Contacts of the helix formed by residues 93 - 120 (chain A) in PDB entry 4P9U
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP* 3.0 38.4 + - + +
91A ALA 3.0 0.8 - - - -
92A GLU* 1.3 84.9 + - - +
94A ALA* 1.3 57.3 + - - +
95A THR* 3.0 7.6 - - - +
96A SER* 2.9 36.7 + - - +
97A ILE* 3.3 11.4 + - + +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 3.6 33.8 - - + +
90A ASP 3.3 4.3 + - - -
91A ALA* 2.9 19.0 + - - +
93A ASN* 1.3 74.8 - - - +
95A THR* 1.3 66.0 + - - +
96A SER 3.5 0.3 + - - -
97A ILE* 4.1 1.6 - - - -
98A VAL* 3.3 27.0 + - - +
263A TRP* 5.3 0.5 - - - -
270A LEU* 5.2 7.6 - - + -
274A PHE* 4.9 5.7 - - + -
275A THR* 3.9 15.7 - - + -
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 4.5 0.8 + - - -
92A GLU 4.4 9.9 + - - -
93A ASN* 4.6 3.4 - - - -
94A ALA* 1.3 81.4 - - - +
96A SER* 1.3 60.5 + - - +
98A VAL* 4.0 2.8 + - - +
99A GLU* 3.0 44.5 + - - +
263A TRP* 4.8 6.0 + - - +
267A LYS* 4.8 18.2 - - + +
270A LEU* 5.6 7.4 - - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 2.9 27.1 + - - +
95A THR* 1.3 79.5 - - - +
97A ILE* 1.3 73.6 + - - +
99A GLU* 2.9 25.3 + - - +
100A ASP* 3.0 20.5 + - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.8 24.8 - - + +
86A LEU* 3.7 34.5 - - + +
87A MET* 3.7 35.4 - - + +
90A ASP* 5.0 2.2 - - + +
93A ASN* 3.3 14.6 + - + +
94A ALA* 4.1 1.6 - - - +
95A THR 3.5 0.4 - - - -
96A SER* 1.3 84.0 + - - +
98A VAL* 1.3 64.3 + - - +
100A ASP* 2.9 22.1 + - - +
101A LEU* 3.0 11.3 + - - +
211A LEU* 3.9 24.6 - - + +
199B GLN* 5.0 5.6 - - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 4.2 16.4 - - + -
94A ALA 3.3 17.9 - - - +
95A THR 4.3 1.3 - - - +
96A SER 3.3 0.4 - - - -
97A ILE* 1.3 74.9 - - - +
99A GLU* 1.3 53.6 + - - +
101A LEU* 2.9 9.9 + - + +
102A LEU* 2.7 43.7 + - + +
211A LEU* 5.3 0.7 - - + -
215A VAL* 3.8 41.1 - - + -
263A TRP* 3.5 41.3 - - + +
274A PHE* 4.6 2.7 - - + -
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 3.0 40.4 - - - +
96A SER* 2.9 12.2 + - - +
98A VAL* 1.3 75.0 - - - +
100A ASP* 1.3 60.6 + - - +
102A LEU* 3.9 10.2 - - - +
103A ALA* 3.1 28.1 + - - +
263A TRP* 4.4 15.3 - - + +
267A LYS* 4.3 13.9 + - - -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 5.5 2.4 - - + +
96A SER* 3.0 19.7 + - - +
97A ILE* 2.9 14.4 + - + +
99A GLU* 1.3 77.5 - - - +
101A LEU* 1.3 58.2 + - - +
103A ALA 2.9 1.2 + - - -
104A ALA* 2.8 32.9 + - - +
197B GLY 3.6 15.6 - - - +
198B ASN* 3.3 34.0 + - - +
199B GLN* 3.7 27.3 + - + +
200B ILE* 3.9 9.0 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE 3.0 10.8 + - - +
98A VAL* 2.9 9.8 + - + +
100A ASP* 1.3 77.1 - - - +
102A LEU* 1.3 67.4 + - + +
104A ALA* 4.2 0.7 - - - +
105A ARG* 3.3 24.3 + - + +
208A LEU* 4.0 29.6 - - + +
211A LEU* 3.6 40.4 - - + +
212A TYR* 4.1 30.3 - - + -
215A VAL* 3.9 25.1 - - + -
200B ILE* 3.6 8.9 - - + +
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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
----------------------------------------------------------
98A VAL* 2.7 41.5 + - + +
99A GLU* 4.2 6.7 - - - +
101A LEU* 1.3 78.3 - - + +
103A ALA* 1.3 58.0 + - - +
105A ARG* 4.1 28.6 + - - +
106A THR* 2.5 36.2 + - - +
215A VAL* 5.0 10.3 - - + -
219A TYR* 6.5 0.2 - - + -
259A SER* 5.4 5.4 - - - +
260A GLY* 5.6 4.9 - - - -
263A TRP* 3.9 32.8 - - + -
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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
----------------------------------------------------------
99A GLU 3.1 20.3 + - - +
100A ASP* 2.9 4.6 + - - +
102A LEU* 1.3 75.1 - - - +
104A ALA* 1.3 60.7 + - - +
106A THR* 2.9 8.6 + - - -
107A ASN* 2.8 40.4 + - - +
198B ASN* 3.7 11.9 - - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP 2.8 19.3 + - - +
101A LEU 4.2 1.1 - - - +
103A ALA* 1.3 72.2 - - - +
105A ARG* 1.3 63.2 + - - +
107A ASN* 2.9 2.8 + - - +
108A ILE* 2.9 36.0 + - + +
208A LEU* 5.7 1.3 - - + -
198B ASN* 3.5 9.0 - - - +
200B ILE* 3.6 34.3 - - + -
201B TYR* 3.9 18.2 - - + +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.3 18.2 + - + +
102A LEU* 4.1 26.1 + - - +
103A ALA 3.3 0.4 - - - -
104A ALA* 1.3 79.7 - - - +
106A THR* 1.3 63.3 + - - +
108A ILE* 4.3 8.1 - - - -
109A SER* 2.2 45.0 + - - +
185A ASP* 3.6 11.5 + - - -
189A PHE* 3.6 33.2 - - + -
205A PHE* 4.1 12.3 - - + -
212A TYR* 2.9 41.0 + - + -
219A TYR* 6.3 0.8 - - - -
220A PHE* 6.1 0.2 - - - -
255A TYR* 3.7 26.1 + - - -
256A GLY* 6.3 0.2 - - - -
259A SER* 4.6 7.9 + - - -
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.5 24.7 + - - +
103A ALA* 2.9 7.9 + - - -
105A ARG* 1.3 82.7 + - - +
107A ASN* 1.3 64.5 + - - +
110A PRO* 3.4 16.7 - - - +
252A ILE* 3.8 30.5 - - + +
253A ARG* 4.5 11.7 - - + +
256A GLY* 4.1 19.3 - - - -
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 2.8 28.5 + - - +
104A ALA 2.9 2.4 + - - +
106A THR* 1.3 82.9 - - - +
108A ILE* 1.3 59.3 + - - +
109A SER 3.4 0.2 - - - -
110A PRO* 3.4 13.9 - - - +
111A ILE* 4.0 9.4 - - - +
111B ILE* 3.7 27.3 - - + +
115B TYR* 4.1 25.0 + - - -
198B ASN* 4.7 0.4 - - - +
201B TYR* 2.8 37.7 + - - +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 2.9 26.6 + - + +
105A ARG* 4.3 4.7 - - - +
107A ASN* 1.3 77.2 - - + +
109A SER* 1.3 65.7 + - - +
110A PRO 3.4 1.3 - - - -
111A ILE* 3.1 22.3 + - + +
112A PHE* 3.0 28.3 - - + -
201A TYR* 4.7 13.2 - - + +
204A ILE* 4.4 34.5 - - + -
205A PHE* 4.8 8.3 - - + -
108B ILE* 4.4 16.8 - - + -
111B ILE* 5.4 2.5 - - + -
200B ILE* 6.3 1.1 - - + -
201B TYR* 4.1 24.7 - - + +
204B ILE* 5.8 3.6 - - + -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 2.2 39.8 + - - +
106A THR* 4.5 0.2 - - - -
108A ILE* 1.3 73.1 - - - +
110A PRO* 1.3 72.4 - - - +
111A ILE 3.0 1.8 - - - -
112A PHE* 3.4 16.8 - - - -
113A MET* 3.1 36.8 + - - +
189A PHE* 3.6 10.1 - - - -
252A ILE* 3.5 20.9 - - - -
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR 3.4 16.4 - - - +
107A ASN 3.4 17.5 - - - +
109A SER* 1.3 91.6 - - - +
111A ILE* 1.3 64.3 + - + +
113A MET 4.3 0.4 - - - -
114A ARG* 3.6 24.4 + - - +
248A LEU* 3.6 20.7 - - + +
249A PRO* 4.6 16.8 - - + -
252A ILE* 3.4 18.1 - - + -
253A ARG* 5.8 3.1 - - + -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN 4.0 8.1 - - - +
108A ILE* 3.3 24.2 - - + +
109A SER 3.0 0.8 - - - -
110A PRO* 1.3 85.1 - - + +
112A PHE* 1.3 62.6 + - - +
114A ARG* 4.0 3.0 - - - +
115A TYR* 3.3 27.5 + - + -
201A TYR* 3.2 31.9 - - + +
107B ASN* 3.7 33.4 - - + +
108B ILE* 5.6 1.8 - - + -
111B ILE* 4.9 12.8 - - + -
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 3.0 24.1 + - + -
109A SER* 3.4 29.8 - - - -
111A ILE* 1.3 78.5 - - - +
113A MET* 1.3 99.0 + - + +
115A TYR* 3.5 3.0 + - - -
116A ALA* 2.9 27.7 + - - +
189A PHE* 3.7 17.7 - + - -
192A LEU 3.6 6.3 - - - -
193A ALA* 3.4 18.2 - - - -
196A SER* 3.3 19.7 - - - +
201A TYR* 3.8 36.3 - + + -
205A PHE* 3.7 32.5 - + - -
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Residues in contact with MET 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER* 3.1 22.4 + - - +
112A PHE* 1.3 97.9 - - + +
114A ARG* 1.3 54.2 + - - +
116A ALA* 3.0 7.2 + - - +
117A PHE* 2.7 52.3 + - + -
188A LEU* 4.3 2.7 - - + -
189A PHE* 3.6 37.0 - - + -
192A LEU* 4.1 26.0 - - + -
232A PHE* 5.1 1.1 - - + -
236A LEU* 4.0 30.1 - - + -
248A LEU* 4.5 5.6 - - + -
252A ILE* 3.9 17.5 - - + -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO 3.6 21.3 + - - +
111A ILE* 4.0 6.3 - - - +
112A PHE 3.4 0.4 - - - -
113A MET* 1.3 74.7 - - - +
115A TYR* 1.3 95.4 + - + +
117A PHE* 3.0 19.9 + - - +
118A LYS* 3.1 24.4 + - + +
245A ARG* 3.2 56.2 - - + +
248A LEU* 4.7 8.6 - - + +
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.3 23.5 + - + -
112A PHE* 3.5 8.4 + - - +
113A MET 3.3 0.4 - - - -
114A ARG* 1.3 108.0 + - + +
116A ALA* 1.3 63.5 + - - +
118A LYS* 3.0 7.8 + - - -
119A LEU* 2.9 43.3 + - + +
196A SER* 3.8 23.6 - - - +
198A ASN* 6.3 1.3 - - + -
201A TYR* 5.4 4.0 - + - -
107B ASN* 3.7 23.8 + - - -
253B ARG* 3.1 28.2 + - - -
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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
----------------------------------------------------------
112A PHE 2.9 18.2 + - - +
113A MET* 3.0 8.9 + - - +
115A TYR* 1.3 78.4 - - - +
117A PHE* 1.3 65.1 + - + +
120A ASN* 3.1 31.2 + - - +
124A ALA* 4.0 2.0 - - + +
192A LEU* 3.6 25.6 - - + +
195A HIS* 3.2 27.8 - - + +
196A SER* 4.1 0.4 - - - +
----------------------------------------------------------
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 2.7 34.8 + - + +
114A ARG* 3.0 9.8 + - - +
116A ALA* 1.3 78.9 - - + +
118A LYS* 1.3 61.3 + - + +
121A LYS* 3.4 26.2 - - - +
124A ALA* 4.1 3.4 - - + -
128A MET* 3.9 19.3 - - - -
192A LEU* 4.2 18.8 - - + -
236A LEU* 3.9 31.2 - - + -
239A VAL* 4.0 11.2 - - + -
240A CYS* 3.6 37.8 - - + +
243A GLY* 6.1 0.7 - - - -
245A ARG* 5.2 8.7 - - + -
248A LEU* 3.8 27.6 - - + -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.1 17.2 + - - +
115A TYR* 3.0 11.3 + - - +
117A PHE* 1.3 83.8 - - - +
119A LEU* 1.3 76.9 + - + +
121A LYS* 4.2 7.8 + - - +
245A ARG* 3.1 50.9 - - + +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 2.9 40.4 + - + +
118A LYS* 1.3 89.7 - - + +
120A ASN* 1.3 74.5 + - - +
121A LYS* 3.6 2.1 + - - +
195A HIS 5.0 2.7 - - - +
196A SER 4.2 13.7 - - - +
197A GLY* 4.9 8.1 - - - -
----------------------------------------------------------
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA 3.1 14.5 + - - +
119A LEU* 1.3 87.5 - - - +
121A LYS* 1.3 65.0 + - - +
122A GLU 3.5 1.8 - - - -
123A SER* 4.1 11.5 + - - +
124A ALA* 3.1 15.2 + - - +
195A HIS* 3.5 51.3 + - + +
197A GLY* 5.2 4.2 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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