Contacts of the helix formed by residues 191 - 201 (chain B) in PDB entry 3GBA
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 SER 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.5 6.9 - - - -
109B GLY 2.8 32.8 + - - +
111B SER* 5.2 1.1 - - - -
189B MET 3.8 0.4 + - - -
190B GLU* 1.3 69.5 - - - +
192B THR* 1.3 61.7 + - - +
194B ILE* 3.3 12.9 + - - +
195B GLU* 2.9 30.9 + - - +
206B GLN* 4.3 6.9 - - - +
210B LEU* 3.8 26.9 - - - +
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.4 14.9 + - - +
106B MET* 3.6 24.2 - - + -
107B THR 3.4 25.8 - - - +
108B LEU* 3.8 6.9 - - + +
190B GLU* 3.8 6.4 - - - +
191B SER* 1.3 75.8 + - - +
193B SER* 1.3 66.0 + - - +
195B GLU* 3.5 7.3 + - - +
196B TYR* 3.3 6.4 + - - +
216B TYR* 2.8 24.1 + - + -
247B LYS* 5.2 5.6 - - - +
251B TRP* 3.0 30.8 + - + +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 4.3 4.7 + - - -
14B GLU 5.0 5.6 + - - -
16B TYR* 4.4 7.9 - - - -
189B MET* 3.3 22.7 - - - -
190B GLU 3.0 6.2 + - - -
192B THR* 1.3 78.4 + - - +
194B ILE* 1.3 66.7 + - - +
196B TYR* 3.2 7.8 + - - +
197B VAL* 2.9 27.9 + - - +
251B TRP* 5.6 0.2 - - - -
258B DYH 2.8 39.5 + - - -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.8 42.0 - - - -
112B ILE 3.8 11.2 - - - +
113B LEU* 4.2 6.3 - - + -
189B MET* 3.5 33.4 - - + +
190B GLU 3.0 15.5 + - - +
191B SER* 3.3 8.7 + - - +
193B SER* 1.3 76.2 - - - +
195B GLU* 1.3 56.1 + - - +
197B VAL* 4.6 2.7 - - - -
198B THR* 2.8 51.3 + - + +
206B GLN* 3.9 27.8 - - + +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B SER 2.9 12.6 + - - +
192B THR* 3.5 12.5 - - - +
193B SER 3.2 0.2 - - - -
194B ILE* 1.3 77.5 - - - +
196B TYR* 1.3 64.4 + - - +
198B THR* 3.4 6.8 + - - -
199B GLN* 3.3 23.8 + - - +
247B LYS* 3.6 22.7 + - - +
251B TRP* 3.7 23.1 + - + +
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.5 42.1 + - + +
15B PRO* 3.6 38.0 - - + +
18B MET* 4.3 6.2 - - - +
192B THR 3.3 3.8 + - - +
193B SER* 3.2 9.5 + - - +
195B GLU* 1.3 82.5 - - - +
197B VAL* 1.3 73.6 + - + +
199B GLN* 3.5 6.8 + - - +
200B ARG* 3.3 66.9 + - - +
250B TRP 3.7 14.1 - - - -
251B TRP* 3.6 24.1 - + - +
252B ARG 6.1 0.2 - - - -
261B CL 4.4 3.1 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 4.0 24.7 - - + -
177B ILE* 3.6 31.9 - - + -
189B MET* 4.4 5.4 - - + -
193B SER* 2.9 23.9 + - - +
194B ILE* 3.9 4.7 - - - +
196B TYR* 1.3 83.3 - - + +
198B THR* 1.3 59.8 + - - +
200B ARG 3.1 1.7 + - - -
201B ASN* 3.0 46.3 + - - +
204B LEU* 4.1 11.9 - - + -
261B CL 3.9 15.5 - - + -
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 3.6 25.6 - - + -
194B ILE* 2.8 35.3 + - + +
195B GLU* 3.4 9.0 + - - -
197B VAL* 1.3 73.0 - - - +
199B GLN* 1.3 64.5 + - - +
201B ASN 3.1 23.7 + - - +
202B CYS* 3.8 0.3 - - - -
204B LEU* 3.8 8.9 - - - +
205B THR* 3.7 23.1 - - - -
206B GLN 4.1 0.9 - - - +
256B CYS* 3.3 11.3 - - - -
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Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLU* 3.3 16.1 + - - +
196B TYR* 3.9 6.9 + - - +
197B VAL 3.3 0.8 - - - -
198B THR* 1.3 83.0 + - - +
200B ARG* 1.3 63.7 + - + +
201B ASN 3.6 0.3 + - - -
202B CYS* 3.9 4.0 - - - -
251B TRP* 2.8 30.9 + - - +
252B ARG 3.7 2.8 + - - -
253B GLY* 3.1 25.7 + - - +
254B ASN 4.5 0.9 - - - +
255B GLY* 2.9 39.1 + - - +
256B CYS* 3.7 16.3 - - - -
210D LEU 5.0 0.2 - - - +
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.7 17.0 + - - -
196B TYR* 3.3 55.2 + - - +
197B VAL 3.1 8.3 + - - +
199B GLN* 1.3 81.4 - - + +
201B ASN* 1.3 71.0 + - - +
202B CYS 4.1 0.9 - - - -
252B ARG 6.2 0.4 - - - +
261B CL 3.5 15.5 - - + +
121D ASP* 4.3 19.2 + - - -
209D GLY* 3.5 21.5 + - - -
210D LEU 4.0 2.8 - - - +
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Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ILE* 4.9 1.8 - - - +
181B LEU* 3.8 26.3 - - + +
197B VAL* 3.0 26.8 + - - +
198B THR 3.1 9.8 - - - +
199B GLN 3.3 0.4 - - - -
200B ARG* 1.3 84.9 + - - +
202B CYS* 1.3 58.1 + - - +
203B ASN* 3.1 13.1 - - - +
204B LEU* 2.9 39.6 + - + +
261B CL 3.2 26.1 - - - +
209D GLY* 3.9 12.6 - - - -
210D LEU 3.9 4.2 + - - +
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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