Contacts of the helix formed by residues 186 - 198 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D LYS 3.1 21.6 + - - +
82D ASN 2.8 19.0 + - - +
83D LEU 4.1 1.0 + - - -
84D SER* 3.4 31.2 - - - -
87D GLY* 4.7 3.6 - - - -
185D VAL* 1.3 73.9 - - - +
187D TRP* 1.3 53.9 + - - +
188D ALA* 3.1 19.8 + - - +
189D ASP* 2.9 29.3 + - - +
190D VAL* 3.6 4.7 + - - +
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Residues in contact with TRP 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D GLY* 5.5 0.8 - - - -
88D GLY* 3.6 22.6 + - - -
89D ASP 3.5 14.1 + - - -
90D LYS 4.1 8.7 - - - +
91D PRO* 3.7 37.9 - - + -
95D LEU* 4.1 3.1 - - + +
99D ILE* 4.1 9.2 - - + -
106D PHE* 3.5 35.0 - + - -
109D PHE* 4.3 6.7 - + - -
128D LEU* 5.8 0.7 - - + -
157D LEU* 4.2 13.5 - - + -
182D TRP* 3.8 24.5 + + - -
185D VAL* 3.5 25.7 + - + +
186D ASN* 1.3 69.3 - - - +
188D ALA* 1.3 61.8 + - - +
189D ASP 3.1 0.4 - - - -
190D VAL* 4.0 29.8 - - + +
191D GLN* 3.0 34.1 + - - +
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D ASN* 2.9 12.9 + - - +
187D TRP* 1.3 78.1 - - - +
189D ASP* 1.3 59.1 + - - +
191D GLN* 4.0 8.6 - - - +
192D SER* 3.2 26.2 + - - -
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LYS* 3.7 21.9 - - - +
82D ASN* 2.8 21.1 + - - +
186D ASN* 2.9 27.5 + - - +
188D ALA* 1.3 78.8 - - - +
190D VAL* 1.3 66.0 + - - +
192D SER* 2.9 8.9 + - - -
193D ARG* 2.7 63.6 + - - +
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Residues in contact with VAL 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ASN* 4.3 6.1 - - + +
95D LEU* 3.4 22.2 - - + -
128D LEU* 4.7 8.1 - - + -
156D LEU* 4.1 27.8 - - + +
157D LEU* 4.0 32.3 - - + -
185D VAL* 4.6 0.9 - - + -
186D ASN 3.6 13.7 + - - +
187D TRP* 4.1 24.2 - - + +
189D ASP* 1.3 73.2 + - - +
191D GLN* 1.3 52.6 + - - +
193D ARG* 3.0 10.7 + - - +
194D TYR* 2.8 33.8 + - - +
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Residues in contact with GLN 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PRO* 3.6 4.7 - - - +
92D THR* 2.6 53.2 + - - +
95D LEU* 3.1 38.1 - - + +
187D TRP* 3.0 21.0 + - - +
188D ALA* 4.0 8.1 - - - +
190D VAL* 1.3 79.1 - - - +
192D SER* 1.3 63.7 + - - +
194D TYR* 3.3 4.6 + - - +
195D ALA* 3.1 23.6 + - - +
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Residues in contact with SER 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ALA 3.2 13.9 + - - -
189D ASP* 2.9 16.6 + - - -
191D GLN* 1.3 82.2 - - - +
193D ARG* 1.3 62.1 + - - +
195D ALA* 3.2 8.6 + - - +
196D ALA* 3.1 21.3 + - - +
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D THR* 6.1 1.0 - - - +
78D ILE* 3.9 37.3 - - - +
81D LYS* 3.8 21.4 - - - +
82D ASN* 3.8 2.0 - - - +
154D VAL* 5.3 2.1 - - + +
155D PRO* 4.0 10.6 + - - +
156D LEU* 3.3 37.2 - - + +
189D ASP* 2.7 51.3 + - - +
190D VAL* 3.4 4.3 - - - +
192D SER* 1.3 75.6 - - - +
194D TYR* 1.3 60.9 - - - +
196D ALA* 3.4 6.3 + - - +
197D ALA* 2.9 29.8 + - - +
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Residues in contact with TYR 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLU* 4.2 23.6 + - + -
95D LEU* 3.6 33.0 - - + -
98D ALA* 3.4 30.6 - - + +
130D TRP* 4.2 19.3 - + - -
137D LEU* 4.3 7.4 - - + -
156D LEU* 3.8 25.3 - - + +
190D VAL 2.8 15.4 + - - +
191D GLN 3.6 4.9 - - - +
192D SER 3.2 0.2 - - - -
193D ARG* 1.3 77.8 - - - +
195D ALA* 1.3 53.0 + - + +
197D ALA* 3.2 2.0 + - + +
198D THR* 2.7 71.2 + - + +
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Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D GLN 3.1 12.7 + - - +
192D SER* 3.3 11.9 - - - +
194D TYR* 1.3 82.9 - - + +
196D ALA* 1.3 61.1 + - - +
198D THR* 3.5 7.6 + - - -
199D SER* 3.4 22.0 + - - -
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D SER* 3.1 10.0 + - - +
193D ARG* 3.4 8.7 + - - +
195D ALA* 1.3 76.8 - - - +
197D ALA* 1.3 66.5 + - - +
199D SER* 3.2 19.0 + - - +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D TRP* 3.7 41.2 + - + -
132D THR* 5.2 2.9 - - - +
154D VAL* 4.2 20.9 - - + -
156D LEU* 4.2 3.8 - - + -
193D ARG 2.9 18.6 + - - +
194D TYR* 3.5 6.1 - - + +
196D ALA* 1.3 78.5 - - - +
198D THR* 1.3 60.5 + - - +
199D SER 3.2 5.7 + - - -
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Residues in contact with THR 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D TRP* 3.7 33.2 - - + +
194D TYR* 2.7 66.3 + - + +
195D ALA* 3.6 9.7 + - - -
196D ALA 3.3 0.4 - - - -
197D ALA* 1.3 71.4 - - - +
199D SER* 1.3 59.9 + - - +
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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