Contacts of the helix formed by residues 93 - 108 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74S HIS* 6.2 0.2 - - - -
77S ALA* 3.4 13.4 - - + +
78S CYS* 2.8 46.9 + - - +
89S MET* 2.9 28.8 + - - +
92S ASN* 1.3 83.0 + - - +
94S TYR* 1.3 63.9 + - - +
97S SER* 2.8 32.7 + - - -
140S PHE* 4.0 7.9 - - - -
143S SER* 3.2 28.6 + - - +
144S LYS* 4.6 6.9 - - + +
147S PHE* 6.0 0.4 - - - -
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Residues in contact with TYR 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89S MET 3.7 0.2 + - - -
90S MET* 3.2 38.4 + - + +
93S ASN* 1.3 76.0 - - - +
95S GLN* 1.3 74.0 + - - +
97S SER* 3.2 6.4 + - - -
98S LYS* 2.9 40.6 + - + +
143S SER* 4.1 9.2 - - - +
146S LEU* 3.5 44.9 - - + +
147S PHE* 3.6 27.3 - + + -
150S TYR* 3.7 18.9 - - + +
48T ALA 4.2 1.0 + - - -
49T ASP* 2.6 37.4 + - - -
50T TYR* 3.8 13.0 - + + -
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Residues in contact with GLN 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S MET 2.8 15.4 + - - +
91S ASP* 3.3 27.1 - - - +
94S TYR* 1.3 77.0 - - + +
96S TYR* 1.3 64.8 + - - +
98S LYS* 3.0 43.2 + - - +
99S GLU* 3.0 47.2 + - - +
50T TYR 4.1 10.6 - - - +
51T MET* 5.6 3.8 - - - +
55T ASP* 5.9 1.8 - - - +
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Residues in contact with TYR 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S THR* 5.4 0.7 - - + -
30S VAL* 4.1 0.2 - - - +
53S LYS* 2.7 40.5 + - + -
54S GLU* 5.4 1.6 - - - -
56S PHE* 3.5 18.7 - + - -
57S LEU* 3.6 35.3 + - + -
74S HIS* 3.9 16.4 - + - +
91S ASP 2.9 12.9 + - - +
92S ASN* 3.1 26.7 - - - +
93S ASN 4.0 0.2 - - - +
94S TYR 3.3 0.4 - - - -
95S GLN* 1.3 74.0 - - - +
97S SER* 1.3 64.0 + - - +
99S GLU* 3.0 16.6 + - - +
100S LEU* 3.0 32.0 + - + +
400S NAP 3.3 36.6 + + - -
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Residues in contact with SER 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S HIS* 2.8 32.1 + - - -
76S GLY 5.2 0.2 + - - -
93S ASN* 2.8 21.6 + - - -
94S TYR 3.5 4.0 - - - -
96S TYR* 1.3 80.3 - - - +
98S LYS* 1.3 63.9 + - - +
100S LEU* 3.3 2.9 + - - +
101S LEU* 2.9 24.3 + - - +
111S PHE* 4.1 1.2 - - - -
113S TYR* 5.9 0.3 - - - -
144S LYS* 5.7 2.8 + - - -
147S PHE* 3.6 33.1 - - - -
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Residues in contact with LYS 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94S TYR* 2.9 29.4 + - + +
95S GLN* 3.0 44.4 + - - +
97S SER* 1.3 76.9 - - - +
99S GLU* 1.3 65.2 + - - +
101S LEU* 3.2 2.8 + - - +
102S HIS* 3.0 37.0 + - + +
147S PHE* 3.7 12.3 - - + -
150S TYR* 3.6 46.3 + - + +
49T ASP* 2.9 31.5 + - - -
50T TYR 4.3 1.8 + - - -
51T MET* 5.4 4.0 - - - +
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Residues in contact with GLU 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57S LEU* 4.0 14.4 - - + -
60S ILE* 3.9 7.6 - - + +
61S MET* 3.4 43.7 - - + +
95S GLN* 3.0 38.3 + - - +
96S TYR* 3.2 10.3 - - - +
98S LYS* 1.3 79.4 - - - +
100S LEU* 1.3 62.2 + - - +
102S HIS* 3.4 8.2 + - - +
103S TYR* 3.2 21.3 + - - +
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Residues in contact with LEU 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S THR* 4.1 14.1 - - + -
56S PHE* 3.7 25.1 - - + -
57S LEU* 5.2 2.0 - - + -
60S ILE* 3.9 18.8 - - + -
72S ILE* 4.5 12.8 - - + -
74S HIS* 3.3 46.0 - - + +
96S TYR* 3.0 24.2 + - + +
97S SER 3.6 7.4 - - - +
99S GLU* 1.3 73.8 - - - +
101S LEU* 1.3 66.5 + - - +
103S TYR* 3.1 7.6 + - - +
104S CYS* 2.9 26.5 + - - -
111S PHE* 3.7 12.6 - - + -
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Residues in contact with LEU 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S SER 2.9 17.1 + - - +
98S LYS 3.5 3.6 - - - +
100S LEU* 1.3 76.3 - - - +
102S HIS* 1.3 59.7 + - + +
104S CYS* 3.3 1.0 + - - +
105S LEU* 2.8 42.2 + - + +
111S PHE* 3.8 31.1 - - + -
147S PHE* 4.0 20.2 - - + -
150S TYR* 4.0 28.9 - - + -
151S VAL* 4.3 9.2 - - + -
154S ILE* 4.3 13.9 - - + -
162S ILE* 3.8 29.2 - - + -
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Residues in contact with HIS 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98S LYS* 3.0 34.5 + - + +
99S GLU* 3.9 8.3 - - - +
101S LEU* 1.3 77.6 - - + +
103S TYR* 1.3 63.4 + - - +
105S LEU* 3.3 12.8 + - + +
106S GLU* 3.0 30.3 + - - +
150S TYR* 2.6 38.7 + + - -
154S ILE* 4.5 14.8 - - + -
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Residues in contact with TYR 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S ILE* 6.0 0.4 - - + -
60S ILE* 3.5 58.1 - - + +
63S GLY* 4.3 0.7 - - - -
64S GLU 2.6 27.5 + - - -
65S GLU* 3.8 5.2 + - - -
66S PHE* 3.3 18.1 + + - -
69S VAL* 5.6 3.2 - - + +
72S ILE* 4.7 7.2 - - + -
99S GLU 3.2 13.1 + - - +
100S LEU 3.1 8.3 + - - +
102S HIS* 1.3 77.4 - - - +
104S CYS* 1.3 72.9 + - - +
106S GLU* 4.8 1.3 - - - -
107S ARG* 3.1 78.3 + - - +
109S ILE* 4.1 12.3 - - + -
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Residues in contact with CYS 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S ILE* 3.4 36.3 - - - -
100S LEU 2.9 15.0 + - - +
101S LEU* 3.6 7.4 - - + +
103S TYR* 1.3 78.4 - - - +
105S LEU* 1.3 55.4 + - + +
107S ARG 3.0 2.1 + - - -
108S GLU 2.7 32.2 + - - -
109S ILE* 2.9 41.8 + - - +
111S PHE* 3.8 26.2 - - + -
160S SER* 5.0 0.2 - - - -
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Residues in contact with LEU 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S LEU* 2.8 31.6 + - + +
102S HIS* 3.5 16.4 - - - +
104S CYS* 1.3 77.2 - - + +
106S GLU* 1.3 62.9 + - - +
108S GLU* 3.3 17.8 + - - +
109S ILE 6.1 0.2 - - - +
111S PHE* 6.3 0.4 - - + -
154S ILE* 3.5 33.0 - - + -
158S ALA* 4.3 13.9 - - + -
159S ASN* 5.3 3.0 - - - +
160S SER* 4.3 14.6 + - - +
162S ILE* 3.7 28.9 - - + -
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Residues in contact with GLU 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102S HIS* 3.0 19.3 + - - +
103S TYR* 3.8 6.1 - - - +
105S LEU* 1.3 77.7 - - - +
107S ARG* 1.3 79.3 + - + +
108S GLU* 3.4 3.9 - - - +
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Residues in contact with ARG 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S GLY* 3.5 29.9 + - - -
65S GLU* 3.3 37.6 + - - +
103S TYR* 3.1 63.4 + - - +
104S CYS 3.0 1.8 + - - -
106S GLU* 1.3 101.1 + - + +
108S GLU* 1.3 70.2 + - - +
109S ILE* 3.2 24.6 + - + +
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Residues in contact with GLU 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S CYS 2.7 6.7 + - - -
105S LEU 3.3 10.4 + - - +
106S GLU 4.9 2.7 - - - +
107S ARG* 1.3 82.1 - - - +
109S ILE* 1.3 58.9 + - - +
110S PRO* 3.4 10.9 - - - +
159S ASN* 3.9 30.9 + - + +
160S SER* 3.4 27.0 - - - +
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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