Contacts of the helix formed by residues 184 - 193 (chain A) in PDB entry 2P6U
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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183A PRO* 1.3 72.7 - - - +
185A VAL* 1.3 52.0 + - - +
186A THR* 2.7 18.6 + - - -
187A GLU* 2.7 54.2 + - - +
188A ILE* 3.5 3.1 + - - +
404A ARG* 3.2 30.0 - - - +
405A ILE* 2.5 60.0 + - - +
442A PHE* 4.7 0.8 - - - -
446A GLN* 3.3 3.4 - - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.2 18.9 - - + +
46A ALA* 4.1 8.1 - - + -
179A SER* 4.0 7.2 - - - +
180A ALA 4.0 10.3 - - - +
182A ALA* 2.9 51.4 - - + +
183A PRO 4.3 1.6 - - - +
184A ASN* 1.3 76.6 + - - +
186A THR* 1.3 69.9 + - - +
188A ILE* 3.2 17.3 - - + +
189A ALA 3.2 15.8 + - - -
196A TYR* 5.8 0.2 - - + -
198A VAL* 4.0 28.7 - - + -
405A ILE* 4.3 4.0 - - + -
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Residues in contact with THR 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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183A PRO 3.7 13.0 + - - -
184A ASN* 2.7 5.4 + - - -
185A VAL* 1.3 77.0 - - - +
187A GLU* 1.3 58.7 + - - -
189A ALA* 3.0 9.0 + - - +
190A GLU* 2.9 36.7 + - + +
196A TYR* 3.3 51.7 - - + +
198A VAL* 5.8 0.2 - - - +
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Residues in contact with GLU 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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184A ASN* 2.7 53.7 + - + +
186A THR* 1.3 71.8 - - - +
188A ILE* 1.3 60.8 + - - +
190A GLU* 3.0 22.0 + - - +
191A TRP* 2.8 28.9 + - - +
404A ARG* 2.8 28.9 + - - -
442A PHE* 4.2 13.1 - - + -
445A LYS* 4.3 10.3 - - + +
446A GLN* 3.2 24.4 + - - +
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Residues in contact with ILE 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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44A LEU* 3.7 12.1 - - + -
147A ILE* 4.6 17.7 - - + +
148A HIS* 5.0 0.2 - - - -
150A LEU* 4.5 11.4 - - + -
179A SER* 5.0 1.3 - - - +
184A ASN 4.1 2.2 - - - +
185A VAL* 3.2 23.8 - - + +
186A THR 3.1 0.2 - - - -
187A GLU* 1.3 79.8 - - - +
189A ALA* 1.3 57.2 + - - +
191A TRP* 2.9 14.3 + - + +
192A LEU* 2.8 49.0 + - + +
405A ILE* 3.7 35.2 - - + -
442A PHE* 3.7 27.4 - - + -
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Residues in contact with ALA 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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44A LEU* 4.0 15.9 - - + -
185A VAL 3.2 6.1 + - - +
186A THR* 3.0 13.6 + - - +
188A ILE* 1.3 79.9 - - - +
190A GLU* 1.3 50.1 + - + +
192A LEU* 3.2 5.2 + - - -
193A ASP 2.7 28.2 + - - -
194A ALA* 2.7 31.7 + - - +
196A TYR* 3.9 26.9 - - + -
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Residues in contact with GLU 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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186A THR* 2.9 25.0 + - + +
187A GLU* 3.2 18.2 - - - +
188A ILE 3.0 0.4 - - - -
189A ALA* 1.3 72.9 - - + +
191A TRP* 1.3 62.5 + - - +
192A LEU 2.9 1.3 - - - -
193A ASP* 2.8 29.9 + - - +
445A LYS* 3.4 31.1 + - - +
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Residues in contact with TRP 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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147A ILE* 4.5 7.4 - - + -
150A LEU* 3.6 24.5 - - + -
160A GLU* 4.1 22.4 - - - -
163A VAL* 3.9 38.4 - - + -
164A THR* 4.4 3.1 + - - -
167A ARG* 3.3 16.8 + - - +
187A GLU 2.8 16.5 + - - +
188A ILE* 2.9 8.7 + - + +
190A GLU* 1.3 72.8 - - - +
192A LEU* 1.3 78.8 + - + +
193A ASP* 4.3 2.4 - - - +
440A ASP 3.0 26.2 + - - -
441A THR 3.7 3.8 - - - -
442A PHE* 3.3 52.9 - + + +
445A LYS* 3.9 20.3 - - + +
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Residues in contact with LEU 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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42A ASN* 2.7 32.9 + - + +
44A LEU* 4.3 15.5 - - + -
147A ILE* 4.1 16.8 - - + -
163A VAL* 4.1 20.0 - - + -
167A ARG* 3.4 8.7 + - - +
175A VAL* 3.6 28.9 - - + +
177A GLY* 4.6 9.9 - - - +
188A ILE* 2.8 36.3 + - + +
189A ALA* 3.6 6.3 - - - +
191A TRP* 1.3 93.7 - - + +
193A ASP* 1.3 60.1 + - - +
194A ALA* 4.2 9.4 - - + -
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Residues in contact with ASP 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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41A LYS* 4.0 16.7 - - - +
42A ASN* 3.4 11.0 - - - +
167A ARG* 3.3 28.9 + - - +
171A LYS* 5.7 1.3 + - - -
189A ALA 2.7 7.3 + - - -
190A GLU* 2.8 16.7 + - - +
191A TRP 4.3 2.1 - - - +
192A LEU* 1.3 79.5 - - - +
194A ALA* 1.3 56.5 + - - +
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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