - - +
196A GLN* 4.4 11.3 + - - +
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Residues in contact with SER 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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100A PHE* 3.9 24.8 - - - -
188A ARG 3.2 9.5 + - - -
189A PHE* 2.6 23.6 + - - -
190A LEU 3.3 0.2 - - - -
191A GLU* 1.3 77.6 - - - +
193A GLU* 1.3 63.7 + - - +
194A PHE* 3.7 8.1 + - - +
195A TYR* 2.9 19.8 + - - +
196A GLN* 3.0 22.2 + - - +
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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