Contacts of the helix formed by residues 187 - 199 (chain A) in PDB entry 3RZE
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 VAL 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ASP 5.2 0.9 - - - +
184A PHE* 2.7 44.8 + - + +
186A ASP* 1.4 70.4 - - + +
188A THR* 1.3 58.7 + - - +
189A TRP* 3.4 38.1 - - + +
190A PHE* 3.8 17.9 - - + +
191A LYS* 3.3 23.2 + - - +
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Residues in contact with THR 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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185A TYR 4.8 5.6 - - - +
186A ASP 3.2 15.0 + - - +
187A VAL* 1.3 72.4 - - - +
189A TRP* 1.4 63.5 + - - +
190A PHE 3.5 0.4 - - - -
191A LYS* 4.0 11.7 - - + -
192A VAL* 3.4 27.4 + - - +
438A ILE* 5.4 2.0 - - + +
439A ALA* 3.9 33.0 + - - +
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Residues in contact with TRP 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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167A HIS* 4.1 30.7 - + - -
187A VAL* 3.4 27.3 - - + +
188A THR* 1.4 80.0 + - - +
190A PHE* 1.4 81.1 + + + +
192A VAL* 3.4 19.3 - - - +
193A MET* 3.4 26.8 + - + +
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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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158A TRP* 4.9 2.0 - + - -
161A PRO* 4.1 25.8 - - + -
184A PHE* 3.6 50.9 - + + -
187A VAL* 3.8 21.4 - - + +
189A TRP* 1.4 100.8 - + + +
191A LYS* 1.4 65.2 + - - +
192A VAL 3.2 0.4 - - - -
193A MET* 3.3 15.7 + - + +
194A THR* 3.1 50.2 + - + +
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Residues in contact with LYS 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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108A TYR* 4.5 4.0 + - - -
182A THR* 4.1 12.5 - - - +
184A PHE* 4.4 12.9 - - + +
185A TYR* 3.4 33.2 - - - +
187A VAL 3.3 19.6 + - - +
188A THR* 4.1 13.5 - - + +
189A TRP 3.5 0.2 - - - -
190A PHE* 1.4 80.5 - - - +
192A VAL* 1.4 57.4 + - + +
194A THR* 3.3 15.1 + - - -
195A ALA* 3.4 15.1 + - - +
435A PHE* 3.5 41.9 - - + -
438A ILE* 6.4 3.4 - - + -
1200A 5EH 4.9 0.2 - - - -
1202A PO4 3.0 28.0 + - - -
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Residues in contact with VAL 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 THR 3.4 20.8 + - - +
189A TRP* 3.4 15.5 - - - +
191A LYS* 1.4 77.7 - - + +
193A MET* 1.3 63.3 + - - +
194A THR 3.4 0.4 - - - -
195A ALA* 3.4 9.2 - - + +
196A ILE* 3.4 33.0 + - + +
435A PHE* 5.3 4.7 - - + +
436A MET* 6.2 1.1 - - - -
439A ALA* 4.0 25.8 - - + -
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Residues in contact with MET 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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189A TRP* 3.4 32.6 + - + +
190A PHE* 3.3 23.0 + - + +
192A VAL* 1.3 79.2 - - + +
194A THR* 1.4 62.4 + - + +
196A ILE* 3.7 4.7 + - - +
197A ILE* 3.1 45.4 + - + +
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Residues in contact with THR 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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158A TRP* 3.6 33.0 - - + -
184A PHE* 5.5 1.9 - - - -
190A PHE* 3.1 48.1 + - + +
191A LYS* 3.3 12.5 + - - -
193A MET* 1.4 78.2 - - + +
195A ALA* 1.4 59.7 + - - +
196A ILE 3.3 0.4 - - - -
197A ILE* 4.6 1.8 - - + -
198A ASN* 3.1 39.9 + - - +
199A PHE 4.2 0.2 + - - -
432A PHE* 5.2 0.2 - - - -
1200A 5EH 3.9 15.8 - - - -
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Residues in contact with ALA 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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191A LYS 3.4 15.9 + - - +
192A VAL* 3.4 13.5 - - + +
193A MET 3.3 0.2 - - - -
194A THR* 1.4 80.5 + - - +
196A ILE* 1.3 57.2 + - + +
199A PHE* 3.2 13.7 + - - +
200A TYR* 3.1 40.4 + - + -
432A PHE* 4.1 18.2 - - + -
435A PHE* 4.8 10.5 - - + -
1200A 5EH 4.7 1.6 - - - -
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Residues in contact with ILE 196 (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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192A VAL* 3.4 25.0 + - + +
193A MET* 4.3 3.6 - - - +
194A THR 3.3 0.2 - - - -
195A ALA* 1.3 75.7 - - + +
197A ILE* 1.4 67.7 + - + +
199A PHE 3.2 0.3 + - - -
200A TYR* 3.1 36.0 + - + -
201A LEU* 2.7 41.0 + - + +
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Residues in contact with ILE 197 (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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116A PHE* 5.1 6.7 - - + -
154A LEU* 6.3 2.7 - - + -
193A MET* 3.1 37.3 + - + +
194A THR* 5.1 1.3 - - + -
196A ILE* 1.4 77.3 - - + +
198A ASN* 1.3 73.3 + - - +
201A LEU* 4.2 28.8 - - + +
202A PRO* 3.4 15.1 - - - +
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Residues in contact with ASN 198 (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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112A THR* 3.4 17.1 - - + +
115A ILE* 3.3 27.1 - - - +
116A PHE* 4.5 8.9 - - - -
154A LEU* 5.0 2.4 - - - +
158A TRP* 3.1 39.4 + - + -
194A THR* 3.1 25.4 + - - +
197A ILE* 1.3 92.6 - - - +
199A PHE* 1.3 58.5 + - - +
202A PRO* 3.5 5.9 - - - +
1200A 5EH 3.8 21.6 - - + +
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Residues in contact with PHE 199 (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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115A ILE* 3.8 19.9 - - + +
195A ALA 3.2 12.3 + - - +
196A ILE 3.2 1.2 + - - -
198A ASN* 1.3 78.7 - - - +
200A TYR* 1.4 77.5 + + - +
201A LEU 3.3 1.1 - - - -
202A PRO* 3.3 4.1 - - - +
203A THR* 2.9 45.1 + - + +
424A PHE* 4.5 9.2 - + - -
425A ILE* 4.7 12.1 - - + -
428A TRP* 3.7 20.2 - - + -
429A ILE* 4.0 37.2 - - + -
432A PHE* 3.6 52.7 - + + -
1200A 5EH 4.2 5.6 - + - -
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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