Contacts of the helix formed by residues 185 - 196 (chain A) in PDB entry 1N0N
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A THR 3.5 13.4 + - - +
80A ASN 2.8 26.2 + - - +
81A LEU 3.8 9.8 + - - -
82A SER* 3.7 22.2 + - - -
84A ASN* 5.3 1.7 - - - +
85A GLY* 4.5 2.5 - - - -
183A VAL 3.3 1.6 + - - -
184A ILE* 1.3 70.5 - - - +
186A TRP* 1.3 62.2 + - - +
187A GLU* 3.1 23.7 + - - +
188A ASN* 3.1 21.8 + - - +
189A VAL* 3.1 14.7 + - - +
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Residues in contact with TRP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY* 5.4 0.2 - - - -
86A GLY 3.4 25.6 - - - +
87A GLY 3.3 18.4 + - - -
88A GLU 4.2 3.6 - - - +
89A PRO* 3.7 37.7 - - + -
93A LEU* 3.9 8.1 - - + -
97A ILE* 4.3 6.1 - - + -
104A PHE* 3.6 22.4 - + - -
107A PHE* 3.5 24.7 - + - -
126A LEU* 4.8 3.1 - - + -
156A LEU* 3.9 11.0 - - + -
181A TRP* 4.0 17.2 + + - -
184A ILE* 3.1 31.1 + - + +
185A ASN* 1.3 70.6 + - - +
187A GLU* 1.3 56.5 + - - +
189A VAL* 3.7 31.7 - - + +
190A THR* 2.7 38.3 + - - -
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASN* 5.7 3.6 + - - +
185A ASN* 3.1 12.9 - - - +
186A TRP* 1.3 79.3 - - - +
188A ASN* 1.3 58.7 + - - +
190A THR* 3.4 5.8 + - - -
191A GLU* 3.0 45.7 + - + +
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Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 3.1 42.1 + - - +
80A ASN* 2.9 27.9 + - - -
185A ASN* 3.1 17.2 + - - +
187A GLU* 1.3 78.2 - - - +
189A VAL* 1.3 63.6 + - - +
191A GLU* 3.2 19.1 + - - +
192A ARG* 3.0 41.6 + - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 4.2 8.7 - - - +
93A LEU* 3.9 7.2 - - + -
126A LEU* 4.6 4.3 - - + -
155A LEU* 3.7 40.7 - - + +
156A LEU* 4.1 21.5 - - + -
184A ILE* 4.3 2.5 - - + -
185A ASN 3.1 18.2 + - - +
186A TRP* 3.8 35.2 - - + +
188A ASN* 1.3 75.5 - - - +
190A THR* 1.3 64.1 + - - +
192A ARG* 3.3 3.6 + - - +
193A TYR* 3.0 21.0 + - - +
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PRO* 4.1 7.3 - - - +
90A LYS 4.9 7.0 + - - +
93A LEU* 3.4 31.7 - - + +
186A TRP 2.7 23.5 + - - -
187A GLU* 3.6 7.1 - - - -
189A VAL* 1.3 79.1 - - - +
191A GLU* 1.3 58.4 + - + +
193A TYR* 3.1 3.5 + - + +
194A MET* 2.9 43.5 + - + +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.0 33.9 + - + +
188A ASN* 3.2 21.2 + - - +
190A THR* 1.3 77.9 - - + +
192A ARG* 1.3 56.8 - - + +
194A MET* 3.4 6.2 + - - +
195A ALA* 3.0 27.2 + - - +
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER 4.8 0.4 + - - -
76A ILE* 3.8 34.0 - - - +
79A THR* 2.8 27.9 + - - +
80A ASN* 3.7 4.8 - - - +
153A ILE* 5.1 2.4 - - + +
154A PRO* 3.9 15.7 + - - +
155A LEU* 3.4 35.9 - - + +
188A ASN* 3.0 38.3 + - - +
189A VAL 3.7 4.3 - - - +
191A GLU* 1.3 76.1 - - + +
193A TYR* 1.3 61.5 + - - +
195A ALA* 3.3 19.0 + - - +
196A CYS* 3.4 14.0 - - - -
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLU* 3.8 19.2 + - + +
93A LEU* 3.8 37.7 - - + -
96A ALA* 3.5 24.1 - - + +
128A PHE* 4.2 13.5 - + - -
135A LEU* 4.0 30.3 - - + -
155A LEU* 3.9 15.4 - - + +
189A VAL 3.0 14.6 + - - +
190A THR 3.1 6.0 + - - +
192A ARG* 1.3 74.9 - - - +
194A MET* 1.3 76.6 + - + +
196A CYS* 3.1 15.5 + - - -
197A LYS* 2.6 48.7 + - - -
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Residues in contact with MET 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLU* 3.4 42.2 - - + +
190A THR* 2.9 33.4 + - + +
191A GLU* 3.9 7.0 - - - +
193A TYR* 1.3 87.1 - - + +
195A ALA* 1.3 58.2 + - - +
197A LYS* 2.9 34.9 + - + +
198A LYS* 4.3 5.0 + - - -
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU 3.0 15.2 + - - +
192A ARG* 3.3 18.4 - - - +
193A TYR 3.1 0.4 - - - -
194A MET* 1.3 78.3 - - - +
196A CYS* 1.3 56.4 + - - +
197A LYS 3.2 0.7 - - - -
198A LYS* 3.5 17.5 - - - +
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Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.6 48.7 - - + -
130A LYS* 5.2 3.6 - - + -
153A ILE* 3.8 30.3 - - + -
155A LEU* 4.3 3.4 - - - -
192A ARG 3.4 16.8 - - - -
193A TYR 3.1 12.7 + - - +
195A ALA* 1.3 76.8 - - - +
197A LYS* 1.3 54.1 - - - +
198A LYS* 2.8 25.8 + - - +
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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