Contacts of the helix formed by residues 187 - 195 (chain A) in PDB entry 4R8A
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 TRP 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASN* 4.8 2.0 + - + +
26A PHE* 3.9 30.6 - + - -
29A VAL* 4.5 25.6 - - + +
67A VAL* 3.6 38.1 - - + -
68A MET* 3.6 53.0 - - + +
169A MET* 5.6 1.1 - - - -
172A CYS* 4.1 14.1 - - + -
173A ASP* 4.8 4.7 - - - -
175A LEU* 6.1 0.9 - - + -
176A ARG* 3.4 48.2 - - + +
180A PHE* 4.9 2.2 - + - -
186A ASP* 1.3 83.3 + - + +
188A SER* 1.3 58.6 + - - +
189A GLU 3.2 4.0 + - - -
190A PHE* 3.7 29.8 + + + +
191A VAL* 4.3 6.4 + - - +
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Residues in contact with SER 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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186A ASP* 2.9 25.1 + - - -
187A TRP* 1.3 76.0 - - - +
189A GLU* 1.3 63.6 + - - +
190A PHE 3.2 1.1 - - - -
191A VAL* 3.4 11.2 + - - +
192A LEU* 3.0 43.8 + - - +
9C T 5.7 3.8 - - - -
10C G 4.2 18.4 - - - -
13D C 4.7 3.7 + - - -
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Residues in contact with GLU 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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180A PHE* 4.0 11.4 - - + -
184A TRP* 4.7 6.4 - - - -
185A GLN* 3.1 39.1 + - + +
186A ASP* 3.2 19.7 + - - +
187A TRP 3.2 0.6 - - - -
188A SER* 1.3 81.7 + - - +
190A PHE* 1.3 58.1 + - - +
192A LEU* 3.4 10.2 + - - +
193A ALA* 2.8 34.5 + - - +
198A TYR* 5.3 4.8 - - - +
200A TYR* 2.6 30.8 + - - -
414A PHE* 3.4 18.4 - - + +
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Residues in contact with PHE 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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25A ASN* 3.4 47.1 - - + +
28A ALA* 4.7 9.4 - - + -
29A VAL* 3.6 30.7 - - + -
179A TYR* 3.5 35.7 - + - -
180A PHE* 4.3 11.0 - + - -
187A TRP* 3.8 22.9 - + + +
188A SER 3.2 0.4 - - - -
189A GLU* 1.3 77.2 - - - +
191A VAL* 1.3 56.4 + - - +
193A ALA* 3.5 1.2 + - - +
194A ASP* 3.0 37.3 + - - +
413A PRO* 6.0 0.4 - - + -
414A PHE* 3.6 24.0 - + - -
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.5 31.4 - - + -
22A TYR* 6.1 0.2 - - - -
25A ASN* 4.3 4.7 - - - +
68A MET* 6.6 0.2 - - + -
187A TRP 4.3 12.3 - - - +
188A SER* 3.4 9.4 + - - +
189A GLU 3.3 0.4 - - - -
190A PHE* 1.3 76.6 - - - +
192A LEU* 1.3 55.3 + - - +
194A ASP* 3.0 8.5 + - + +
195A LEU* 2.8 58.5 + - + +
10C G 3.7 43.1 - - + +
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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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188A SER* 3.0 31.6 + - - +
189A GLU* 3.9 7.9 - - - +
191A VAL* 1.3 77.0 - - - +
193A ALA* 1.3 58.1 + - - +
195A LEU* 3.9 2.9 - - - +
196A GLY 3.5 0.9 + - - -
197A ILE* 3.0 38.7 + - + +
198A TYR* 2.8 53.4 + - + -
10C G 4.3 7.0 - - + +
13D C 3.5 57.4 - - + +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLU 2.8 18.4 + - - +
190A PHE 3.8 2.2 - - - +
192A LEU* 1.3 75.9 - - - +
194A ASP* 1.3 65.8 + - - +
195A LEU 3.2 0.2 - - - -
196A GLY* 3.2 12.8 + - - -
198A TYR* 3.3 20.7 - - - +
199A ARG* 5.6 0.7 - - - +
200A TYR* 4.4 6.3 - - + -
414A PHE* 3.5 24.0 - - + -
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Residues in contact with ASP 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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16A LEU 6.4 0.2 - - - +
21A TYR* 6.1 0.9 - - - +
25A ASN* 4.4 13.0 + - - +
190A PHE* 3.0 28.9 + - - +
191A VAL* 3.0 7.8 + - - +
193A ALA* 1.3 78.0 - - - +
195A LEU* 1.3 67.3 + - + +
196A GLY 3.1 1.5 + - - -
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Residues in contact with LEU 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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16A LEU* 5.0 22.7 - - + +
191A VAL* 2.8 33.1 + - + +
192A LEU* 5.1 0.2 - - - -
193A ALA 3.2 0.4 - - - -
194A ASP* 1.3 80.1 - - + +
196A GLY* 1.3 61.0 + - - +
197A ILE* 3.1 32.3 + - + +
10C G 3.6 43.3 - - + +
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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