Contacts of the helix formed by residues 94 - 117 (chain A) in PDB entry 2I2X
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 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 2.9 32.3 + - - +
91A MET 3.3 6.4 - - - +
93A ASN* 1.3 83.4 - - - +
95A PRO* 1.3 70.3 - - - +
96A SER* 3.1 3.6 - - - +
97A TRP* 2.8 51.3 + - + +
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Residues in contact with PRO 95 (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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91A MET 4.1 6.0 - - - +
92A SER 3.7 5.6 - - - +
93A ASN 3.4 11.7 - - - +
94A ASN* 1.3 82.6 - - - +
96A SER* 1.3 62.6 + - - +
97A TRP 3.2 0.5 + - - -
98A GLY* 3.3 4.5 + - - -
99A ALA* 3.1 19.6 + - - +
145A VAL* 4.0 16.8 - - + +
148A GLU* 3.7 53.6 - - + +
149A ALA* 4.0 5.6 - - - +
152A GLN* 4.0 12.9 - - + +
153A CYS* 4.8 2.3 - - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 5.1 1.6 + - - -
94A ASN* 2.9 4.9 + - - +
95A PRO* 1.3 77.1 - - - +
97A TRP* 1.3 69.0 + - - +
99A ALA* 3.5 9.3 - - - +
100A GLU* 2.9 46.6 + - - +
152A GLN* 5.1 7.1 - - - +
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Residues in contact with TRP 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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52A GLY 5.0 2.0 - - - -
53A ALA 4.9 4.7 - - - -
54A SER* 4.1 6.1 - - - -
55A LYS* 3.4 64.5 - - + +
58A LEU* 4.0 18.4 - - + -
59A ILE* 5.3 0.7 - - - +
90A GLN* 3.8 38.8 - - + -
91A MET* 3.9 12.1 - - + -
94A ASN* 2.8 39.1 + - + +
96A SER* 1.3 80.8 - - - +
98A GLY* 1.3 65.0 + - - +
100A GLU* 3.1 3.2 + - - +
101A VAL* 3.0 29.5 + - + +
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Residues in contact with GLY 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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87A HIS* 3.8 17.9 - - - -
91A MET* 3.2 31.5 + - - +
95A PRO 3.3 2.4 + - - -
97A TRP* 1.3 78.1 - - - +
99A ALA* 1.3 62.4 + - - +
101A VAL* 3.4 0.5 + - - +
102A ALA* 2.9 23.9 + - - +
124A HIS* 3.5 5.7 + - - -
153A CYS* 3.5 7.2 - - - -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO 3.1 14.0 + - - +
96A SER* 3.5 13.2 - - - +
97A TRP 3.2 0.2 - - - -
98A GLY* 1.3 75.0 - - - +
100A GLU* 1.3 59.6 + - + +
102A ALA* 3.2 4.7 + - - +
103A HIS* 2.9 23.0 + - - +
152A GLN* 3.7 31.6 - - + +
153A CYS* 3.8 7.2 - - - +
156A ASN* 3.4 25.4 - - - +
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Residues in contact with GLU 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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55A LYS* 2.7 37.6 + - - -
59A ILE* 3.8 21.0 - - + +
96A SER* 2.9 30.9 + - - +
97A TRP* 3.1 3.8 + - - +
99A ALA* 1.3 75.5 - - + +
101A VAL* 1.3 66.9 + - - +
103A HIS* 3.7 7.0 - - + +
104A ALA* 3.0 24.9 + - - +
156A ASN* 6.0 1.3 - - - +
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Residues in contact with VAL 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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55A LYS* 6.3 0.7 - - + -
58A LEU* 4.8 4.0 - - + -
59A ILE* 4.0 22.4 - - + +
62A TYR* 3.4 45.5 - - + -
85A THR* 4.4 0.2 - - + -
91A MET* 4.0 22.0 - - + -
97A TRP* 3.0 20.5 + - + +
98A GLY 3.8 3.8 - - - +
100A GLU* 1.3 73.4 - - - +
102A ALA* 1.3 66.0 + - - +
104A ALA* 3.2 4.0 + - - +
105A GLN* 2.9 43.0 + - - +
124A HIS* 4.3 0.9 - - - +
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Residues in contact with ALA 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 GLY 2.9 15.7 + - - +
99A ALA* 3.3 11.4 - - - +
101A VAL* 1.3 76.3 - - - +
103A HIS* 1.3 59.5 + - - +
106A LYS* 3.0 28.9 + - - +
122A LEU* 3.8 6.9 - - - +
124A HIS* 3.7 25.5 + - + +
153A CYS* 4.1 17.3 - - - +
156A ASN 3.3 13.7 - - - +
158A ALA 4.1 6.7 - - - +
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Residues in contact with HIS 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 ALA 2.9 13.9 + - - +
100A GLU* 3.7 9.0 - - + +
101A VAL 3.1 0.4 - - - -
102A ALA* 1.3 75.6 - - - +
104A ALA* 1.3 65.2 + - - +
106A LYS* 4.0 3.7 - - + +
107A THR* 2.8 46.3 + - - -
156A ASN* 3.1 36.7 + - + +
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Residues in contact with ALA 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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59A ILE* 3.9 20.4 - - + +
62A TYR* 6.3 0.7 - - + -
63A GLU* 3.8 27.4 - - + +
100A GLU 3.0 16.6 + - - +
101A VAL* 3.8 4.0 - - - +
103A HIS* 1.3 80.4 + - - +
105A GLN* 1.3 63.2 + - + +
107A THR* 3.6 6.8 + - - -
108A ILE* 3.5 25.7 + - - +
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Residues in contact with GLN 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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45A TYR* 3.0 24.8 + - - -
62A TYR* 4.3 12.9 - - + +
63A GLU* 5.9 0.2 - - - -
65A ILE* 5.4 0.2 - - - +
66A THR* 3.2 34.2 + - - +
83A LEU* 4.3 3.3 - - - +
85A THR* 2.5 23.8 + - - +
101A VAL* 2.9 31.8 + - + +
102A ALA 3.8 3.4 - - - +
104A ALA* 1.3 73.3 - - + +
106A LYS* 1.3 63.5 + - - +
108A ILE 3.2 3.3 + - - -
109A MET* 3.1 35.0 + - + +
122A LEU* 3.9 8.9 - - + +
124A HIS* 3.2 23.6 - - - -
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Residues in contact with LYS 106 (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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29A GLY* 4.7 1.2 - - - -
30A LEU* 4.0 31.2 - - + -
102A ALA 3.0 18.0 + - - +
103A HIS* 4.1 4.9 - - + +
105A GLN* 1.3 76.5 - - - +
107A THR* 1.3 53.3 + - - +
109A MET* 3.2 20.5 + - + +
110A GLU* 2.8 50.5 + - - +
120A CYS 5.5 0.9 - - - -
121A ALA* 5.6 0.4 - - - +
122A LEU* 4.4 2.4 - - + +
157A GLY* 2.9 32.5 + - - +
159A ASP* 2.7 40.9 + - - +
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Residues in contact with THR 107 (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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103A HIS* 2.8 41.4 + - - -
104A ALA* 3.7 8.2 - - - -
105A GLN 3.2 0.4 - - - -
106A LYS* 1.3 77.5 - - - +
108A ILE* 1.3 65.4 + - + +
110A GLU* 3.3 14.1 + - - +
111A LYS* 3.1 20.5 + - - +
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Residues in contact with ILE 108 (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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63A GLU* 3.8 36.6 - - + +
66A THR* 3.8 20.2 - - + -
67A THR* 3.6 29.6 - - - +
70A MET* 4.4 2.0 - - + -
104A ALA 3.5 15.0 + - - +
105A GLN 3.2 6.7 + - - +
107A THR* 1.3 76.9 - - + +
109A MET* 1.3 66.0 + - - +
111A LYS* 3.1 19.9 + - + +
112A TYR* 3.1 34.4 + - + -
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Residues in contact with MET 109 (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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30A LEU* 4.0 3.4 - - + +
66A THR* 4.0 7.9 - - + -
70A MET* 4.3 19.5 - - - -
83A LEU* 3.7 33.4 - - + -
105A GLN* 3.1 29.8 + - + +
106A LYS* 3.2 21.7 + - + +
108A ILE* 1.3 76.6 - - - +
110A GLU* 1.3 55.7 + - - +
112A TYR* 3.4 2.9 + - - +
113A HIS* 2.9 29.6 + - - +
120A CYS* 4.2 17.5 - - - -
121A ALA 4.5 5.2 - - - +
122A LEU* 3.4 48.9 - - + -
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Residues in contact with GLU 110 (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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30A LEU* 4.1 28.1 - - + +
106A LYS* 2.8 37.4 + - + +
107A THR* 3.6 15.3 + - - +
109A MET* 1.3 72.8 - - - +
111A LYS* 1.3 66.3 + - - +
113A HIS* 3.2 1.7 + - - +
114A ASP* 2.8 40.0 + - - +
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Residues in contact with LYS 111 (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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107A THR* 3.1 9.6 + - + +
108A ILE* 3.1 15.0 + - + +
110A GLU* 1.3 79.4 - - - +
112A TYR* 1.3 82.9 + - + +
114A ASP* 3.8 6.6 - - - +
115A GLU* 3.1 46.3 + - + +
116A TYR* 5.7 2.4 + - - -
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Residues in contact with TYR 112 (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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67A THR* 4.1 16.1 + - + +
70A MET* 3.5 49.6 - - + -
71A GLU* 2.8 48.2 + - - +
74A VAL* 4.1 5.4 - - + -
108A ILE* 3.1 36.5 + - + -
109A MET 3.8 2.7 - - - +
111A LYS* 1.3 96.7 + - + +
113A HIS* 1.3 61.5 + - - +
116A TYR* 2.9 65.8 + + - +
117A GLY 3.8 0.3 + - - -
118A ILE* 3.9 4.7 - - + +
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Residues in contact with HIS 113 (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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30A LEU* 3.8 43.0 - - + +
31A ASP* 3.9 22.5 + - + +
109A MET 2.9 17.8 + - - +
110A GLU* 3.2 3.3 + - - +
112A TYR* 1.3 78.1 - - - +
114A ASP* 1.3 68.6 + - - +
117A GLY* 2.8 36.8 + - - -
118A ILE* 3.0 35.8 - - - +
119A LYS* 4.6 0.7 - - - -
120A CYS* 4.6 1.3 - - - -
4I LYS* 5.4 7.5 - - - -
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Residues in contact with ASP 114 (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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110A GLU* 2.8 34.2 + - - +
111A LYS* 3.8 6.3 + - - +
113A HIS* 1.3 87.1 + - - +
115A GLU* 1.3 61.7 + - - +
117A GLY 4.5 0.9 + - - -
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Residues in contact with GLU 115 (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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111A LYS* 3.1 35.7 + - + +
113A HIS 3.4 0.2 - - - -
114A ASP* 1.3 79.6 - - + +
116A TYR* 1.3 92.3 + - + +
20D LEU* 3.9 44.0 - - - +
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Residues in contact with TYR 116 (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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71A GLU* 4.7 4.7 + - - -
74A VAL* 3.8 13.7 - - + +
111A LYS* 5.7 2.8 + - - -
112A TYR* 2.9 54.0 + + - +
115A GLU* 1.3 99.5 + - + +
117A GLY* 1.3 60.4 + - - +
118A ILE 4.3 2.2 - - - +
234C LEU* 3.6 29.7 - - + +
14D THR* 5.4 1.0 - - - +
16D TYR* 3.3 50.9 - + + -
20D LEU* 3.6 30.0 - - + +
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Residues in contact with GLY 117 (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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31A ASP* 5.4 1.6 - - - +
79A PRO 4.9 0.7 - - - +
113A HIS* 2.8 29.7 + - - -
114A ASP 4.5 1.2 + - - -
115A GLU 3.7 0.6 - - - -
116A TYR* 1.3 77.0 - - - +
118A ILE* 1.3 63.2 + - - +
119A LYS* 3.5 10.4 + - - +
16D TYR* 4.6 2.0 - - - -
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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
------------------------------------------------------------
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