Contacts of the helix formed by residues 186 - 198 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS 3.1 21.6 + - - +
82B ASN 2.8 19.4 + - - +
83B LEU 4.1 1.2 + - - -
84B SER* 3.4 31.2 + - - -
87B GLY* 4.7 3.6 - - - -
184B VAL 3.3 0.2 + - - -
185B VAL* 1.3 74.2 - - - +
187B TRP* 1.3 54.5 + - - +
188B ALA* 3.1 20.2 + - - +
189B ASP* 2.9 28.8 + - - +
190B VAL* 3.6 5.4 + - - +
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Residues in contact with TRP 187 (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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87B GLY* 5.5 0.6 - - - -
88B GLY* 3.6 23.3 + - - -
89B ASP 3.5 14.3 + - - -
90B LYS 4.1 9.4 - - - +
91B PRO* 3.7 37.0 - - + -
95B LEU* 4.1 2.7 - - + -
99B ILE* 4.1 9.6 - - + -
106B PHE* 3.5 34.8 - + - -
109B PHE* 4.3 7.2 - + - -
128B LEU* 5.8 0.4 - - + -
157B LEU* 4.2 13.0 - - + -
182B TRP* 3.8 24.3 + + - -
185B VAL* 3.5 24.4 + - + +
186B ASN* 1.3 68.8 - - - +
188B ALA* 1.3 61.6 + - - +
189B ASP 3.1 0.4 - - - -
190B VAL* 4.0 30.7 - - + +
191B GLN* 3.0 33.7 + - - +
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Residues in contact with ALA 188 (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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186B ASN* 2.9 12.5 + - - +
187B TRP* 1.3 78.7 - - - +
189B ASP* 1.3 58.5 - - - +
191B GLN* 4.0 8.2 - - - +
192B SER* 3.2 26.5 + - - -
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LYS* 3.7 22.8 - - - +
82B ASN* 2.8 21.5 + - - +
186B ASN* 2.9 26.7 + - - +
188B ALA* 1.3 79.1 - - - +
190B VAL* 1.3 65.1 + - - +
192B SER* 2.9 9.8 + - - -
193B ARG* 2.7 63.0 + - - +
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Residues in contact with VAL 190 (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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82B ASN* 4.3 4.9 - - + +
95B LEU* 3.4 22.2 - - + -
128B LEU* 4.7 7.4 - - + -
156B LEU* 4.1 27.1 - - + +
157B LEU* 4.0 32.3 - - + -
185B VAL* 4.6 0.4 - - + -
186B ASN 3.6 13.9 + - - +
187B TRP* 4.1 25.6 - - + +
189B ASP* 1.3 73.6 + - - +
191B GLN* 1.3 52.8 - - - +
193B ARG* 3.0 10.9 + - - +
194B TYR* 2.8 33.4 + - - +
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Residues in contact with GLN 191 (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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90B LYS 4.9 0.2 - - - +
91B PRO* 3.6 4.9 - - - +
92B THR* 2.6 53.8 + - - +
95B LEU* 3.1 37.2 - - + +
187B TRP* 3.0 20.9 + - - +
188B ALA* 4.0 8.1 - - - +
190B VAL* 1.3 79.5 - - - +
192B SER* 1.3 64.3 + - - +
194B TYR* 3.3 5.2 + - - +
195B ALA* 3.1 22.7 + - - +
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Residues in contact with SER 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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188B ALA 3.2 14.5 + - - -
189B ASP* 2.9 16.4 + - - -
191B GLN* 1.3 82.2 - - - +
193B ARG* 1.3 60.8 + - - +
195B ALA* 3.2 9.4 + - - +
196B ALA* 3.1 21.8 + - - +
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Residues in contact with ARG 193 (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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77B THR* 6.1 1.2 - - - +
78B ILE* 3.9 36.8 - - - +
81B LYS* 3.8 21.2 - - - +
82B ASN* 3.8 2.0 - - - +
154B VAL* 5.3 2.3 - - + +
155B PRO 4.0 10.4 + - - +
156B LEU* 3.3 36.1 - - + +
189B ASP* 2.7 51.2 + - - +
190B VAL* 3.0 4.9 + - - +
192B SER* 1.3 74.0 - - - +
194B TYR* 1.3 60.8 + - - +
196B ALA* 3.4 6.4 + - - +
197B ALA* 2.9 29.8 + - - +
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Residues in contact with TYR 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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94B GLU* 4.2 23.5 + - + -
95B LEU* 3.6 32.1 - - + -
98B ALA* 3.4 29.6 - - + +
130B TRP* 4.2 19.6 - + - -
137B LEU* 4.3 7.4 - - + -
156B LEU* 3.8 25.3 - - + +
190B VAL 2.8 15.4 + - - +
191B GLN 3.6 5.4 - - - +
193B ARG* 1.3 78.4 - - - +
195B ALA* 1.3 52.5 + - + +
197B ALA* 3.2 1.8 + - + +
198B THR* 2.7 70.8 + - + +
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Residues in contact with ALA 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 GLN 3.1 12.5 + - - +
192B SER* 3.2 12.1 + - - +
194B TYR* 1.3 82.4 - - + +
196B ALA* 1.3 60.4 + - - +
198B THR* 3.5 8.3 + - - -
199B SER* 3.4 21.7 + - - -
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Residues in contact with ALA 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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192B SER* 3.1 10.4 + - - +
193B ARG* 3.9 8.7 - - - +
194B TYR 3.3 0.2 - - - -
195B ALA* 1.3 78.1 - - - +
197B ALA* 1.3 66.4 + - - +
199B SER* 3.2 19.7 + - - +
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Residues in contact with ALA 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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130B TRP* 3.7 40.3 + - + -
132B THR* 5.2 3.1 - - - +
154B VAL* 4.2 22.4 - - + -
156B LEU* 4.2 4.5 - - + -
193B ARG 2.9 18.6 + - - +
194B TYR* 3.5 5.2 - - - +
196B ALA* 1.3 79.1 - - - +
198B THR* 1.3 59.2 + - - +
199B SER 3.1 6.3 + - - -
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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
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130B TRP* 3.7 33.2 - - + +
194B TYR* 2.7 67.4 + - + +
195B ALA* 3.6 9.3 + - - -
196B ALA 3.3 0.2 - - - -
197B ALA* 1.3 71.8 - - - +
199B SER* 1.3 60.3 + - - +
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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