Contacts of the helix formed by residues 101 - 121 (chain U) in PDB entry 4HOK
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 SER 101 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U PHE* 1.3 74.1 - - - +
102U LEU* 1.3 53.3 + - - +
103U LYS* 3.9 6.9 + - - +
104U THR* 2.8 15.9 + - - -
105U VAL* 2.5 33.9 + - - +
289U ASP* 2.4 33.3 + - - -
25W LEU* 6.2 4.9 - - - -
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Residues in contact with LEU 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U PHE 4.1 0.6 + - - +
101U SER* 1.3 68.7 - - - +
103U LYS* 1.3 59.5 + - - +
105U VAL* 4.0 4.3 - - + +
106U LEU* 2.5 50.8 + - + +
207U ASN* 4.3 13.0 - - - +
244U TYR* 5.8 3.8 - - + -
245U PRO* 4.4 19.5 - - + -
248U PHE* 3.8 28.5 - - + -
276U LEU* 4.1 26.5 - - + -
280U GLN* 4.5 10.8 - - - +
282U PHE* 4.1 13.0 - - + -
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Residues in contact with LYS 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101U SER* 3.4 6.9 + - - +
102U LEU* 1.3 76.5 - - - +
104U THR* 1.3 58.8 + - - +
106U LEU* 4.0 1.5 - - - +
107U LEU* 3.0 36.9 + - + +
277U PHE* 3.9 4.0 - - + -
282U PHE* 3.3 55.9 - - + -
283U SER* 3.2 18.5 + - - +
285U ASP* 2.5 40.3 + - - -
287U VAL* 3.5 29.9 + - - +
288U PHE* 5.6 0.4 - - - +
34W GLU* 4.3 17.4 + - - +
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Residues in contact with THR 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U PHE* 3.5 28.5 - - + -
101U SER* 2.8 18.5 + - - -
103U LYS* 1.3 78.1 - - - +
105U VAL* 1.3 65.6 + - - +
106U LEU 3.2 1.3 - - - -
107U LEU* 3.7 4.3 + - - +
108U LEU* 3.3 25.0 + - + +
287U VAL 4.4 1.0 + - - -
288U PHE* 2.9 20.4 - - + +
289U ASP* 2.6 46.4 + - - +
290U TRP* 4.6 4.7 - - + -
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Residues in contact with VAL 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100U PHE* 3.8 22.9 - - + +
101U SER 2.5 30.8 + - - +
102U LEU* 3.8 11.0 - - + +
104U THR* 1.3 72.8 - - - +
106U LEU* 1.3 60.0 + - + +
108U LEU* 3.1 8.8 + - + +
109U ALA* 2.9 25.3 + - - +
203U LEU* 3.8 33.4 - - + +
206U PHE* 4.6 11.2 - - + +
207U ASN* 3.9 15.3 - - - +
248U PHE* 4.2 18.6 - - + -
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Residues in contact with LEU 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U LEU* 2.5 36.9 + - + +
103U LYS 4.0 2.5 - - - +
105U VAL* 1.3 69.5 - - - +
107U LEU* 1.3 54.7 + - - +
108U LEU 2.7 15.5 + - - -
109U ALA* 2.9 16.0 + - + +
110U ASP* 3.3 11.1 + - - +
248U PHE* 4.2 15.9 - - + -
273U PHE* 3.8 42.5 - - + +
276U LEU* 4.0 18.2 - - + -
277U PHE* 3.6 45.3 - - + +
282U PHE* 5.1 2.5 - - + -
284U TYR* 5.6 1.8 - - - +
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Residues in contact with LEU 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U LYS* 3.0 41.1 + - - +
104U THR* 4.2 2.7 - - - +
106U LEU* 1.3 71.9 - - - +
108U LEU* 1.3 60.1 + - - +
110U ASP* 4.0 4.6 - - - +
111U GLN* 3.9 27.4 + - - +
277U PHE* 3.1 29.2 - - + -
283U SER 4.5 1.3 - - - +
284U TYR* 3.2 33.1 - - + -
286U TYR* 3.5 48.5 - - + +
287U VAL 4.6 0.2 - - - +
288U PHE* 4.2 20.8 - - + +
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Residues in contact with LEU 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89U LEU* 3.9 27.1 - - + -
100U PHE* 4.8 6.7 - - + -
104U THR* 3.3 16.1 + - + +
105U VAL* 3.1 10.7 + - - +
106U LEU 2.7 2.2 + - - -
107U LEU* 1.3 78.7 - - - +
109U ALA* 1.3 63.6 + - - +
110U ASP 3.1 1.8 - - - -
111U GLN* 3.9 1.5 + - - +
112U MET* 3.0 35.6 + - - +
136U MET* 4.3 2.5 - - - -
145U VAL* 3.5 28.7 - - + -
203U LEU* 5.7 1.8 - - + -
206U PHE* 4.6 11.7 - - + -
288U PHE* 3.7 23.8 - - + -
290U TRP* 4.0 22.2 - - + -
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Residues in contact with ALA 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105U VAL 2.9 14.5 + - - +
106U LEU* 2.9 8.2 + - + +
108U LEU* 1.3 74.5 - - - +
110U ASP* 1.3 55.4 + - - +
112U MET* 3.7 5.5 - - - +
113U ILE* 2.5 40.2 + - + +
203U LEU* 3.3 39.9 - - + -
273U PHE* 3.9 22.0 - - + -
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Residues in contact with ASP 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106U LEU 3.3 8.4 + - - +
107U LEU* 4.0 11.7 - - - +
108U LEU 3.1 0.4 - - - -
109U ALA* 1.3 83.0 - - - +
111U GLN* 1.3 69.1 + - + +
113U ILE* 3.4 10.3 + - - +
114U SER* 3.3 16.1 + - - -
270U ARG* 2.8 43.4 + - - +
273U PHE* 5.5 3.2 - - + +
274U ARG* 3.0 39.8 + - + -
284U TYR* 4.6 13.5 - - + +
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Residues in contact with GLN 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107U LEU 3.9 17.1 + - - +
108U LEU 3.9 1.4 + - - +
110U ASP* 1.3 81.0 - - + +
112U MET* 1.3 62.7 + - - +
114U SER* 3.5 2.5 + - - -
115U ARG* 3.0 52.2 + - - +
143U ASN* 2.7 22.7 + - - +
144U LEU* 3.2 12.2 - - - +
145U VAL* 2.6 46.9 + - + +
286U TYR* 4.4 18.2 - - - -
288U PHE* 4.9 4.0 - - - -
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Residues in contact with MET 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89U LEU* 3.9 20.4 - - + -
108U LEU* 3.0 34.1 + - - +
109U ALA* 3.7 5.6 - - - +
110U ASP 3.1 0.6 - - - -
111U GLN* 1.3 74.1 - - - +
113U ILE* 1.3 66.3 + - - +
115U ARG* 3.2 15.6 + - - +
116U ILE* 2.8 22.4 + - - +
134U PHE* 3.8 34.8 - - + -
145U VAL* 4.2 9.4 - - + -
199U LEU* 2.9 42.4 - - + -
202U VAL* 3.8 22.0 - - + -
203U LEU* 4.8 3.8 - - + -
206U PHE* 4.4 5.8 - - + -
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Residues in contact with ILE 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109U ALA* 2.5 29.4 + - + +
110U ASP* 3.4 6.5 + - - +
112U MET* 1.3 73.4 - - - +
114U SER* 1.3 64.9 + - - +
116U ILE* 3.3 11.8 + - - +
117U GLU* 2.9 19.8 + - - +
196U LEU* 3.6 20.9 - - + -
199U LEU* 4.0 6.7 - - + -
251U TYR* 3.6 29.4 - - + -
266U TYR* 3.8 31.3 - - + +
269U LEU* 4.9 2.2 - - + -
270U ARG* 4.2 27.6 - - + +
273U PHE* 4.3 11.7 - - + -
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Residues in contact with SER 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U ASP* 3.3 13.8 + - - -
111U GLN* 3.5 2.7 - - - -
112U MET 3.2 0.8 - - - -
113U ILE* 1.3 77.0 - - - +
115U ARG* 1.3 77.7 + - - +
117U GLU* 2.6 31.9 + - - +
118U TYR* 2.8 9.4 + - - +
270U ARG* 3.4 28.8 + - - +
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Residues in contact with ARG 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259O ARG* 6.1 0.2 - - - +
63U VAL* 3.5 34.8 + - - +
64U GLY* 3.9 11.9 - - - -
65U ILE* 5.8 2.8 - - - +
111U GLN* 3.0 51.9 + - - +
112U MET* 3.2 11.2 + - - +
114U SER* 1.3 100.1 - - - +
116U ILE* 1.3 64.4 + - - +
117U GLU 2.8 1.4 + - - -
118U TYR* 3.2 6.9 + - - +
119U ILE* 3.2 27.2 + - - +
134U PHE* 4.6 4.5 - - + -
144U LEU* 4.2 12.7 - - - +
145U VAL* 3.2 34.7 + - + +
146U TYR 4.8 0.2 - - - -
147U ILE* 4.2 26.7 - - + -
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Residues in contact with ILE 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112U MET 2.8 32.8 + - - +
113U ILE* 3.8 6.3 - - - +
115U ARG* 1.3 76.6 - - + +
117U GLU* 1.3 58.7 + - - +
119U ILE* 3.9 9.0 - - - +
120U HIS* 2.9 74.2 + - + +
126U HIS* 5.7 2.5 - - + -
129U VAL* 4.5 15.7 - - + -
134U PHE* 4.5 14.4 - - + -
147U ILE* 5.2 4.0 - - + +
195U ASP* 3.7 19.1 - - + +
196U LEU* 4.3 12.3 - - + -
199U LEU* 3.7 29.6 - - + -
266U TYR* 5.5 0.4 - - + -
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Residues in contact with GLU 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113U ILE 2.9 9.8 + - - +
114U SER* 2.6 17.8 + - - +
116U ILE* 1.3 74.4 - - - +
118U TYR* 1.3 48.8 + - - +
119U ILE 2.7 4.4 + - - -
120U HIS* 2.6 26.7 + - - +
121U SER* 2.7 20.7 + - - -
263U LYS* 5.8 0.2 - - - -
266U TYR* 2.9 56.5 - - + +
270U ARG* 2.5 29.6 + - - -
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Residues in contact with TYR 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U MET* 3.1 14.7 + - + -
60U GLN 2.5 29.3 + - - -
61U GLY* 3.4 3.1 - - - -
62U GLY* 2.7 34.4 + - - -
63U VAL* 5.0 7.2 - - + +
65U ILE* 3.7 20.4 - - + -
114U SER 2.8 13.0 + - - +
115U ARG* 3.9 9.0 - - - +
117U GLU* 1.3 72.2 - - - +
119U ILE* 1.3 61.1 + - + +
121U SER* 2.7 27.1 + - - -
122U LYS* 2.8 52.1 - - + +
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Residues in contact with ILE 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U MET* 4.0 15.5 - - + -
65U ILE* 4.7 9.9 - - + -
115U ARG 3.2 14.1 + - - +
116U ILE* 3.9 5.8 - - - +
117U GLU 2.7 5.1 + - - -
118U TYR* 1.3 73.4 - - + +
120U HIS* 1.3 58.4 + - + +
122U LYS* 2.5 38.2 + - - +
124U PHE* 3.0 26.2 + - + +
125U ILE 4.4 10.3 - - - +
126U HIS* 4.3 9.9 - - + +
147U ILE* 3.7 38.4 - - + -
150U PHE* 3.5 31.2 - - + -
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Residues in contact with HIS 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116U ILE* 2.9 47.9 + - + +
117U GLU 2.6 9.8 + - - +
119U ILE* 1.3 70.6 - - + +
121U SER* 1.3 53.4 + - - +
122U LYS 2.7 15.2 + - - -
123U ASN 3.0 8.1 + - - -
124U PHE 3.5 17.0 - - - -
125U ILE* 4.1 6.5 - - - -
156U TYR* 2.4 24.3 + - - -
157U ARG* 3.5 3.5 + - - -
192U ARG* 3.2 45.2 - - + +
195U ASP* 3.5 14.9 + - - +
196U LEU* 4.6 1.3 - - + -
266U TYR* 2.6 41.1 + + + +
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Residues in contact with SER 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117U GLU* 2.7 17.7 + - - -
118U TYR* 2.7 29.3 + - - -
120U HIS* 1.3 72.0 - - - +
122U LYS* 1.3 63.8 + - - +
123U ASN* 4.8 1.2 + - - -
157U ARG* 3.1 19.6 + - - +
266U TYR* 6.2 0.2 - - - -
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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