Contacts of the helix formed by residues 189 - 197 (chain A) in PDB entry 2GH1
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 LYS 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A THR* 5.6 1.8 - - - +
183A ASP* 2.6 36.3 + - - +
185A ASN* 3.4 21.8 + - - +
186A ILE* 2.8 8.7 + - - +
188A MSE 1.3 78.4 - - - +
190A ILE* 1.3 65.6 + - - +
191A PRO* 3.1 3.4 - - - -
192A ILE* 2.9 25.3 + - + +
193A TYR* 3.0 44.4 + - + +
154B LEU* 3.6 35.6 - - + +
156B ASP* 6.0 1.1 - - - +
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Residues in contact with ILE 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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116A LEU* 3.5 28.3 - - + -
126A LEU* 4.6 6.3 - - + -
141A CYS* 4.0 19.1 - - + +
143A GLU* 4.1 13.0 - - + -
186A ILE* 3.1 32.1 + - + +
187A GLY* 3.8 12.1 - - - +
189A LYS* 1.3 76.8 - - - +
191A PRO* 1.3 62.0 - - + +
193A TYR* 3.8 6.4 - - + +
194A LEU* 2.8 48.6 + - + +
285A LYS 6.0 0.4 - - - +
287A THR* 3.6 26.2 - - + +
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Residues in contact with PRO 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLY 4.1 0.9 - - - +
188A MSE 3.3 17.7 - - - +
189A LYS 3.2 5.4 - - - -
190A ILE* 1.3 95.9 - - + +
192A ILE* 1.3 56.1 + - - +
194A LEU* 3.6 2.3 - - - +
195A SER* 2.9 29.5 + - - -
202A ILE* 4.0 8.3 - - + +
204A CYS* 4.0 17.9 - - + -
287A THR* 3.7 26.2 - - + +
212B PHE* 3.5 37.8 - - + -
279B VAL* 4.4 7.6 - - + -
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Residues in contact with ILE 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 MSE 4.7 0.4 - - - +
189A LYS* 2.9 17.0 + - + +
191A PRO* 1.3 73.7 - - - +
193A TYR* 1.3 69.8 + - + +
195A SER* 3.1 5.3 + - - -
196A GLU* 3.0 41.0 + - + +
154B LEU* 3.4 32.5 - - + -
156B ASP* 3.6 42.8 - - + +
212B PHE* 4.1 19.7 - - + -
277B SER* 4.1 14.8 - - - +
279B VAL* 4.2 11.0 - - + -
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Residues in contact with TYR 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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122A PRO* 4.0 19.5 - - + +
123A GLU* 3.3 44.2 + - + -
126A LEU* 3.6 24.5 - - + -
183A ASP* 4.8 3.3 + - - +
186A ILE* 4.0 17.4 - - + +
189A LYS* 3.0 51.6 + - + +
190A ILE* 3.9 4.5 - - + +
192A ILE* 1.3 79.0 - - + +
194A LEU* 1.3 64.1 + - - +
196A GLU* 3.3 18.8 + - - +
197A LEU* 3.1 30.3 + - + +
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Residues in contact with LEU 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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126A LEU* 3.9 33.2 - - + -
130A ILE* 4.7 2.7 - - + -
139A ILE* 4.4 17.9 - - + -
141A CYS* 5.4 0.9 - - - -
190A ILE* 2.8 20.7 + - + +
191A PRO 3.6 4.9 - - - +
193A TYR* 1.3 77.0 - - - +
195A SER* 1.3 62.6 + - - +
197A LEU* 3.3 9.3 + - + +
198A GLY 3.4 0.2 + - - -
199A VAL* 3.1 48.5 + - + +
202A ILE* 3.7 13.2 - - + -
287A THR* 3.7 28.9 - - + +
288A PHE* 4.3 19.3 - - - +
289A GLY 4.5 0.7 - - - +
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Residues in contact with SER 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 PRO 2.9 14.1 + - - -
192A ILE* 3.1 10.5 + - - -
194A LEU* 1.3 73.1 - - - +
196A GLU* 1.3 60.3 + - - +
197A LEU 3.0 1.6 - - - -
198A GLY* 2.9 21.8 + - - -
199A VAL 4.9 1.2 - - - +
202A ILE* 3.5 10.7 - - - +
212B PHE* 4.2 2.9 - - - -
214B ASP* 2.7 37.9 + - - -
216B ASN* 2.8 30.0 + - - +
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Residues in contact with GLU 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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123A GLU* 4.6 7.4 - - - +
192A ILE* 3.0 32.4 + - + +
193A TYR* 3.3 23.5 + - - +
195A SER* 1.3 75.4 - - - +
197A LEU* 1.3 62.2 + - + +
198A GLY 3.2 1.1 + - - -
156B ASP* 4.3 8.3 - - - +
216B ASN* 3.9 13.9 - - - +
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Residues in contact with LEU 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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123A GLU* 4.1 13.2 - - + +
126A LEU* 3.7 33.2 - - + -
127A GLN* 3.9 42.7 - - + +
130A ILE* 4.5 13.6 - - + +
193A TYR* 3.1 23.1 + - + +
194A LEU* 3.6 9.2 - - + +
195A SER 3.0 1.4 - - - -
196A GLU* 1.3 81.4 - - + +
198A GLY* 1.3 59.5 + - - +
199A VAL* 3.4 8.0 + - + +
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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