Contacts of the helix formed by residues 95 - 121 (chain A) in PDB entry 2IB0
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.6 18.2 - - - +
94A SER* 1.3 83.7 + - - +
96A ALA* 1.3 65.8 + - - +
97A ALA* 3.6 12.5 + - - +
98A ASP* 3.0 28.1 + - - +
99A ALA 3.5 4.0 + - - -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.8 25.7 + - - +
47A SER* 4.7 0.5 + - - -
48A PRO* 3.6 29.3 - - + +
95A SER* 1.3 74.0 - - - +
97A ALA* 1.3 59.6 + - - +
99A ALA* 3.5 14.0 + - - +
100A ALA 4.0 1.2 + - - -
151A TRP* 3.6 15.9 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 3.2 8.9 + - - +
96A ALA* 1.3 72.7 - - - +
98A ASP* 1.3 66.9 + - - +
99A ALA 3.1 2.5 + - - -
100A ALA 3.6 1.7 + - - -
101A ARG* 3.6 40.9 + - - +
148A LEU* 4.0 5.4 - - + +
151A TRP* 3.7 20.8 - - + -
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.6 8.5 - - + +
92A GLN 4.4 4.3 - - - -
93A VAL* 3.5 23.1 - - + +
94A SER* 2.6 32.6 + - - -
95A SER* 3.0 19.6 + - - +
97A ALA* 1.3 78.1 - - - +
99A ALA* 1.3 57.8 + - - +
101A ARG* 2.9 32.2 + - - +
102A LEU* 2.9 26.3 + - - +
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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
----------------------------------------------------------
43A VAL* 3.5 41.2 - - - +
46A LEU* 3.9 23.1 - - + +
47A SER* 4.0 6.7 - - - +
93A VAL* 4.9 0.7 - - - -
95A SER 3.5 1.2 + - - -
96A ALA 3.5 12.3 + - - +
97A ALA 3.1 0.6 - - - -
98A ASP* 1.3 76.9 - - - +
100A ALA* 1.3 60.6 + - - +
102A LEU* 3.3 8.6 + - - +
103A ALA* 2.9 24.6 + - - +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 4.0 2.0 + - - -
97A ALA 3.6 0.8 + - - +
99A ALA* 1.3 74.7 - - - +
101A ARG* 1.3 64.3 + - - +
103A ALA* 3.3 3.3 + - - +
104A VAL* 3.0 28.6 + - - +
144A TRP* 3.7 31.2 - - + +
147A VAL* 4.5 2.5 - - + -
148A LEU* 3.7 26.5 - - + -
151A TRP* 3.7 22.6 - - + -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.7 19.7 - - + +
97A ALA* 3.6 24.9 + - - +
98A ASP* 2.9 42.2 + - - +
100A ALA* 1.3 73.9 - - - +
102A LEU* 1.3 66.1 + - - +
104A VAL* 3.3 4.4 + - - +
105A ARG* 3.0 23.7 + - - +
148A LEU* 3.7 31.4 - - + +
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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
----------------------------------------------------------
39A GLY 4.0 9.6 - - - +
42A ILE* 4.3 7.9 - - + -
43A VAL* 3.9 16.4 - - + +
89A LEU* 3.9 28.5 - - + -
90A PRO* 3.7 34.3 - - + -
91A MET* 3.7 21.5 - - + -
93A VAL* 4.0 11.2 - - + -
98A ASP 2.9 14.2 + - - +
99A ALA* 3.3 9.6 - - - +
100A ALA 3.2 0.2 - - - -
101A ARG* 1.3 76.1 - - - +
103A ALA* 1.3 59.8 + - - +
105A ARG* 3.2 2.5 + - + +
106A MET* 2.9 47.2 + - + +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.9 11.4 - - + +
43A VAL* 4.3 2.7 - - + +
99A ALA 2.9 14.0 + - - +
100A ALA 3.5 4.3 - - - +
101A ARG 3.3 0.2 - - - -
102A LEU* 1.3 76.9 - - - +
104A VAL* 1.3 62.6 + - - +
106A MET* 3.3 13.7 + - - +
107A GLU* 3.1 29.2 + - - +
144A TRP* 3.4 44.2 - - + +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 3.0 15.7 + - - +
101A ARG* 3.7 7.2 - - - +
102A LEU 3.2 0.2 - - - -
103A ALA* 1.3 75.3 - - - +
105A ARG* 1.3 66.0 + - - +
107A GLU* 3.2 6.0 + - - +
108A ASN* 2.9 41.3 + - - +
141A ALA* 4.1 7.2 - - + +
144A TRP* 3.5 22.4 - - + -
145A ASN* 3.6 41.3 - - - +
148A LEU* 4.2 7.4 - - + -
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Residues in contact with ARG 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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90A PRO* 3.6 50.3 + - + +
91A MET* 4.9 8.8 - - - +
101A ARG 3.0 17.8 + - - +
102A LEU* 3.6 6.1 - - - +
104A VAL* 1.3 78.3 - - - +
106A MET* 1.3 57.9 + - - +
108A ASN* 3.5 7.4 + - - +
109A ASP* 2.9 53.8 + - - +
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Residues in contact with MET 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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35A ALA 4.2 2.5 - - - +
36A THR* 3.8 39.1 + - + +
39A GLY* 3.6 39.9 - - - -
40A TYR* 3.8 16.2 - - + +
43A VAL* 3.9 18.6 - - + -
62A HIS* 6.0 0.2 - - - -
89A LEU* 5.4 0.4 - - - -
90A PRO* 4.1 14.4 - - + -
102A LEU* 2.9 35.0 + - + +
103A ALA* 3.8 7.6 - - - +
105A ARG* 1.3 76.4 - - - +
107A GLU* 1.3 58.2 + - + +
109A ASP* 3.4 8.3 + - - +
110A GLY* 2.9 24.3 + - - -
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Residues in contact with GLU 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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36A THR* 5.2 0.2 - - - -
40A TYR* 2.6 28.8 + - + +
61A GLN* 4.8 0.2 - - - +
62A HIS* 2.7 36.5 + - - -
103A ALA 3.1 21.8 + - - +
104A VAL 3.7 0.4 - - - +
106A MET* 1.3 72.6 - - - +
108A ASN* 1.3 61.8 + - - +
110A GLY* 3.2 2.7 + - - -
111A ALA* 2.8 26.6 + - - +
137A SER* 3.4 41.2 + - - +
140A MET* 3.4 26.1 - - + +
141A ALA* 3.7 15.0 - - + +
144A TRP* 4.7 0.4 - - + -
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Residues in contact with ASN 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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104A VAL* 2.9 34.1 + - - +
105A ARG* 3.7 7.9 - - - +
107A GLU* 1.3 73.8 - - - +
109A ASP* 1.3 64.6 + - - +
111A ALA* 3.4 9.9 + - - +
112A THR* 3.1 25.7 + - - -
138A ALA* 5.7 1.8 - - - +
141A ALA* 3.5 20.6 - - - +
145A ASN* 5.4 0.2 - - - +
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Residues in contact with ASP 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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32A VAL* 4.2 14.3 - - + +
90A PRO* 4.2 8.1 - - - +
105A ARG* 2.9 60.4 + - - +
106A MET* 3.4 7.3 + - - +
108A ASN* 1.3 74.4 - - - +
110A GLY* 1.3 57.4 + - - +
112A THR* 3.4 9.6 + - - -
113A ALA* 3.1 26.7 + - - +
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Residues in contact with GLY 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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32A VAL* 3.9 17.0 - - - +
33A GLU* 5.2 2.7 - - - -
36A THR* 5.6 0.7 - - - -
62A HIS* 6.4 1.6 - - - -
106A MET 2.9 15.1 + - - -
107A GLU* 3.2 4.9 + - - -
109A ASP* 1.3 74.4 - - - +
111A ALA* 1.3 58.9 + - - +
113A ALA* 3.3 1.1 + - - -
114A TRP* 2.9 44.0 + - - -
137A SER* 3.9 7.0 - - - -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU 2.8 16.2 + - - +
108A ASN* 3.4 14.8 + - - +
110A GLY* 1.3 70.7 - - - +
112A THR* 1.3 54.5 + - - +
114A TRP* 3.3 1.8 + - - -
115A ARG* 2.8 46.3 + - - +
134A LEU* 3.9 26.3 - - + +
137A SER* 3.7 13.5 - - - -
138A ALA* 4.8 7.4 - - + +
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Residues in contact with THR 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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108A ASN 3.1 12.2 + - - -
109A ASP* 3.5 12.8 - - - -
110A GLY 3.3 0.2 - - - -
111A ALA* 1.3 78.9 - - - +
113A ALA* 1.3 60.3 + - - +
115A ARG* 3.7 20.9 + - - +
116A ALA* 3.4 18.7 + - - +
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Residues in contact with ALA 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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25A ALA 4.7 1.2 - - - +
28A ASP* 4.8 4.5 - - + +
29A ALA* 4.0 20.0 - - - +
32A VAL* 4.0 25.4 - - + -
109A ASP 3.1 16.9 + - - +
110A GLY 3.3 4.2 + - - +
111A ALA 3.3 0.2 - - - -
112A THR* 1.3 75.1 - - - +
114A TRP* 1.3 64.4 + - + +
116A ALA* 3.2 15.6 + - - +
117A VAL* 3.3 16.1 + - - +
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Residues in contact with TRP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.8 22.9 - - + -
29A ALA* 3.8 18.1 + - + +
32A VAL* 6.0 0.4 - - - +
33A GLU* 2.9 29.8 + - + +
65A ARG* 3.7 19.8 - - - +
69A VAL* 3.5 29.2 - - + -
110A GLY* 2.9 34.5 + - - +
111A ALA 3.9 0.4 - - - +
113A ALA* 1.3 74.4 - - + +
115A ARG* 1.3 65.0 + - - +
117A VAL* 3.2 16.4 + - + +
118A VAL* 3.0 24.9 + - - +
129A PHE* 3.7 18.6 - + - -
130A ALA* 3.7 33.9 - - + +
133A ALA* 3.5 15.0 - - + -
134A LEU* 3.8 15.0 - - - -
137A SER* 4.0 9.2 - - - -
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 2.8 25.8 + - - +
112A THR* 3.9 26.3 + - - +
113A ALA 3.4 0.2 - - - -
114A TRP* 1.3 73.1 - - - +
116A ALA* 1.3 61.7 + - - +
118A VAL* 3.4 4.5 + - + +
119A GLU* 3.1 25.1 + - - +
134A LEU* 3.9 33.7 - - + +
128B VAL* 4.1 29.7 - - + +
131B SER* 4.6 6.9 + - - +
132B THR* 4.7 9.7 + - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.8 12.5 - - + +
112A THR 3.4 10.2 + - - +
113A ALA* 3.2 12.9 + - - +
114A TRP 3.1 0.6 - - - -
115A ARG* 1.3 77.2 - - - +
117A VAL* 1.3 60.6 + - - +
119A GLU* 3.4 11.7 + - - +
120A HIS* 3.1 40.8 + - + +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 5.0 4.0 - - - +
25A ALA* 3.2 39.0 - - + +
26A LEU* 3.7 17.3 - - + +
29A ALA* 3.7 14.4 - - + -
72A MET* 5.9 1.3 - - + -
76A ARG* 5.6 2.2 - - - +
113A ALA 3.6 10.5 - - - +
114A TRP* 3.2 20.0 + - + +
116A ALA* 1.3 74.7 - - - +
118A VAL* 1.3 58.4 + - - +
121A ALA* 2.7 47.9 + - + +
126A ASP* 4.7 3.6 - - + +
130A ALA* 3.5 20.2 - - + -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP 3.0 19.0 + - - +
115A ARG* 3.6 7.9 - - - +
116A ALA 3.4 0.2 - - - -
117A VAL* 1.3 77.3 - - - +
119A GLU* 1.3 64.4 + - - +
121A ALA 3.8 1.0 + - - -
127A ARG* 3.6 26.0 - - - +
130A ALA* 3.7 6.0 - - + +
131A SER* 3.6 36.6 - - - +
134A LEU* 4.3 13.2 - - + -
118B VAL* 4.4 12.8 - - + -
127B ARG* 3.6 35.2 + - + +
128B VAL* 4.6 3.1 - - + +
131B SER* 4.0 10.3 - - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 3.1 17.8 + - - +
116A ALA* 3.5 13.3 - - - +
118A VAL* 1.3 79.3 - - - +
120A HIS* 1.3 80.7 + - + +
124B ALA* 3.6 21.3 - - + +
125B ASP* 5.8 0.3 - - - +
127B ARG* 2.8 24.3 + - - +
128B VAL* 3.7 21.3 - - + +
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.2 3.8 + - - +
21A ALA* 3.9 39.5 - - + +
22A ASP* 3.4 19.2 + - - +
25A ALA* 4.2 11.9 - - + -
116A ALA* 3.1 32.7 + - + +
117A VAL 3.6 0.4 - - - -
119A GLU* 1.3 101.1 + - + +
121A ALA* 1.3 64.9 + - - +
122A GLU* 3.4 7.1 + - - +
127B ARG* 5.1 0.2 - - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 3.4 14.1 - - - +
117A VAL* 2.7 28.9 + - + +
118A VAL 3.8 0.4 + - - -
119A GLU 3.6 1.0 - - - -
120A HIS* 1.3 72.2 - - - +
122A GLU* 1.3 63.8 + - - +
126A ASP* 4.0 13.0 - - + -
127A ARG* 3.4 47.3 + - + +
127B ARG* 4.2 7.4 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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