Contacts of the helix formed by residues 158 - 167 (chain N) in PDB entry 5XS0
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 PHE 158 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76M ASN* 3.5 16.4 + - - +
81M TYR* 3.5 27.8 - + - +
43N LEU* 3.5 27.3 - - + +
79N PHE* 4.3 5.2 - + - -
113N VAL* 4.0 24.7 - - + -
115N LEU* 3.5 39.3 - - + -
119N SER* 3.9 10.1 - - - -
120N TYR* 4.6 1.6 - - - -
121N HIS* 3.2 40.2 - + + -
154N ALA 4.5 1.3 - - - -
155N LEU* 3.2 24.8 + - + +
156N ARG 3.0 1.8 + - - -
157N SER* 1.3 76.9 - - - +
159N GLY* 1.3 56.4 + - - +
162N LEU* 3.8 20.9 - - + -
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Residues in contact with GLY 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M ILE* 5.1 0.2 - - - -
73M ASN* 4.4 5.8 - - - -
76M ASN* 3.7 11.2 - - - +
43N LEU* 4.0 10.2 - - - +
155N LEU 4.7 0.2 + - - -
156N ARG 3.3 7.5 + - - +
157N SER 3.4 1.4 - - - -
158N PHE* 1.3 80.5 - - - +
160N ASN* 1.3 66.0 + - - -
161N ALA 3.3 3.4 - - - -
162N LEU* 3.3 8.9 + - - -
163N GLY 3.5 0.2 + - - -
164N ASN* 3.3 21.5 + - - -
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Residues in contact with ASN 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M HIS* 5.7 1.0 - - - -
73M ASN* 3.2 34.7 + - - +
43N LEU 3.2 3.6 + - - -
44N ARG* 3.4 27.1 + - - +
45N GLN 3.6 14.4 - - - +
46N ARG* 4.4 11.9 + - - +
47N LEU* 4.2 1.7 - - - +
159N GLY* 1.3 73.4 - - - -
161N ALA* 1.3 62.8 + - - +
163N GLY* 3.0 11.8 + - - -
164N ASN* 3.8 7.7 - - - +
165N CYS* 3.4 43.2 + - + +
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Residues in contact with ALA 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M LYS* 4.8 11.7 - - + -
42N ALA 3.6 16.2 - - - +
43N LEU* 3.0 28.0 + - + +
45N GLN 3.1 16.8 + - - +
47N LEU* 3.5 23.3 - - - +
74N LEU* 3.6 15.0 - - + +
78N MET* 4.6 9.4 - - + +
159N GLY 3.3 0.2 - - - -
160N ASN* 1.3 76.5 - - - +
162N LEU* 1.3 59.2 + - - +
163N GLY 3.8 0.2 + - - -
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Residues in contact with LEU 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N LEU* 4.1 11.9 - - + +
66N ILE* 4.8 4.4 - - - +
71N VAL* 4.4 18.2 - - + +
74N LEU* 3.8 18.4 - - + +
75N ALA* 3.7 33.9 - - + +
78N MET* 4.7 3.6 - - + -
79N PHE* 3.6 30.5 - - + -
152N LYS 4.7 1.4 - - - +
155N LEU* 3.4 34.8 - - + +
156N ARG* 3.8 13.6 + - - +
158N PHE* 3.8 18.2 - - + -
159N GLY 3.3 8.0 + - - +
160N ASN 3.1 0.8 - - - -
161N ALA* 1.3 78.7 - - - +
163N GLY* 1.3 57.7 + - - +
164N ASN 3.9 0.7 - - - -
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Residues in contact with GLY 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N LEU* 4.8 1.1 - - - -
66N ILE* 3.7 23.5 - - - +
156N ARG* 3.6 13.2 - - - +
160N ASN 3.0 7.7 + - - -
161N ALA 3.4 1.2 + - - -
162N LEU* 1.3 79.9 - - - +
164N ASN* 1.3 66.4 + - - +
165N CYS* 3.3 3.1 - - - -
166N ILE* 3.1 25.4 - - - +
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Residues in contact with ASN 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M HIS* 3.0 47.4 + - - +
72M ILE* 3.4 35.1 - - - +
73M ASN* 3.5 14.3 + - - +
156N ARG* 3.5 16.0 - - - +
159N GLY 3.3 24.6 + - - +
160N ASN* 3.6 4.0 + - - +
163N GLY* 1.3 79.0 - - - +
165N CYS* 1.3 64.3 + - - +
167N LEU* 3.0 23.2 + - - +
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Residues in contact with CYS 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M HIS* 5.7 1.1 - - - -
46N ARG* 4.2 15.0 - - + +
47N LEU* 3.9 31.6 - - - -
52N ILE* 5.6 0.9 - - - -
160N ASN* 3.4 41.4 + - + +
163N GLY 4.7 1.3 - - - -
164N ASN* 1.3 73.2 - - - +
166N ILE* 1.3 61.3 + - - +
167N LEU 2.9 5.6 - - - -
168N ASP* 2.8 27.5 + - + +
171N TYR* 3.3 34.8 - - + -
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Residues in contact with ILE 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N ILE* 3.6 44.9 - - + -
64N CYS* 3.7 29.1 - - + +
65N TYR* 4.3 8.3 - - - +
66N ILE* 4.7 11.7 - - + -
156N ARG* 5.4 1.8 - - - -
163N GLY* 3.1 23.4 + - - +
164N ASN 3.1 1.4 + - - -
165N CYS* 1.3 80.9 - - - +
167N LEU* 1.3 75.4 + - + +
168N ASP 3.3 0.6 + - - -
171N TYR* 4.5 4.7 - - + -
172N LEU* 4.0 24.0 - - + +
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Residues in contact with LEU 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M GLU* 4.4 2.3 - - - +
68M GLY* 5.3 2.7 - - - -
69M HIS* 3.7 30.0 + - + +
72M ILE* 5.4 0.7 - - + -
156N ARG* 3.5 44.4 - - - +
164N ASN* 3.0 19.5 + - - +
165N CYS 2.9 1.6 - - - -
166N ILE* 1.3 91.5 - - + +
168N ASP* 1.3 59.3 - - - +
169N LYS* 3.4 11.1 + - - +
172N LEU* 5.3 1.6 - - - -
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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