Contacts of the helix formed by residues 84 - 105 (chain O) in PDB entry 5A0Q
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 THR 84 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O LEU* 5.9 2.1 - - - +
68O HIS* 5.1 11.7 - - + +
82O GLY 3.5 5.3 + - - -
83O MET* 1.4 70.9 - - - +
85O ALA* 1.3 64.9 + - - +
87O SER* 3.4 10.4 - - - -
88O ARG* 3.2 40.0 + - - +
156U VAL* 3.7 23.1 - - + -
158U TYR* 3.6 25.4 + - + +
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Residues in contact with ALA 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O MET 3.4 0.2 - - - -
84O THR* 1.3 79.0 - - - +
86O ASP* 1.4 67.0 + - - +
87O SER 3.4 0.5 + - - -
88O ARG* 3.4 16.6 + - - +
120U HIS* 3.3 26.9 + - + +
123U THR* 5.5 0.4 - - - +
154U SER* 3.1 37.5 - - - +
155U GLY 4.0 9.4 - - - +
156U VAL* 3.6 13.3 - - + +
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Residues in contact with ASP 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O MET* 3.2 44.5 - - + +
84O THR 3.2 0.4 - - - -
85O ALA* 1.4 80.0 - - - +
87O SER* 1.3 63.6 + - - +
88O ARG 3.4 0.2 + - - -
89O SER* 3.5 8.1 + - - -
90O GLN 3.8 2.6 + - - -
132O ARG* 3.2 28.5 + - - -
134O LEU* 3.5 42.1 - - + +
135O GLY 4.2 7.0 - - - +
136O CYS* 3.9 7.0 - - - -
120U HIS* 3.6 18.9 - - - -
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Residues in contact with SER 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O HIS* 5.9 1.0 + - - -
70O PHE* 4.7 4.5 - - - -
80O MET* 3.4 38.1 - - - +
81O THR 4.7 0.5 + - - -
82O GLY 5.0 1.6 + - - -
83O MET 3.0 16.2 + - - -
84O THR* 3.4 12.1 + - - -
86O ASP* 1.3 77.5 - - - +
88O ARG* 1.4 71.1 + - - +
89O SER 3.3 0.5 + - - -
90O GLN 3.3 3.5 + - - -
91O VAL* 2.9 30.2 + - - +
136O CYS* 4.1 7.9 - - - +
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Residues in contact with ARG 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O HIS* 4.9 11.1 + - - -
70O PHE* 3.9 32.2 - - - -
84O THR* 3.2 40.9 + - - +
85O ALA 3.8 11.2 - - - +
86O ASP 3.3 1.0 - - - -
87O SER* 1.4 85.8 + - - +
89O SER* 1.4 59.3 + - - +
91O VAL* 3.6 6.7 - - - +
92O GLN* 3.0 34.8 + - + +
113U ASP* 6.2 2.3 - - - -
117U MET* 5.0 9.9 - - + -
120U HIS* 5.7 0.4 - - + -
155U GLY 4.9 8.7 - - - +
156U VAL* 5.9 1.0 - - - +
157U SER* 4.8 8.1 + - - +
158U TYR* 4.4 14.8 - - - -
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Residues in contact with SER 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85O ALA 4.0 2.2 + - - -
86O ASP 3.5 1.2 + - - -
87O SER 3.3 1.0 - - - -
88O ARG* 1.4 77.7 - - - +
90O GLN* 1.4 57.1 + - - +
92O GLN* 3.4 4.3 + - - +
93O ARG* 3.0 26.2 + - - +
125O TYR* 5.0 1.6 + - - -
134O LEU* 3.8 25.4 - - - +
117U MET* 3.8 24.8 - - - +
120U HIS* 3.8 20.2 - - - -
124U LEU* 4.4 7.2 - - - +
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Residues in contact with GLN 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O MET* 3.5 22.5 - - + +
86O ASP 3.8 0.6 + - - -
87O SER 3.3 3.4 + - - +
89O SER* 1.4 75.8 - - - +
91O VAL* 1.4 60.3 + - - +
93O ARG* 3.8 7.4 - - - +
94O ALA* 3.0 27.4 + - - +
118O ILE* 3.4 29.7 - - + +
121O ILE* 3.6 12.9 - - + +
122O SER* 3.8 17.3 - - - -
125O TYR* 3.5 29.2 + - - +
134O LEU* 4.0 12.8 - - + +
136O CYS* 3.4 26.8 - - - +
138O MET* 4.5 4.7 - - - +
154O CYS* 5.8 3.0 - - - -
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Residues in contact with VAL 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O PHE* 3.7 47.3 - - + -
72O ILE* 3.7 19.1 - - + -
78O CYS* 4.9 0.2 - - - -
80O MET* 3.8 13.2 - - + -
87O SER 2.9 20.0 + - - +
88O ARG* 3.6 12.3 - - - +
89O SER 3.3 0.6 - - - -
90O GLN* 1.4 75.8 - - - +
92O GLN* 1.3 62.4 + - + +
94O ALA* 3.2 4.0 + - - +
95O ARG* 3.0 51.3 + - - +
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Residues in contact with GLN 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O ARG* 3.0 21.2 + - + +
89O SER* 3.8 5.8 - - - +
91O VAL* 1.3 77.0 - - + +
93O ARG* 1.3 56.1 + - - +
95O ARG* 3.4 30.7 + - - +
96O TYR* 2.9 27.1 + - - +
113U ASP* 6.2 1.2 - - - +
114U ARG* 3.6 36.5 + - - +
117U MET* 5.4 10.1 - - + -
65V PHE* 4.2 19.9 - - - -
69V GLU* 3.7 13.2 - - - +
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Residues in contact with ARG 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89O SER 3.0 17.6 + - - +
90O GLN* 3.9 9.6 - - + +
91O VAL 3.3 0.2 - - - -
92O GLN* 1.3 72.6 - - - +
94O ALA* 1.3 64.1 + - - +
96O TYR* 3.3 21.5 + - - +
97O GLU* 3.0 45.2 + - + +
117O ARG* 4.6 4.4 - - - +
118O ILE* 3.7 17.5 - - + -
121O ILE* 4.0 40.5 - - + +
125O TYR* 5.9 4.0 + - - -
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Residues in contact with ALA 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O ILE* 3.5 27.8 - - + +
90O GLN 3.0 20.2 + - - +
91O VAL 3.4 5.4 - - - +
93O ARG* 1.3 76.6 - - - +
95O ARG* 1.3 55.8 + - - +
97O GLU* 3.9 1.6 - - - +
98O ALA* 2.9 30.8 + - - +
114O LEU* 5.1 3.4 - - + +
118O ILE* 3.7 15.0 - - + +
138O MET* 3.9 17.9 - - + -
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Residues in contact with ARG 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O PHE* 5.2 5.5 - - - -
71O LYS* 3.4 27.3 + - - +
72O ILE* 3.3 27.1 - - - +
91O VAL* 3.0 39.0 + - - +
92O GLN* 3.4 33.5 - - - +
93O ARG 3.3 0.2 - - - -
94O ALA* 1.3 72.0 - - - +
96O TYR* 1.3 63.5 + - - +
98O ALA* 4.1 0.8 - - - +
99O ALA* 3.2 25.6 + - - +
65V PHE* 3.9 19.4 - - + -
68V ILE* 3.6 31.5 + - + +
69V GLU* 3.7 21.7 + - - +
71V ASN* 4.8 5.3 - - - +
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Residues in contact with TYR 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O GLN 2.9 17.4 + - - +
93O ARG* 3.3 30.7 + - - +
95O ARG* 1.3 77.8 - - - +
97O GLU* 1.4 73.0 + - - +
99O ALA* 3.9 2.6 - - - +
100O ASN* 2.9 43.7 + - + +
61V TYR* 3.9 18.7 + - - -
65V PHE* 4.5 16.4 - + + -
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Residues in contact with GLU 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O ARG* 3.0 35.2 + - - +
94O ALA 4.1 2.2 - - - +
96O TYR* 1.4 90.0 - - - +
98O ALA* 1.3 59.9 + - - +
100O ASN* 3.8 18.9 + - - +
101O TRP* 3.0 28.2 + - - +
109O ILE* 4.2 9.3 - - + +
114O LEU* 5.5 1.6 - - + -
117O ARG* 3.2 55.7 + - + +
118O ILE* 4.2 11.4 - - + -
121O ILE* 4.9 0.5 - - - +
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Residues in contact with ALA 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O ILE* 4.1 8.1 - - + +
73O THR* 3.2 33.9 - - + +
94O ALA 2.9 20.6 + - - +
95O ARG 4.1 3.4 - - - +
97O GLU* 1.3 77.0 - - - +
99O ALA* 1.4 59.9 + - - +
101O TRP* 3.5 14.4 - - - +
102O LYS* 3.8 7.6 + - - +
109O ILE* 4.2 6.1 + - + +
114O LEU* 3.8 22.8 - - + +
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Residues in contact with ALA 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O THR* 6.4 0.2 - - - -
95O ARG 3.2 17.3 + - - +
96O TYR* 3.9 2.9 - - - +
98O ALA* 1.4 75.4 - - - +
100O ASN* 1.3 59.6 + - - +
101O TRP 3.2 0.4 + - - -
102O LYS* 3.4 7.1 + - - +
103O TYR 3.1 20.8 + - - -
61V TYR* 3.1 27.9 - - + +
65V PHE* 4.6 22.7 - - + -
68V ILE* 6.1 4.7 - - + -
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Residues in contact with ASN 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O TYR* 2.9 35.1 + - + +
97O GLU* 3.8 22.4 + - - +
99O ALA* 1.3 74.4 - - - +
101O TRP* 1.3 62.4 + - - +
103O TYR* 3.3 5.7 + - - +
104O LYS* 3.1 43.8 + - - +
61V TYR* 3.4 23.1 + - - +
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Residues in contact with TRP 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O GLU 3.0 12.9 + - - +
98O ALA 3.5 13.2 - - - +
99O ALA 3.2 0.2 - - - -
100O ASN* 1.3 74.6 - - - +
102O LYS* 1.3 51.7 + - - +
104O LYS* 3.1 2.1 + - - -
105O TYR* 2.8 77.3 + + + +
107O TYR* 3.1 49.5 - - - -
109O ILE* 3.4 40.0 - - + +
110O PRO* 4.2 2.7 - - + -
113O MET* 3.8 41.7 - - + -
116O LYS* 6.0 2.7 - - - -
117O ARG* 6.1 2.9 - - + -
66W HIS* 3.4 23.8 - + - -
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Residues in contact with LYS 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O THR* 6.0 5.8 - - - -
74O GLU* 5.3 8.1 - - - -
75O ASN* 5.8 3.8 - - - +
98O ALA 3.8 6.7 + - - +
99O ALA* 3.4 9.5 + - - +
101O TRP* 1.3 79.1 - - - +
103O TYR* 1.3 49.3 + - - +
106O GLY* 3.2 23.7 + - - +
107O TYR* 3.9 33.0 - - - +
108O GLU* 4.0 7.8 - - - +
60V THR* 6.1 5.2 - - + -
81W ARG* 2.2 41.0 + - - +
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Residues in contact with TYR 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99O ALA 3.1 5.7 + - - -
100O ASN* 3.5 11.9 - - - +
101O TRP 3.1 0.4 - - - -
102O LYS* 1.3 67.3 - - - +
104O LYS* 1.4 59.5 + - + +
54V ALA* 4.1 9.7 + - - -
57V ASP* 4.0 11.7 - - + -
58V ALA* 3.9 35.5 - - + +
61V TYR* 3.2 50.2 - + + -
81W ARG* 1.8 65.4 + - - +
85W GLN* 2.9 36.2 + - - +
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Residues in contact with LYS 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O ASN* 3.1 34.8 + - - +
101O TRP 3.1 3.9 + - - +
103O TYR* 1.4 83.5 - - + +
105O TYR* 1.3 88.2 + - + +
78W THR 4.3 0.2 - - - +
81W ARG* 3.5 14.9 - - - +
82W MET* 4.0 17.7 + - + +
85W GLN* 4.0 14.1 - - - +
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Residues in contact with TYR 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O TRP* 2.8 74.3 + + + +
104O LYS* 1.3 107.0 + - + +
106O GLY* 1.3 59.9 + - - +
107O TYR* 3.6 18.8 - - + -
66W HIS* 3.7 24.5 + + + +
77W VAL 3.6 2.8 - - - +
78W THR* 3.1 44.6 + - + +
81W ARG* 3.3 13.2 - - - +
82W MET* 4.2 10.3 - - + -
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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