Contacts of the helix formed by residues 190 - 200 (chain A) in PDB entry 1G5J
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 GLY 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A GLN 2.6 17.4 + - - -
188A GLU 4.3 0.9 - - - -
189A ASN* 1.3 75.0 - - - +
191A GLY* 1.3 65.5 + - - +
193A ASP* 3.3 8.8 - - - +
194A THR* 2.5 29.5 + - - -
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Residues in contact with GLY 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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141A TRP* 4.0 3.5 - - - -
186A ILE* 2.8 19.5 + - - -
187A GLN* 3.1 14.5 + - - +
190A GLY* 1.3 77.4 - - - +
192A TRP* 1.3 55.9 + - - -
193A ASP* 2.9 7.9 - - - -
194A THR* 2.7 29.3 + - - -
195A PHE 3.4 2.6 + - - -
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Residues in contact with TRP 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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5A MET* 4.4 14.6 - - + -
8A SER* 5.6 5.4 - - - -
9A ASN* 2.6 42.9 + - + +
12A LEU* 5.0 1.6 - - + -
46A GLU* 4.8 5.8 - - - +
90A VAL* 3.8 17.6 - - + +
94A LEU* 3.8 14.1 - - + -
141A TRP* 4.9 4.7 - + - -
144A ILE* 3.4 29.8 - - + -
148A PHE* 4.2 12.3 - + - -
178A LEU* 3.5 25.8 - - + -
186A ILE* 3.4 35.3 - - + +
191A GLY* 1.3 69.4 - - - -
193A ASP* 1.3 62.5 + - - +
195A PHE* 3.2 63.0 + + + +
196A VAL* 3.3 7.6 + - - +
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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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46A GLU* 3.6 31.3 + - + +
190A GLY 3.3 11.1 - - - +
191A GLY* 2.8 1.5 + - - -
192A TRP* 1.3 76.4 - - - +
194A THR* 1.3 73.9 + - - +
196A VAL* 3.0 24.2 + - - +
197A GLU* 3.2 18.9 + - - +
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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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141A TRP* 3.7 17.5 - - + +
189A ASN 3.4 19.2 + - - +
190A GLY* 2.5 30.5 + - - -
191A GLY 2.7 10.3 + - - -
193A ASP* 1.3 82.8 + - - +
195A PHE* 1.3 64.2 + - - +
197A GLU* 2.9 11.2 + - + +
198A LEU* 2.8 32.4 + - + +
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Residues in contact with PHE 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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90A VAL* 3.5 17.9 - - + -
93A ALA* 3.4 22.7 - - + -
94A LEU* 3.0 41.5 - - + -
141A TRP* 3.5 55.1 - + + +
144A ILE* 6.0 1.1 - - + -
145A VAL* 4.1 15.9 - - + -
191A GLY 3.4 2.2 + - - -
192A TRP* 3.2 32.0 + + + +
193A ASP 3.2 0.4 - - - -
194A THR* 1.3 79.6 - - - +
196A VAL* 1.3 65.7 + - + +
199A TYR* 2.8 49.4 + + + +
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Residues in contact with VAL 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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46A GLU* 5.8 1.6 - - + -
89A ALA* 3.9 16.6 - - + +
90A VAL* 3.3 52.5 - - + +
93A ALA* 4.4 4.3 - - + -
192A TRP 3.3 1.5 + - - +
193A ASP* 3.0 13.2 + - - +
195A PHE* 1.3 89.0 - - + +
197A GLU* 1.3 66.1 + - + +
200A GLY* 2.7 36.5 + - - +
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Residues in contact with GLU 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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193A ASP* 3.7 23.3 - - - +
194A THR* 2.9 11.2 + - + +
196A VAL* 1.3 84.5 - - + +
198A LEU* 1.3 65.9 + - - +
200A GLY* 3.6 5.4 + - - -
202A ASN* 5.5 5.9 - - - +
203A ALA* 5.2 0.2 - - - +
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Residues in contact with LEU 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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141A TRP* 3.4 25.6 - - + +
189A ASN* 5.4 5.4 - - - +
194A THR* 2.8 28.2 + - + +
195A PHE 3.8 2.0 - - - +
197A GLU* 1.3 76.9 - - - +
199A TYR* 1.3 63.0 + - + +
203A ALA* 2.7 27.9 + - - +
323B PHE* 2.8 45.9 - - + +
324B LYS* 3.7 9.6 - - + +
325B LYS 5.0 1.8 - - - +
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Residues in contact with TYR 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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93A ALA* 4.8 11.2 - - - +
96A GLU* 5.9 0.5 - - - +
97A ALA* 4.5 9.0 - - + +
140A ASN* 4.9 4.2 + - - +
141A TRP* 3.5 39.5 + + + +
142A GLY* 3.3 24.8 + - - -
145A VAL* 4.4 11.0 - - + -
195A PHE* 2.8 28.6 + - + +
196A VAL 3.8 0.4 - - - -
198A LEU* 1.3 82.4 - - + +
200A GLY* 1.3 69.6 + - - +
203A ALA* 3.4 7.3 - - + +
204A ALA* 3.9 10.7 + - - +
319B PHE* 4.9 5.2 - + - -
320B VAL* 2.8 37.3 - - + +
323B PHE* 3.4 41.7 - + + -
324B LYS* 4.8 4.1 + - + +
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Residues in contact with GLY 200 (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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93A ALA* 4.9 8.5 - - - -
96A GLU* 6.4 0.2 - - - -
196A VAL* 2.7 30.4 + - - -
197A GLU 3.6 5.0 + - - -
198A LEU 3.3 4.2 + - - -
199A TYR* 1.3 84.0 - - - +
201A ASN* 1.3 57.8 + - - -
202A ASN* 2.9 4.9 - - - -
203A ALA 2.7 25.1 + - - -
204A ALA 3.2 4.0 + - - -
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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