Contacts of the helix formed by residues 186 - 198 (chain C) in PDB entry 1GN2
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 ASN 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C LYS 3.1 20.9 + - - +
82C ASN* 2.8 19.0 + - - +
83C LEU 4.1 1.2 + - - -
84C SER* 3.4 31.1 - - - -
87C GLY* 4.7 3.1 - - - -
185C VAL* 1.3 75.6 - - - +
187C TRP* 1.3 54.2 + - - +
188C ALA* 3.0 20.7 + - - +
189C ASP* 2.9 28.5 + - - +
190C VAL* 3.6 4.9 + - - +
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Residues in contact with TRP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C GLY* 5.5 0.8 - - - -
88C GLY* 3.6 23.5 + - - -
89C ASP 3.5 13.9 + - - -
90C LYS 4.1 9.2 - - - +
91C PRO* 3.7 38.8 - - + -
95C LEU* 4.1 2.7 - - + -
99C ILE* 4.1 9.0 - - + -
106C PHE* 3.5 35.2 - + - -
109C PHE* 4.3 7.0 - + - -
128C LEU* 5.8 0.7 - - + -
157C LEU* 4.2 13.9 - - + -
182C TRP* 3.8 24.2 + + - -
185C VAL* 3.5 25.0 + - + +
186C ASN* 1.3 69.1 - - - +
188C ALA* 1.3 60.6 + - - +
189C ASP 3.1 0.4 - - - -
190C VAL* 4.0 31.1 - - + +
191C GLN* 3.0 33.3 + - - +
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASN* 2.9 12.9 + - - +
187C TRP* 1.3 78.2 - - - +
189C ASP* 1.3 59.9 + - - +
191C GLN* 4.0 8.6 - - - +
192C SER* 3.2 25.8 + - - -
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Residues in contact with ASP 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LYS* 3.7 22.2 - - - +
82C ASN* 2.8 20.5 + - - +
186C ASN* 2.9 27.6 + - - +
188C ALA* 1.3 79.8 - - - +
190C VAL* 1.3 66.1 + - - +
192C SER* 2.9 9.2 + - - -
193C ARG* 2.7 64.7 + - - +
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASN* 4.4 5.8 - - + +
95C LEU* 3.4 22.0 - - + -
128C LEU* 4.7 7.6 - - + -
156C LEU* 4.1 25.6 - - + +
157C LEU* 4.0 32.5 - - + -
185C VAL* 4.6 0.7 - - + -
186C ASN 3.6 13.7 + - - +
187C TRP* 4.1 25.8 - - + +
189C ASP* 1.3 73.2 + - - +
191C GLN* 1.3 53.0 + - - +
193C ARG* 3.0 11.0 + - - +
194C TYR* 2.8 34.1 + - - +
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Residues in contact with GLN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LYS 4.9 0.2 - - - +
91C PRO* 3.6 4.7 - - - +
92C THR* 2.6 53.0 + - - +
95C LEU* 3.1 38.1 - - + +
187C TRP* 3.0 21.1 + - - +
188C ALA* 4.0 8.7 - - - +
190C VAL* 1.3 78.8 - - - +
192C SER* 1.3 63.4 + - - +
194C TYR* 3.3 4.9 + - - +
195C ALA* 3.1 23.8 + - - +
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Residues in contact with SER 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ALA 3.2 14.6 + - - -
189C ASP* 2.9 16.9 + - - -
191C GLN* 1.3 82.6 - - - +
193C ARG* 1.3 59.9 + - - +
195C ALA* 3.2 9.3 + - - +
196C ALA* 3.1 22.4 + - - +
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Residues in contact with ARG 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR* 5.1 1.2 + - - +
78C ILE* 3.9 37.1 - - - +
81C LYS* 3.8 20.8 - - - +
82C ASN* 3.8 2.4 - - - +
154C VAL* 5.3 2.1 - - + +
155C PRO* 4.0 9.7 + - - +
156C LEU* 3.3 37.3 - - + +
189C ASP* 2.7 50.6 + - - +
190C VAL* 3.4 5.2 - - - +
192C SER* 1.3 75.2 - - - +
194C TYR* 1.3 61.4 + - - +
196C ALA* 3.4 6.2 + - - +
197C ALA* 2.9 30.0 + - - +
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Residues in contact with TYR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLU* 4.2 23.0 + - + -
95C LEU* 3.6 33.9 - - + -
98C ALA* 3.4 29.8 - - + +
130C TRP* 4.2 18.9 - + - -
137C LEU* 4.3 8.3 - - + -
156C LEU* 3.8 25.3 - - + +
190C VAL 2.8 15.0 + - - +
191C GLN 3.6 5.8 - - - +
192C SER 3.2 0.2 - - - -
193C ARG* 1.3 78.6 - - - +
195C ALA* 1.3 53.3 + - + +
197C ALA* 3.2 2.2 + - + +
198C THR* 2.7 71.9 + - + +
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C GLN 3.1 12.4 + - - +
192C SER* 3.3 12.3 - - - +
194C TYR* 1.3 81.9 - - + +
196C ALA* 1.3 60.2 - - - +
198C THR* 3.5 8.2 + - - -
199C SER* 3.4 22.3 + - - -
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Residues in contact with ALA 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C SER* 3.1 10.3 + - - +
193C ARG* 3.9 8.3 - - - +
195C ALA* 1.3 77.7 - - - +
197C ALA* 1.3 66.8 + - - +
199C SER* 3.2 19.4 + - - +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C TRP* 3.7 41.3 + - + -
132C THR* 5.2 2.9 - - - +
154C VAL* 4.2 21.9 - - + +
156C LEU* 4.2 3.6 - - + -
193C ARG 2.9 19.4 + - - +
194C TYR* 3.5 4.9 - - - +
196C ALA* 1.3 80.0 - - - +
198C THR* 1.3 58.8 + - - +
199C SER 3.1 5.9 + - - -
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Residues in contact with THR 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C TRP* 3.7 31.9 - - + +
194C TYR* 2.7 67.2 + - + +
195C ALA* 3.6 9.2 + - - -
196C ALA 3.3 0.4 - - - -
197C ALA* 1.3 72.5 - - - +
199C SER* 1.3 61.1 + - - +
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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