Contacts of the helix formed by residues 93 - 108 (chain F) in PDB entry 2X86
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 93 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74F HIS* 4.9 0.2 + - - -
77F ALA* 3.4 11.5 - - + +
78F CYS* 2.8 47.2 + - - +
89F MET* 2.9 29.2 + - - +
92F ASN* 1.3 84.0 + - - +
94F TYR* 1.3 63.6 + - - +
95F GLN 3.7 0.2 - - - -
97F SER* 2.8 33.1 + - - -
140F PHE* 4.0 8.5 - - - -
143F SER* 3.2 28.2 + - - +
144F LYS* 4.6 7.1 - - - +
147F PHE* 6.0 0.2 - - - -
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Residues in contact with TYR 94 (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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89F MET 3.7 0.4 + - - -
90F MET* 3.2 36.4 + - + +
93F ASN* 1.3 76.6 - - - +
95F GLN* 1.3 73.7 + - + +
97F SER* 3.2 6.1 + - - -
98F LYS* 2.9 40.3 + - + +
143F SER* 4.1 9.9 - - - +
146F LEU* 3.5 45.5 - - + +
147F PHE* 3.6 27.8 - + + -
150F TYR* 3.7 16.0 - - + +
48G ALA 4.3 0.9 + - - -
49G ASP* 2.6 40.0 + - - -
50G TYR* 3.8 14.6 - + + -
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Residues in contact with GLN 95 (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 MET 2.8 16.4 + - - +
91F ASP* 3.3 26.9 - - - +
94F TYR* 1.3 77.6 - - + +
96F TYR* 1.3 63.7 + - - +
98F LYS* 3.0 42.3 + - - +
99F GLU* 3.0 47.0 + - - +
50G TYR 4.0 10.7 - - - +
51G MET* 5.4 4.6 - - - +
55G ASP* 5.8 2.7 - - - +
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Residues in contact with TYR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F THR* 5.4 0.7 - - + -
30F VAL* 4.1 0.2 - - - +
53F LYS* 2.7 41.7 + - + +
54F GLU* 5.5 1.6 - - - -
56F PHE* 3.5 18.8 - + - -
57F LEU* 3.6 36.0 + - + -
74F HIS* 3.9 16.4 - + - -
91F ASP 2.9 12.2 + - - +
92F ASN* 3.1 26.9 - - - +
93F ASN 4.0 0.2 - - - +
95F GLN* 1.3 74.6 - - - +
97F SER* 1.3 64.5 + - - +
99F GLU* 3.0 17.5 + - - +
100F LEU* 3.0 32.0 + - + +
400F NAP 3.4 35.4 + + - -
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Residues in contact with SER 97 (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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74F HIS* 2.8 32.7 + - - -
93F ASN* 2.8 21.6 + - - -
94F TYR 3.5 3.6 - - - -
96F TYR* 1.3 79.5 - - - +
98F LYS* 1.3 61.8 + - - +
99F GLU 3.2 0.2 + - - -
100F LEU* 3.3 3.1 + - - +
101F LEU* 2.9 25.3 + - - +
111F PHE* 4.1 1.0 - - - -
113F TYR* 5.9 0.5 - - - -
144F LYS* 5.6 3.1 + - - -
147F PHE* 3.6 33.1 - - - -
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Residues in contact with LYS 98 (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 TYR* 2.9 25.2 + - + +
95F GLN* 3.0 44.1 + - - +
97F SER* 1.3 77.1 - - - +
99F GLU* 1.3 63.7 + - - +
101F LEU* 3.2 3.0 + - - +
102F HIS* 3.0 38.5 + - + +
147F PHE* 3.5 12.8 - - + -
150F TYR* 3.6 46.8 + - + +
49G ASP* 2.7 36.5 + - - +
50G TYR 4.1 2.2 + - - -
51G MET* 5.4 4.2 - - - +
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Residues in contact with GLU 99 (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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57F LEU* 4.0 14.8 - - + -
60F ILE* 3.9 7.7 - - + +
61F MET* 3.4 45.0 - - + +
95F GLN* 3.0 38.2 + - - +
96F TYR* 3.0 10.1 + - - +
98F LYS* 1.3 80.1 - - - +
100F LEU* 1.3 62.7 + - - +
102F HIS* 3.4 7.8 + - - +
103F TYR* 3.2 21.7 + - - +
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Residues in contact with LEU 100 (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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5F THR* 4.1 14.4 - - + -
56F PHE* 3.7 25.1 - - + -
57F LEU* 5.2 2.2 - - + -
60F ILE* 3.9 17.9 - - + -
72F ILE* 4.4 11.9 - - + -
74F HIS* 3.3 46.7 - - + +
96F TYR* 3.0 24.7 + - + +
97F SER 3.6 7.6 - - - +
99F GLU* 1.3 73.8 - - - +
101F LEU* 1.3 66.9 + - - +
103F TYR* 3.1 6.6 + - - +
104F CYS* 2.9 26.5 + - - -
111F PHE* 3.7 13.0 - - + -
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Residues in contact with LEU 101 (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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97F SER 2.9 17.3 + - - +
98F LYS 3.5 3.6 - - - +
100F LEU* 1.3 75.9 - - - +
102F HIS* 1.3 60.3 + - + +
104F CYS* 3.3 1.6 + - - +
105F LEU* 2.8 41.6 + - + +
111F PHE* 3.8 30.5 - - + -
147F PHE* 4.0 20.6 - - + -
150F TYR* 4.0 27.8 - - + -
151F VAL* 4.3 9.2 - - + -
154F ILE* 4.3 14.1 - - + -
162F ILE* 3.8 28.9 - - + -
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Residues in contact with HIS 102 (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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98F LYS* 3.0 35.1 + - + +
99F GLU* 3.9 8.3 - - - +
101F LEU* 1.3 77.7 - - + +
103F TYR* 1.3 63.7 + - - +
105F LEU* 3.3 13.2 + - + +
106F GLU* 3.0 30.3 + - - +
150F TYR* 2.6 38.1 + + - -
154F ILE* 4.5 14.6 - - + -
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Residues in contact with TYR 103 (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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60F ILE* 3.5 59.2 - - + +
63F GLY* 4.3 0.9 - - - -
64F GLU 2.6 28.0 + - - -
65F GLU* 3.8 5.4 + - - -
66F PHE* 3.3 18.4 + + - -
69F VAL* 5.6 3.1 - - + +
72F ILE* 4.7 7.0 - - + -
99F GLU 3.2 12.9 + - - +
100F LEU 3.1 9.5 + - - +
102F HIS* 1.3 76.9 - - - +
104F CYS* 1.3 73.3 + - - +
106F GLU* 5.0 1.8 - - - -
107F ARG* 3.1 78.3 + - - +
109F ILE* 4.1 12.7 - - + +
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Residues in contact with CYS 104 (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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72F ILE* 3.4 37.2 - - - -
100F LEU 2.9 15.2 + - - +
101F LEU* 3.6 7.0 - - + +
103F TYR* 1.3 78.3 - - - +
105F LEU* 1.3 55.4 + - + +
107F ARG 3.0 1.7 + - - -
108F GLU 2.7 31.7 + - - -
109F ILE* 2.9 40.7 + - - +
111F PHE* 3.8 26.5 - - + -
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Residues in contact with LEU 105 (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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101F LEU* 2.8 31.8 + - + +
102F HIS* 3.5 15.9 - - - +
104F CYS* 1.3 77.1 - - + +
106F GLU* 1.3 64.0 + - - +
108F GLU* 3.3 17.3 + - - +
109F ILE 6.1 0.4 - - - +
111F PHE* 6.3 0.7 - - + -
154F ILE* 3.5 32.8 - - + -
158F ALA* 4.3 13.9 - - + -
159F ASN* 5.2 2.9 + - - +
160F SER* 4.3 15.3 + - - +
161F GLN 5.7 0.2 - - - +
162F ILE* 3.7 29.4 - - + -
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Residues in contact with GLU 106 (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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102F HIS* 3.0 18.4 + - - +
103F TYR* 3.8 5.6 - - - +
104F CYS 3.1 0.2 - - - -
105F LEU* 1.3 78.9 - - - +
107F ARG* 1.3 80.5 + - + +
108F GLU* 3.4 3.4 + - - +
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Residues in contact with ARG 107 (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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63F GLY* 3.5 29.3 + - - -
65F GLU* 3.3 37.4 + - - +
103F TYR* 3.1 63.7 + - - +
104F CYS 3.0 1.8 + - - -
106F GLU* 1.3 101.7 + - + +
108F GLU* 1.3 72.4 + - - +
109F ILE* 3.2 24.5 + - + +
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Residues in contact with GLU 108 (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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104F CYS 2.7 7.1 + - - -
105F LEU 3.3 10.1 + - - +
106F GLU 4.9 3.4 - - - +
107F ARG* 1.3 81.3 - - - +
109F ILE* 1.3 57.9 + - - +
110F PRO* 3.4 11.4 - - - +
159F ASN* 3.9 29.9 + - + +
160F SER* 3.4 23.8 - - - +
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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