Contacts of the helix formed by residues 82 - 108 (chain A) in PDB entry 4TXQ
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 GLN 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.8 38.9 + - + +
79A ALA 3.6 2.1 - - - +
80A ILE 4.4 2.2 - - - -
81A THR* 1.3 83.2 + - - +
83A GLU* 1.3 67.4 + - - +
84A ILE* 3.2 11.6 - - + +
85A VAL* 3.0 25.6 + - + +
86A GLY 3.2 9.0 + - - -
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.5 8.1 - - + +
80A ILE 4.6 3.8 + - - +
81A THR 4.0 3.7 + - - +
82A GLN* 1.3 70.1 - - - +
84A ILE* 1.3 57.9 + - - +
86A GLY* 3.0 4.0 + - - -
87A CYS 2.7 24.9 + - - -
130A VAL 4.5 0.3 - - - +
131A PHE* 3.5 37.7 - - + +
196C ARG* 3.5 36.4 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 4.9 11.7 - - + +
83A GLU* 1.3 80.2 - - - +
85A VAL* 1.3 70.1 + - + +
87A CYS* 3.5 16.3 - - + +
88A ALA* 2.9 29.5 + - + +
131A PHE* 6.4 0.4 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 3.8 30.5 - - + +
79A ALA* 3.7 22.7 - - + +
82A GLN* 3.0 25.9 + - + +
84A ILE* 1.3 82.7 - - + +
86A GLY* 1.3 63.6 + - - +
88A ALA* 3.4 6.4 + - + +
89A HIS* 3.0 23.4 + - + +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.9 11.0 - - - -
79A ALA* 3.2 26.7 + - - -
82A GLN 3.2 5.5 + - - -
83A GLU 3.0 6.9 + - - -
85A VAL* 1.3 78.6 - - - +
87A CYS* 1.3 61.4 + - - +
89A HIS* 3.3 4.6 + - - +
90A LEU* 3.1 28.6 + - - +
131A PHE* 3.6 6.5 - - - -
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Residues in contact with CYS 87 (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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83A GLU 2.7 15.9 + - - +
84A ILE* 3.5 24.2 - - + +
85A VAL 3.2 0.2 - - - -
86A GLY* 1.3 74.4 - - - +
88A ALA* 1.3 58.4 + - - +
90A LEU* 3.3 1.0 + - - +
91A GLU* 2.9 46.4 + - - +
128A ILE* 4.5 14.0 - - - +
131A PHE* 3.6 41.4 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 2.9 17.1 + - + +
85A VAL* 3.8 7.0 - - + +
87A CYS* 1.3 77.2 - - - +
89A HIS* 1.3 56.5 + - - +
91A GLU* 4.3 9.6 - - - +
92A ASN* 2.8 46.8 + - - +
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 2.7 35.8 + - - -
33A VAL* 3.5 29.0 - - + +
34A VAL* 4.0 4.7 - - + -
79A ALA* 4.8 5.8 - - + +
85A VAL* 3.0 15.0 + - + +
86A GLY* 3.4 12.3 - - - +
87A CYS 3.2 0.2 - - - -
88A ALA* 1.3 77.0 - - - +
90A LEU* 1.3 69.4 + - + +
92A ASN* 4.0 4.5 - - - +
93A TYR* 3.2 26.7 + - + +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.1 20.9 - - + +
37A TYR* 3.9 27.1 - - + -
86A GLY 3.1 21.2 + - - +
87A CYS 3.9 2.2 - - - +
89A HIS* 1.3 91.1 - - + +
91A GLU* 1.3 55.3 + - - +
93A TYR* 3.2 5.8 + - - +
94A ALA* 2.8 36.6 + - - +
124A LEU* 4.4 15.8 - - + +
127A VAL* 3.5 36.1 - - + -
128A ILE* 4.0 17.3 - - + -
131A PHE* 4.2 9.9 - - + -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A CYS* 2.9 30.7 + - - +
88A ALA* 3.8 8.0 - - - +
90A LEU* 1.3 76.6 - - - +
92A ASN* 1.3 70.1 + - - +
94A ALA* 3.3 4.2 + - - +
95A LEU* 3.0 28.0 + - + +
128A ILE* 3.7 19.9 - - + +
138A ASN* 5.0 11.9 + - - +
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 2.8 36.8 + - - +
89A HIS* 4.0 4.8 - - - +
91A GLU* 1.3 80.1 - - - +
93A TYR* 1.3 57.8 + - - +
95A LEU* 3.5 11.1 + - - +
96A LYS* 3.0 28.4 + - - +
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Residues in contact with TYR 93 (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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27A HIS* 2.8 43.0 + + - -
30A ARG* 5.9 1.0 - - - +
31A ASP* 5.1 5.2 - - + -
34A VAL* 4.0 22.0 - - + -
89A HIS* 3.2 22.5 + - + +
90A LEU* 3.6 3.6 - - - +
92A ASN* 1.3 75.1 - - - +
94A ALA* 1.3 65.3 + - - +
96A LYS* 3.3 29.1 + - + +
97A MET* 3.0 51.2 + - + +
124A LEU* 3.4 26.9 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 2.8 19.8 + - - +
91A GLU* 3.7 7.4 - - - +
93A TYR* 1.3 72.8 - - - +
95A LEU* 1.3 56.7 + - - +
97A MET* 3.3 1.7 + - - -
98A PHE* 3.0 29.4 + - - +
121A ALA* 3.6 19.6 - - + +
124A LEU* 3.8 31.0 - - + +
125A ILE* 4.6 13.0 - - + -
128A ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 3.0 20.4 + - + +
92A ASN* 3.8 11.9 - - - +
94A ALA* 1.3 73.4 - - - +
96A LYS* 1.3 56.8 + - - +
98A PHE* 3.2 13.5 + - + +
99A LEU* 2.7 67.1 + - + +
141A HIS* 5.1 12.1 - - + +
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Residues in contact with LYS 96 (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 ASN 3.0 18.2 + - - +
93A TYR* 3.4 28.3 - - + +
95A LEU* 1.3 77.3 - - - +
97A MET* 1.3 59.2 + - + +
99A LEU* 4.0 5.8 - - - +
100A TYR* 3.0 27.8 + - + +
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Residues in contact with MET 97 (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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27A HIS* 6.3 0.2 - - + -
93A TYR* 3.0 45.8 + - + +
94A ALA 3.8 5.6 - - - +
96A LYS* 1.3 76.0 - - + +
98A PHE* 1.3 60.5 + - - +
100A TYR* 3.4 6.6 + - - +
101A ALA* 2.8 31.9 + - - +
116A LYS* 4.8 1.6 - - + -
117A SER* 3.5 46.3 - - - +
120A THR* 3.6 34.3 - - + +
121A ALA* 4.3 2.2 - - + -
124A LEU* 4.3 7.2 - - - -
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Residues in contact with PHE 98 (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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94A ALA 3.0 17.3 + - - +
95A LEU* 3.6 10.1 - - + +
97A MET* 1.3 76.9 - - - +
99A LEU* 1.3 70.6 + - + +
101A ALA* 3.3 5.0 + - - +
102A ASP* 2.8 44.9 + - + +
117A SER 5.0 0.2 - - - -
118A PHE* 4.3 8.0 - + - -
121A ALA* 4.1 10.5 - - + +
125A ILE* 6.0 1.1 - - + -
141A HIS* 3.7 50.5 - + + -
144A TYR* 3.5 39.7 - + + -
145A ALA* 4.0 18.2 - - + -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 2.7 50.3 + - + +
96A LYS* 4.2 4.3 - - - +
98A PHE* 1.3 79.8 - - + +
100A TYR* 1.3 67.0 + - - +
102A ASP* 3.8 12.4 - - - +
103A ASN* 3.0 24.6 + - - +
106A ARG* 5.3 0.7 + - - +
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Residues in contact with TYR 100 (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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96A LYS* 3.0 19.8 + - + +
97A MET* 3.4 5.2 - - - +
98A PHE 3.3 0.2 - - - -
99A LEU* 1.3 79.5 - - - +
101A ALA* 1.3 74.7 + - - +
103A ASN* 3.1 13.3 + - + +
104A GLU* 3.2 36.4 + - + +
111A HIS* 3.4 21.5 - - - -
113A ASN* 3.7 16.0 + - + +
114A MET* 3.9 17.5 - - - -
117A SER* 3.4 26.5 - - - -
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Residues in contact with ALA 101 (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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97A MET 2.8 19.9 + - - +
98A PHE 3.9 0.4 - - - +
100A TYR* 1.3 80.1 - - - +
102A ASP* 1.3 58.3 + - - +
104A GLU* 3.3 1.6 + - - +
105A ASP* 2.9 23.2 + - - +
114A MET* 3.3 43.2 - - - +
117A SER* 4.0 2.9 - - - -
118A PHE* 3.5 29.8 - - + +
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Residues in contact with ASP 102 (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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98A PHE* 2.8 34.8 + - + +
99A LEU* 3.8 14.3 - - + +
101A ALA* 1.3 75.0 - - - +
103A ASN* 1.3 58.0 + - - +
105A ASP* 3.3 4.7 + - - +
106A ARG* 2.9 60.0 + - - +
118A PHE* 3.7 10.7 - - + -
144A TYR* 3.9 20.1 + - - -
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Residues in contact with ASN 103 (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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99A LEU 3.0 13.5 + - - +
100A TYR* 3.1 11.2 + - + +
102A ASP* 1.3 74.1 + - - +
104A GLU* 1.3 70.1 + - - +
106A ARG* 2.8 38.6 + - - +
107A ALA* 3.2 22.2 + - - +
109A ARG* 4.2 14.6 - - - +
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Residues in contact with GLU 104 (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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100A TYR* 3.2 47.0 + - + +
101A ALA 3.5 7.2 - - - +
102A ASP 3.3 0.2 - - - -
103A ASN* 1.3 79.4 + - - +
105A ASP* 1.3 64.0 + - - +
107A ALA* 3.0 7.6 + - - +
109A ARG* 2.9 79.0 + - - +
111A HIS* 2.8 26.8 + - - +
114A MET* 3.9 8.7 - - + -
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Residues in contact with ASP 105 (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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101A ALA 2.9 17.1 + - - +
102A ASP* 3.4 12.2 - - - +
104A GLU* 1.3 77.5 - - - +
106A ARG* 1.3 65.2 + - - +
108A GLY* 3.1 14.0 + - - -
110A PHE* 3.3 29.1 - - - -
114A MET* 3.7 12.1 - - + +
118A PHE* 4.2 3.8 - - + -
144A TYR* 4.1 8.0 + - - -
148A LYS* 3.2 39.2 + - - -
152A ILE* 3.9 3.8 - - - +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 5.3 0.8 + - - +
102A ASP* 2.9 39.9 + - - +
103A ASN* 2.8 40.2 + - - +
105A ASP* 1.3 80.3 - - - +
107A ALA* 1.3 58.6 + - - +
108A GLY 3.6 0.3 + - - -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 3.2 15.6 + - - +
104A GLU 3.0 6.9 + - - +
106A ARG* 1.3 76.7 - - - +
108A GLY* 1.3 62.0 + - - +
109A ARG* 3.4 37.1 + - + +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP 3.1 11.8 + - - -
106A ARG 3.3 1.0 - - - -
107A ALA* 1.3 78.6 - - - +
109A ARG* 1.3 60.0 + - - +
110A PHE* 3.2 34.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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