Contacts of the helix formed by residues 186 - 198 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E LYS 3.1 21.5 + - - +
82E ASN 2.8 19.2 + - - +
83E LEU 4.1 1.4 + - - -
84E SER* 3.4 31.3 - - - -
87E GLY* 4.7 3.1 - - - -
184E VAL 3.3 0.2 + - - -
185E VAL* 1.3 73.8 - - - +
187E TRP* 1.3 54.8 + - - +
188E ALA* 3.1 20.4 + - - +
189E ASP* 2.9 29.4 + - - +
190E VAL* 3.6 5.3 + - - +
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Residues in contact with TRP 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E GLY* 5.5 1.0 - - - -
88E GLY* 3.6 23.7 + - - -
89E ASP 3.5 13.9 + - - -
90E LYS 4.1 8.7 - - - +
91E PRO* 3.7 37.9 - - + -
95E LEU* 4.1 2.5 - - + -
99E ILE* 4.1 9.4 - - + -
106E PHE* 3.5 35.2 - + - -
109E PHE* 4.3 6.7 - + - -
128E LEU* 5.8 0.9 - - + -
157E LEU* 4.2 13.5 - - + -
182E TRP* 3.8 24.3 + + - -
185E VAL* 3.5 24.9 + - + +
186E ASN* 1.3 69.7 + - - +
188E ALA* 1.3 62.3 + - - +
189E ASP 3.1 0.4 - - - -
190E VAL* 4.0 30.5 - - + +
191E GLN* 3.0 33.5 + - - +
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Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ASN* 2.9 12.7 + - - +
187E TRP* 1.3 78.8 - - - +
189E ASP* 1.3 58.4 + - - +
191E GLN* 4.0 8.6 - - - +
192E SER* 3.2 26.2 + - - -
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Residues in contact with ASP 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LYS* 3.7 22.6 - - - +
82E ASN* 2.8 20.8 + - - +
186E ASN* 2.9 27.6 + - - +
188E ALA* 1.3 79.1 - - - +
190E VAL* 1.3 64.7 + - - +
192E SER* 2.9 9.5 + - - -
193E ARG* 2.7 63.6 + - - +
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Residues in contact with VAL 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E ASN* 4.3 6.3 - - + +
95E LEU* 3.4 22.4 - - + -
128E LEU* 4.7 7.6 - - + -
156E LEU* 4.1 26.5 - - + +
157E LEU* 4.0 31.4 - - + -
185E VAL* 4.6 0.9 - - + -
186E ASN 3.9 13.2 - - - +
187E TRP* 4.1 26.0 - - + +
189E ASP* 1.3 74.4 + - - +
191E GLN* 1.3 52.7 + - - +
193E ARG* 3.0 11.1 + - - +
194E TYR* 2.8 33.3 + - - +
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Residues in contact with GLN 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PRO* 3.6 4.7 - - - +
92E THR* 2.6 53.1 + - - +
95E LEU* 3.1 38.1 - - + +
187E TRP* 3.0 20.8 + - - +
188E ALA* 4.0 8.3 - - - +
190E VAL* 1.3 78.4 - - - +
192E SER* 1.3 64.2 + - - +
194E TYR* 3.3 4.8 + - - +
195E ALA* 3.1 23.2 + - - +
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Residues in contact with SER 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ALA 3.2 15.4 + - - -
189E ASP* 2.9 16.3 + - - -
191E GLN* 1.3 81.6 - - - +
193E ARG* 1.3 61.6 + - - +
195E ALA* 3.2 9.3 + - - +
196E ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E THR* 6.1 1.2 - - - +
78E ILE* 3.9 37.7 - - - +
81E LYS* 3.8 21.2 - - - +
82E ASN* 3.8 2.0 - - - +
154E VAL* 5.3 2.5 - - + +
155E PRO 4.0 9.5 + - - +
156E LEU* 3.3 36.1 - - + +
189E ASP* 2.7 51.8 + - - +
190E VAL* 3.4 4.5 - - - +
192E SER* 1.3 75.2 - - - +
194E TYR* 1.3 60.8 - - - +
196E ALA* 3.8 6.0 - - - +
197E ALA* 2.9 30.3 + - - +
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Residues in contact with TYR 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLU* 4.2 22.7 + - + -
95E LEU* 3.6 33.0 - - + -
98E ALA* 3.4 30.6 - - + +
130E TRP* 4.2 19.1 - + - -
137E LEU* 4.3 7.6 - - + -
156E LEU* 3.8 25.7 - - + +
190E VAL 2.8 14.8 + - - +
191E GLN 3.6 5.6 - - - +
193E ARG* 1.3 78.7 - - - +
195E ALA* 1.3 52.7 + - - +
197E ALA* 3.2 1.8 + - + +
198E THR* 2.7 71.5 + - + +
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Residues in contact with ALA 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E GLN 3.1 12.5 + - - +
192E SER* 3.3 12.3 - - - +
194E TYR* 1.3 81.9 - - + +
196E ALA* 1.3 61.7 + - - +
198E THR* 3.5 8.3 + - - -
199E SER* 3.4 21.3 + - - -
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Residues in contact with ALA 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E SER* 3.1 10.6 + - - +
193E ARG* 3.9 8.7 - - - +
194E TYR 3.3 0.2 - - - -
195E ALA* 1.3 76.2 - - - +
197E ALA* 1.3 67.0 + - - +
199E SER* 3.2 19.1 + - - +
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E TRP* 3.7 41.6 + - + -
132E THR* 5.2 2.8 - - - +
154E VAL* 4.2 21.8 - - + -
156E LEU* 4.2 3.6 - - + -
193E ARG 2.9 19.1 + - - +
194E TYR* 3.2 5.8 + - + +
196E ALA* 1.3 79.7 - - - +
198E THR* 1.3 58.5 + - - +
199E SER 3.2 6.2 + - - -
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Residues in contact with THR 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E TRP* 3.7 32.1 - - + +
194E TYR* 2.7 66.9 + - + +
195E ALA* 3.6 9.3 + - - -
196E ALA 3.3 0.2 - - - -
197E ALA* 1.3 71.4 - - - +
199E SER* 1.3 61.7 + - - +
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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