Contacts of the helix formed by residues 80 - 105 (chain A) in PDB entry 3F4M
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 GLY 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A SER 3.7 2.2 + - - -
79A PHE* 1.3 73.0 - - - +
81A PRO* 1.3 71.3 - - - +
82A SER 3.4 2.7 - - - -
83A GLU* 3.0 15.7 + - - -
84A LEU* 2.8 29.4 + - - +
201A CL 3.6 11.2 - - - -
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Residues in contact with PRO 81 (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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80A GLY* 1.3 82.2 - - - +
82A SER* 1.3 63.7 + - - +
84A LEU* 3.3 11.8 + - + +
85A ALA* 3.1 21.5 + - - +
201A CL 4.3 5.4 - - + -
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Residues in contact with SER 82 (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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80A GLY 3.4 0.4 - - - -
81A PRO* 1.3 79.2 - - - +
83A GLU* 1.3 58.2 + - - +
85A ALA* 3.3 8.3 + - - +
86A LEU* 3.0 31.3 + - - +
201A CL 3.7 14.1 - - - +
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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
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78A SER 4.1 0.2 - - - +
79A PHE* 3.4 13.9 - - + -
80A GLY 3.0 23.7 + - - +
82A SER* 1.3 76.6 - - - +
84A LEU* 1.3 60.0 + - - +
86A LEU* 3.0 11.4 + - + -
87A ALA* 2.9 24.6 + - - +
129A GLU 5.3 2.1 - - - +
130A LEU* 3.1 26.7 - - + +
133A HIS* 4.2 19.9 - - - +
134A HIS* 2.7 38.4 + - - -
201A CL 3.7 17.0 - - + +
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Residues in contact with LEU 84 (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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74A HIS* 4.4 15.0 - - + +
79A PHE* 3.8 36.8 - - + +
80A GLY 2.8 23.1 + - - +
81A PRO* 3.8 8.5 - - + +
83A GLU* 1.3 75.8 - - - +
85A ALA* 1.3 61.9 + - - +
87A ALA* 3.4 6.3 + - + +
88A THR* 3.2 24.5 + - - -
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Residues in contact with ALA 85 (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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81A PRO 3.1 13.6 + - - +
82A SER* 3.6 11.7 - - - +
84A LEU* 1.3 76.0 - - - +
86A LEU* 1.3 60.0 + - - +
88A THR* 3.3 9.5 + - - +
89A ARG* 3.0 25.7 + - - +
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Residues in contact with LEU 86 (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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82A SER* 3.0 18.3 + - - +
83A GLU* 3.0 16.6 + - + +
85A ALA* 1.3 75.2 - - - +
87A ALA* 1.3 59.2 + - - +
89A ARG* 3.1 22.7 + - - +
90A PHE* 2.8 24.4 + - - +
126A VAL* 3.5 27.0 - - + +
129A GLU* 3.8 30.3 - - + +
130A LEU* 3.8 35.4 - - + +
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Residues in contact with ALA 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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74A HIS* 3.7 33.4 - - + +
83A GLU 2.9 12.7 + - - +
84A LEU* 3.6 11.4 - - + +
85A ALA 3.3 0.2 - - - -
86A LEU* 1.3 76.6 - - - +
88A THR* 1.3 63.0 + - - +
90A PHE* 3.2 6.6 + - - +
91A ARG* 3.0 28.8 + - + +
130A LEU* 4.1 17.9 - - + +
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Residues in contact with THR 88 (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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84A LEU 3.2 13.9 + - - -
85A ALA* 3.4 12.2 - - - +
86A LEU 3.2 0.4 - - - -
87A ALA* 1.3 75.2 - - - +
89A ARG* 1.3 63.4 + - - +
91A ARG* 3.3 9.9 + - - +
92A GLN* 3.1 38.9 + - + +
95A ARG* 6.0 0.7 - - - +
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Residues in contact with ARG 89 (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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85A ALA 3.0 13.0 + - - +
86A LEU* 3.1 26.9 + - - +
88A THR* 1.3 77.1 - - - +
90A PHE* 1.3 56.5 + - - +
92A GLN* 3.2 19.2 + - - +
93A LYS* 2.9 45.6 + - + +
122A GLU* 5.8 4.0 + - - +
126A VAL* 3.6 31.1 - - + +
129A GLU* 4.8 7.3 + - - -
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Residues in contact with PHE 90 (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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86A LEU 2.8 14.0 + - - +
87A ALA* 3.5 12.1 - - - +
89A ARG* 1.3 74.8 - - - +
91A ARG* 1.3 67.7 + - + +
93A LYS* 3.2 6.1 + - - +
94A LEU* 2.8 58.5 + - + +
123A CYS* 3.5 42.6 - - + -
126A VAL* 3.7 11.4 - - + +
127A LEU* 3.8 37.0 - - + +
130A LEU* 5.4 4.0 - - + -
147A PHE* 4.1 11.7 - + - -
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Residues in contact with ARG 91 (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 ALA* 3.0 15.4 + - + +
88A THR* 3.7 9.2 - - - +
89A ARG 3.2 0.2 - - - -
90A PHE* 1.3 87.1 - - + +
92A GLN* 1.3 57.1 + - - +
94A LEU* 3.3 8.7 + - + +
95A ARG* 2.9 50.5 + - - +
182A GLY 3.9 14.5 + - - -
183A LYS 4.7 1.8 - - - -
184A LEU* 3.1 36.9 + - - +
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Residues in contact with GLN 92 (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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88A THR* 3.1 28.5 + - + +
89A ARG* 3.2 26.3 + - - +
91A ARG* 1.3 76.3 - - - +
93A LYS* 1.3 61.5 + - + +
95A ARG* 3.4 25.6 + - - +
96A GLN* 3.0 30.2 + - - +
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Residues in contact with LYS 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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89A ARG* 2.9 38.8 + - + +
90A PHE* 3.2 5.8 + - - +
92A GLN* 1.3 77.5 - - + +
94A LEU* 1.3 60.2 + - - +
96A GLN* 2.9 32.5 + - - +
97A GLY* 2.8 25.5 + - - -
119A LEU* 3.3 22.9 - - - +
122A GLU* 2.7 37.9 + - + +
123A CYS* 3.6 22.4 - - - -
126A VAL* 4.5 13.0 - - + -
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Residues in contact with LEU 94 (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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90A PHE* 2.8 47.3 + - + +
91A ARG* 3.7 8.3 - - + +
93A LYS* 1.3 78.2 - - - +
95A ARG* 1.3 57.1 + - - +
97A GLY* 3.3 1.8 + - - -
98A ALA* 3.0 27.9 + - - +
120A LEU* 5.6 5.4 - - + -
123A CYS* 3.7 15.7 - - + -
147A PHE* 5.0 8.1 - - + -
184A LEU* 3.7 34.7 - - + +
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Residues in contact with ARG 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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88A THR* 5.0 1.0 + - - +
91A ARG* 2.9 35.5 + - - +
92A GLN* 3.6 34.8 - - - +
94A LEU* 1.3 73.4 - - - +
96A GLN* 1.3 60.5 + - - +
98A ALA* 3.2 6.7 + - - +
99A MET* 2.8 47.4 + - + +
179A LEU* 3.7 19.1 - - + -
184A LEU* 3.2 48.1 + - + +
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Residues in contact with GLN 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 GLN* 3.0 13.8 + - - +
93A LYS* 2.9 45.6 + - - +
95A ARG* 1.3 77.2 - - - +
97A GLY* 1.3 57.4 + - - +
99A MET* 3.4 7.5 + - + +
100A THR* 2.9 38.8 + - - +
119A LEU* 3.7 16.3 - - + +
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Residues in contact with GLY 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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93A LYS 2.8 14.8 + - - -
94A LEU* 3.7 3.6 - - - -
96A GLN* 1.3 76.3 - - - +
98A ALA* 1.3 56.1 + - - +
100A THR* 3.7 1.6 - - - -
101A ALA* 2.9 30.9 + - - +
116A LEU* 3.9 9.4 - - - +
119A LEU* 4.0 21.2 - - - +
120A LEU* 5.6 7.2 - - - -
123A CYS* 5.6 3.1 - - - -
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Residues in contact with ALA 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 LEU 3.0 16.9 + - - +
95A ARG 3.2 4.9 + - - +
97A GLY* 1.3 75.6 - - - +
99A MET* 1.3 57.9 + - - +
101A ALA* 3.3 4.1 + - - +
102A LEU* 3.0 32.9 + - - +
175A LEU* 4.1 22.7 - - + +
179A LEU* 4.0 12.6 - - + -
184A LEU* 3.7 26.2 - - + -
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Residues in contact with MET 99 (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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95A ARG* 2.8 31.6 + - + +
96A GLN* 4.0 5.8 - - - +
98A ALA* 1.3 75.9 - - - +
100A THR* 1.3 58.9 + - - +
102A LEU* 3.3 10.8 + - + +
103A SER* 2.9 31.8 + - - +
179A LEU* 3.9 33.2 - - + -
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Residues in contact with THR 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 GLN* 2.9 25.4 + - - +
97A GLY 3.7 2.0 - - - -
99A MET* 1.3 75.1 - - - +
101A ALA* 1.3 64.7 + - - +
103A SER* 3.1 7.8 + - - -
104A PHE* 2.9 53.7 + - + +
115A VAL* 4.4 8.1 - - + -
116A LEU* 4.5 5.6 - - + -
119A LEU* 3.3 25.9 - - + +
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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 GLY 2.9 17.4 + - - +
98A ALA* 3.3 6.5 + - - +
100A THR* 1.3 76.5 - - - +
102A LEU* 1.3 60.9 + - - +
104A PHE 3.5 0.3 + - - -
105A GLY* 3.2 14.9 + - - -
116A LEU* 4.3 16.7 - - + +
160A TYR* 2.7 29.7 + - - +
171A ILE* 6.2 0.2 - - + -
172A CYS* 4.4 5.9 - - - -
175A LEU* 4.1 17.9 - - + -
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Residues in contact with LEU 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 ALA 3.0 18.8 + - - +
99A MET* 3.5 10.3 - - + +
100A THR 3.2 0.2 - - - -
101A ALA* 1.3 74.5 - - - +
103A SER* 1.3 65.4 + - - +
105A GLY* 3.0 14.2 + - - -
106A GLU* 3.5 12.3 + - - +
172A CYS* 3.4 48.1 - - + +
175A LEU* 4.4 7.0 - - + -
176A ARG* 4.3 40.2 - - + +
179A LEU* 3.8 25.8 - - + -
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Residues in contact with SER 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 MET* 2.9 19.7 + - - +
100A THR* 3.1 9.7 + - - -
102A LEU* 1.3 75.8 - - - +
104A PHE* 1.3 62.9 + - - +
106A GLU* 2.9 36.1 + - - +
109A PHE* 3.4 25.3 - - - +
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Residues in contact with PHE 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 THR* 2.9 41.1 + - + +
101A ALA 3.9 0.7 - - - +
103A SER* 1.3 81.0 - - - +
105A GLY* 1.3 60.1 + - - +
106A GLU 3.4 6.6 + - - +
109A PHE* 4.0 15.2 - - + +
110A THR 3.4 27.1 - - - -
111A PHE* 3.7 25.5 - + + +
112A GLU* 3.5 45.8 - - + -
115A VAL* 4.1 12.6 - - + -
116A LEU* 4.2 12.6 - - + -
160A TYR* 3.7 26.2 - - + -
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Residues in contact with GLY 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 3.2 10.1 + - - -
102A LEU 3.0 12.3 + - - -
104A PHE* 1.3 75.1 - - - +
106A GLU* 1.3 61.6 + - - +
107A VAL* 3.5 5.0 + - - +
160A TYR* 3.8 9.6 - - - -
168A LEU* 4.8 11.1 - - - +
172A CYS* 4.9 7.6 - - - -
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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