Contacts of the helix formed by residues 93 - 115 (chain H) in PDB entry 4B86
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235F GLN* 4.9 2.1 + - - -
239F GLN* 6.4 0.2 - - - -
1H MET 3.2 29.1 + - - +
2H ASN* 4.6 2.5 - - - +
3H PRO* 4.1 3.0 - - - +
54H PRO* 3.6 10.4 + - + +
56H ALA* 3.8 17.2 + - + +
58H THR* 6.3 1.2 - - - +
92H GLU* 1.3 76.4 + - - +
94H LYS* 1.3 66.5 + - - +
95H GLN* 3.3 15.1 + - - +
96H LEU* 3.3 42.5 + - + +
97H SER* 3.5 20.7 + - - -
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Residues in contact with LYS 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F GLN* 3.4 33.9 + - + +
238F GLN* 5.4 6.1 + - - +
92H GLU* 4.2 2.9 + - + +
93H ASN* 1.3 69.5 + - - +
95H GLN* 1.3 66.7 + - - +
96H LEU 3.1 0.4 - - - -
97H SER* 3.0 9.5 + - - -
98H ILE* 3.0 32.8 + - + +
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Residues in contact with GLN 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E GLN* 2.9 28.9 - - - +
240E LEU* 4.2 2.3 - - - +
232F LEU* 3.7 21.3 - - + +
235F GLN* 3.5 19.8 - - + +
236F GLN* 3.6 19.7 + - + +
239F GLN* 4.2 15.2 - - - +
2H ASN* 3.5 12.9 - - + +
3H PRO* 3.4 26.5 - - + +
7H THR* 3.5 10.5 - - + +
93H ASN* 3.3 11.0 + - - +
94H LYS* 1.3 78.1 - - - +
96H LEU* 1.3 57.4 + - - +
98H ILE* 3.5 3.7 + - - +
99H LEU* 3.0 33.6 + - - +
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Residues in contact with LEU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H PRO* 3.7 22.9 - - + -
6H ALA* 4.9 0.4 - - + -
42H LEU* 4.0 22.4 - - + -
51H LEU* 4.1 7.2 - - + -
54H PRO* 3.7 20.9 - - + -
56H ALA* 3.9 3.8 - - + -
65H TYR* 3.6 52.7 - - + -
93H ASN* 3.3 30.9 + - + +
94H LYS 3.1 0.4 - - - -
95H GLN* 1.3 77.3 - - - +
97H SER* 1.3 59.3 + - - +
99H LEU* 3.1 5.5 + - - +
100H VAL* 2.9 32.6 + - - +
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Residues in contact with SER 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLN 5.8 0.4 - - - -
53H ASP* 5.1 1.0 + - - -
54H PRO* 3.3 29.1 - - - +
93H ASN 3.5 7.7 + - - -
94H LYS* 3.0 11.3 + - - -
96H LEU* 1.3 76.3 - - - +
98H ILE* 1.3 64.2 + - - +
100H VAL* 3.2 7.2 + - - +
101H ASN* 3.0 31.9 + - - +
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Residues in contact with ILE 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F LEU* 3.4 29.7 - - + +
231F ASP* 3.6 37.0 - - + +
232F LEU* 3.8 18.2 - - + +
235F GLN* 3.9 18.6 - - + -
94H LYS* 3.0 18.9 + - + +
95H GLN* 3.7 7.9 - - - +
97H SER* 1.3 78.1 - - - +
99H LEU* 1.3 56.4 + - - +
101H ASN* 3.5 7.4 + - - +
102H CYS* 2.9 34.3 + - - +
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Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F LEU* 4.2 15.0 - - + -
3H PRO* 3.7 20.4 - - + -
6H ALA* 3.8 17.5 - - + +
7H THR* 3.4 32.8 - - + -
10H TYR* 4.0 38.4 - - + -
38H PHE* 4.3 2.9 - - + -
42H LEU* 3.5 22.7 - - + +
95H GLN* 3.0 22.0 + - + +
96H LEU* 3.1 5.6 + - - +
98H ILE* 1.3 73.6 - - - +
100H VAL* 1.3 60.6 + - - +
102H CYS* 3.4 5.1 - - + +
103H TYR 2.9 22.0 + - - -
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Residues in contact with VAL 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LEU* 4.2 22.9 - - + +
50H LEU* 3.8 23.1 - - + -
51H LEU* 3.5 44.9 - - + +
54H PRO* 5.0 0.4 - - + -
96H LEU 2.9 20.5 + - - +
97H SER* 3.5 10.3 - - - +
99H LEU* 1.3 73.7 - - - +
101H ASN* 1.3 69.5 + - - +
103H TYR* 3.0 7.6 + - - +
104H LYS* 3.0 28.9 + - + +
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Residues in contact with ASN 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F LEU* 3.4 23.0 - - + +
97H SER* 3.0 22.2 + - - +
98H ILE* 3.9 3.4 - - - +
100H VAL* 1.3 79.7 - - - +
102H CYS* 1.3 57.8 + - - +
104H LYS* 3.2 22.7 + - - +
105H LYS* 2.9 41.3 + - - +
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Residues in contact with CYS 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ILE* 4.0 5.2 - - - +
228F LEU* 3.4 31.8 - - - +
229F GLN* 4.6 3.4 - - - -
232F LEU* 5.1 4.5 - - - -
10H TYR* 3.5 41.3 - - + -
98H ILE* 2.9 30.3 + - - +
99H LEU* 3.4 10.5 - - - +
100H VAL 3.2 0.2 - - - -
101H ASN* 1.3 76.9 - - - +
103H TYR* 1.3 56.2 + - - +
105H LYS* 3.3 3.9 + - - +
106H LEU* 2.9 31.5 + - - +
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Residues in contact with TYR 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H LEU* 4.8 14.7 - - + +
38H PHE* 3.5 39.2 - + + -
39H ARG* 3.0 45.8 + - + +
42H LEU* 3.8 10.3 - - + -
50H LEU* 3.7 32.3 - - + -
99H LEU 2.9 13.5 + - - +
100H VAL 3.0 7.6 + - - +
102H CYS* 1.3 75.9 - - - +
104H LYS* 1.3 58.5 + - + +
106H LEU* 3.3 5.1 + - + +
107H CYS* 2.9 59.8 + - - -
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Residues in contact with LYS 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LEU* 3.9 24.2 - - + -
100H VAL* 3.0 22.9 + - + +
101H ASN* 3.2 23.5 + - - +
103H TYR* 1.3 79.9 - - + +
105H LYS* 1.3 63.6 + - + +
107H CYS* 3.4 6.7 + - - +
108H GLU* 3.0 27.0 + - - +
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Residues in contact with LYS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F CYS* 3.9 10.2 - - - +
224F GLN* 2.8 45.9 + - + +
225F ILE* 4.3 23.1 - - + +
228F LEU* 3.8 23.3 - - + -
101H ASN* 2.9 30.6 + - - +
102H CYS 3.9 3.4 - - - +
104H LYS* 1.3 77.4 - - + +
106H LEU* 1.3 60.0 + - - +
108H GLU* 3.2 19.1 + - - +
109H TYR* 2.9 27.7 + - - +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ILE* 4.0 15.4 - - + +
10H TYR* 4.5 6.7 - - + -
13H ALA* 4.3 13.9 - - + +
14H SER* 3.3 48.2 - - - +
17H VAL* 4.4 16.6 - - + -
18H LEU* 5.5 5.4 - - + -
35H LEU* 4.8 3.8 - - + -
38H PHE* 4.5 11.7 - - + -
102H CYS 2.9 18.4 + - - +
103H TYR* 3.7 5.2 - - + +
105H LYS* 1.3 76.0 - - - +
107H CYS* 1.3 57.3 + - - +
109H TYR* 3.3 11.6 + - + +
110H ILE* 2.9 45.4 + - + +
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Residues in contact with CYS 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H LEU* 5.1 6.1 - - - -
103H TYR* 2.9 56.2 + - - +
104H LYS* 3.4 11.2 - - - +
106H LEU* 1.3 73.7 - - - +
108H GLU* 1.3 59.1 + - - +
110H ILE* 3.1 15.4 + - - +
111H THR* 2.9 35.1 + - + +
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Residues in contact with GLU 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F CYS* 4.3 14.0 - - - +
224F GLN* 5.1 5.8 + - - -
104H LYS 3.0 14.1 + - - +
105H LYS* 3.2 26.4 + - - +
107H CYS* 1.3 75.0 - - - +
109H TYR* 1.3 57.6 + - - +
111H THR* 3.1 8.8 + - - +
112H GLN* 2.9 52.9 + - + +
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Residues in contact with TYR 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E LYS* 4.0 23.7 + - - +
218F GLN* 4.0 33.8 + - + -
221F CYS* 4.1 8.0 - - + -
222F LEU* 4.0 32.0 - - + +
225F ILE* 6.2 2.7 - - + -
17H VAL* 3.7 35.4 + - + -
18H LEU* 4.7 12.1 - - + -
105H LYS 2.9 12.7 + - - +
106H LEU* 3.5 13.9 - - + +
107H CYS 3.2 0.2 - - - -
108H GLU* 1.3 75.4 - - - +
110H ILE* 1.3 59.1 + - - +
112H GLN* 3.3 9.5 + - - +
113H THR* 3.0 48.8 + - + +
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Residues in contact with ILE 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H VAL* 3.7 37.5 - - + -
28H PHE* 5.6 6.5 - - + -
31H ILE* 4.9 4.7 - - + -
32H ASN* 6.0 1.6 - - - +
35H LEU* 3.8 35.7 - - + -
106H LEU* 2.9 29.2 + - + +
107H CYS* 3.1 12.1 + - - +
109H TYR* 1.3 76.6 - - - +
111H THR* 1.3 60.3 + - + +
113H THR* 3.1 8.6 + - - +
114H THR* 2.9 39.6 + - - +
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Residues in contact with THR 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H CYS* 2.9 20.2 + - + +
108H GLU* 3.1 16.3 + - - +
110H ILE* 1.3 80.1 - - + +
112H GLN* 1.3 61.2 + - - +
114H THR* 3.4 9.3 + - + -
115H LEU* 3.3 35.2 + - - +
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Residues in contact with GLN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F SER* 3.5 35.7 + - - +
218F GLN* 3.9 17.8 + - + +
221F CYS* 3.5 30.1 - - - +
108H GLU* 2.9 36.9 + - + +
109H TYR* 3.6 7.0 - - - +
110H ILE 3.3 0.2 - - - -
111H THR* 1.3 78.1 - - - +
113H THR* 1.3 60.5 + - - +
115H LEU* 5.3 1.8 - - - -
116H ALA* 3.4 33.3 + - - +
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Residues in contact with THR 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F GLN* 3.6 24.0 - - - +
17H VAL* 5.5 2.4 - - - +
20H TYR* 5.5 9.3 - - - -
109H TYR* 3.0 44.4 + - + +
110H ILE* 3.1 14.9 + - - +
112H GLN* 1.3 71.4 - - - +
114H THR* 1.3 64.8 + - - +
115H LEU 3.0 11.7 + - - +
116H ALA* 5.3 0.8 - - - +
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Residues in contact with THR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H PHE* 4.3 20.9 - - + -
110H ILE* 2.9 31.2 + - - +
111H THR* 3.4 13.2 + - + +
113H THR* 1.3 76.7 + - - +
115H LEU* 1.3 71.8 + - + +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H THR* 3.3 22.6 + - - +
112H GLN* 3.7 5.1 + - - +
113H THR 3.0 9.0 - - - +
114H THR* 1.3 92.6 - - + +
116H ALA* 1.3 65.2 + - - +
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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