Contacts of the helix formed by residues 186 - 198 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81F LYS 3.1 21.5 + - - +
82F ASN* 2.8 19.0 + - - +
83F LEU 4.1 1.2 + - - -
84F SER* 3.4 31.9 + - - -
87F GLY* 4.7 2.9 - - - -
185F VAL* 1.3 75.0 - - - +
187F TRP* 1.3 53.9 + - - +
188F ALA* 3.1 20.4 + - - +
189F ASP* 2.9 27.9 + - - +
190F VAL* 3.6 5.5 + - - +
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Residues in contact with TRP 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F GLY* 5.5 1.2 - - - -
88F GLY* 3.6 23.3 + - - -
89F ASP 3.5 13.9 + - - -
90F LYS 4.1 8.7 - - - +
91F PRO* 3.7 38.1 - - + -
95F LEU* 4.1 2.7 - - + -
99F ILE* 4.1 9.0 - - + -
106F PHE* 3.5 34.8 - + - -
109F PHE* 4.3 6.5 - + - -
128F LEU* 5.8 0.9 - - + -
157F LEU* 4.2 13.5 - - + -
182F TRP* 3.8 24.9 + + - -
185F VAL* 3.5 24.6 + - + +
186F ASN* 1.3 70.0 - - - +
188F ALA* 1.3 62.2 + - - +
189F ASP 3.1 0.2 - - - -
190F VAL* 4.0 30.9 - - + +
191F GLN* 3.0 33.2 + - - +
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Residues in contact with ALA 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F ASN* 2.9 12.5 + - - +
187F TRP* 1.3 78.9 - - - +
189F ASP* 1.3 58.1 + - - +
191F GLN* 4.0 8.8 - - - +
192F SER* 3.2 26.2 + - - -
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Residues in contact with ASP 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LYS* 3.7 22.0 - - - +
82F ASN* 2.8 21.6 + - - +
186F ASN* 2.9 26.9 + - - +
188F ALA* 1.3 78.7 - - - +
190F VAL* 1.3 65.9 + - - +
192F SER* 2.9 9.4 + - - -
193F ARG* 2.7 63.5 + - - +
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Residues in contact with VAL 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ASN* 4.3 5.6 - - + +
95F LEU* 3.4 23.3 - - + -
128F LEU* 4.7 7.4 - - + -
156F LEU* 4.1 26.8 - - + +
157F LEU* 4.0 31.6 - - + -
185F VAL* 4.6 1.3 - - + -
186F ASN 3.9 13.2 - - - +
187F TRP* 4.1 25.6 - - + +
189F ASP* 1.3 73.8 + - - +
191F GLN* 1.3 52.2 + - - +
193F ARG* 3.0 10.9 + - - +
194F TYR* 2.8 33.8 + - - +
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Residues in contact with GLN 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LYS 4.9 0.2 - - - +
91F PRO* 3.6 4.7 - - - +
92F THR* 2.6 53.7 + - - +
95F LEU* 3.1 37.8 - - + +
187F TRP* 3.0 20.6 + - - +
188F ALA* 4.0 7.5 - - - +
190F VAL* 1.3 78.2 - - - +
192F SER* 1.3 64.3 + - - +
194F TYR* 3.3 5.0 + - - +
195F ALA* 3.1 23.4 + - - +
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Residues in contact with SER 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F ALA 3.2 15.2 + - - -
189F ASP* 2.9 16.5 + - - -
191F GLN* 1.3 82.4 - - - +
193F ARG* 1.3 61.6 + - - +
195F ALA* 3.2 8.6 + - - +
196F ALA* 3.1 21.5 + - - +
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Residues in contact with ARG 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F THR* 6.1 1.0 - - - +
78F ILE* 3.9 37.0 - - - +
81F LYS* 3.8 21.4 - - - +
82F ASN* 3.8 2.4 - - - +
154F VAL* 5.3 2.3 - - + +
155F PRO 4.0 10.8 + - - +
156F LEU* 3.3 36.8 - - + +
189F ASP* 2.7 50.4 + - - +
190F VAL 3.4 4.3 - - - +
192F SER* 1.3 75.4 - - - +
194F TYR* 1.3 60.7 + - - +
196F ALA* 3.4 6.4 + - - +
197F ALA* 2.9 30.3 + - - +
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Residues in contact with TYR 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLU* 4.2 23.2 + - + -
95F LEU* 3.6 32.5 - - + -
98F ALA* 3.4 30.7 - - + +
130F TRP* 4.2 19.9 - + - -
137F LEU* 4.3 8.1 - - + -
156F LEU* 3.8 24.6 - - + +
190F VAL 2.8 15.3 + - - +
191F GLN 3.6 5.4 - - - +
193F ARG* 1.3 78.9 - - - +
195F ALA* 1.3 53.1 + - + +
197F ALA* 3.2 2.0 + - + +
198F THR* 2.7 71.7 + - + +
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Residues in contact with ALA 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F GLN 3.1 12.3 + - - +
192F SER* 3.3 12.1 - - - +
194F TYR* 1.3 82.0 - - + +
196F ALA* 1.3 60.2 + - - +
198F THR* 3.5 8.8 + - - -
199F SER* 3.4 21.8 + - - -
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Residues in contact with ALA 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F SER 3.1 10.1 + - - +
193F ARG* 3.9 9.4 - - - +
194F TYR 3.3 0.2 - - - -
195F ALA* 1.3 77.0 - - - +
197F ALA* 1.3 66.4 + - - +
199F SER* 3.2 19.4 + - - +
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Residues in contact with ALA 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F TRP* 3.7 40.6 + - + -
132F THR* 5.2 3.3 - - - +
154F VAL* 4.2 22.0 - - + -
156F LEU* 4.2 4.3 - - + -
193F ARG 2.9 18.2 + - - +
194F TYR* 3.2 5.6 + - + +
196F ALA* 1.3 80.1 - - - +
198F THR* 1.3 59.4 + - - +
199F SER 3.2 6.2 + - - -
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Residues in contact with THR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F TRP* 3.7 31.9 - - + +
194F TYR* 2.7 67.3 + - + +
195F ALA* 3.6 9.5 + - - -
196F ALA 3.3 0.2 - - - -
197F ALA* 1.3 72.5 - - - +
199F SER* 1.3 59.6 + - - +
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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