Contacts of the helix formed by residues 90 - 115 (chain A) in PDB entry 2L6X
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 PRO 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 4.2 18.6 - - + +
82A VAL* 6.0 2.7 - - + -
89A SER* 1.3 93.2 + - - +
91A THR* 1.3 65.3 + - - +
92A VAL* 3.1 18.3 + - + +
93A PHE* 3.2 20.8 + - + +
94A ARG* 4.1 2.1 + - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TRP* 3.4 33.7 - - + -
89A SER* 3.0 3.5 + - - +
90A PRO* 1.3 67.0 - - - +
92A VAL* 1.3 61.4 + - - +
93A PHE 2.9 3.7 + - - -
94A ARG* 3.0 14.5 + - - +
95A TYR* 2.7 38.3 + - - +
137A PHE* 6.4 2.7 - - - -
141A GLY 5.9 3.8 - - - +
142A GLU* 6.1 2.1 - - - -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 3.9 20.0 - - + -
91A THR* 1.3 83.1 + - - +
93A PHE* 1.3 70.2 + - + +
95A TYR* 4.3 11.7 - - + -
96A ILE* 3.0 46.2 + - + +
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 3.4 23.3 + + - +
79A MET* 3.4 40.4 - - + -
90A PRO* 3.2 11.9 + - + +
91A THR 3.0 0.6 - - - -
92A VAL* 1.3 92.9 - - + +
94A ARG* 1.3 56.3 + - - +
96A ILE* 4.0 5.6 - - + +
97A ASP* 2.7 38.3 + - - +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 4.1 2.6 - - - -
76A TYR* 3.4 52.6 + - + +
79A MET* 3.9 19.6 + - + +
80A ARG* 3.1 44.4 - - - +
83A TRP* 3.4 52.5 - - - +
89A SER* 4.9 1.6 + - - -
90A PRO 4.1 1.3 + - - +
91A THR* 3.0 17.8 + - - +
93A PHE* 1.3 79.9 - - - +
95A TYR* 1.3 57.2 + - - +
97A ASP* 3.9 4.8 - - - +
98A TRP* 2.9 33.4 + - - +
137A PHE* 5.1 18.3 - - + -
223A TYR* 5.9 0.8 - - - -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 2.7 24.0 + - - +
92A VAL* 3.8 10.3 - - + -
94A ARG* 1.3 71.6 - - - +
96A ILE* 1.3 87.6 + - + +
98A TRP* 3.8 7.0 - - - +
99A LEU* 2.8 54.3 + - + +
134A MET* 3.4 43.6 - - + +
137A PHE* 5.6 10.7 - + + -
138A GLY* 5.8 6.3 - - - -
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Residues in contact with ILE 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 VAL* 3.0 29.3 + - + +
93A PHE* 4.1 5.8 - - + +
95A TYR* 1.3 93.7 - - + +
97A ASP* 1.3 57.4 + - - +
99A LEU* 3.5 7.6 - - + +
100A LEU* 2.7 52.4 + - + +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.5 2.1 - - - +
72A ALA* 3.8 7.6 - - - +
75A HIS* 3.1 42.9 + - + +
76A TYR* 3.5 26.5 - - - +
93A PHE 2.7 24.1 + - - +
94A ARG 3.9 1.5 - - - +
96A ILE* 1.3 72.9 - - - +
98A TRP* 1.3 53.7 + - - +
100A LEU* 3.1 6.4 + - - +
101A THR* 2.6 60.7 + - - +
231A LYS* 4.8 0.3 - - - -
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Residues in contact with TRP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 4.5 15.3 - + + -
94A ARG 2.9 22.4 + - - +
95A TYR* 3.8 4.3 - - - +
97A ASP* 1.3 80.8 + - - +
99A LEU* 1.3 56.3 + - - +
101A THR* 3.3 8.1 - - - -
102A VAL* 2.8 60.9 + - + +
105A LEU* 6.2 0.2 - - + -
130A GLY 6.0 0.2 - - - -
133A VAL* 3.9 18.4 - - + -
134A MET* 4.2 21.3 - - + -
137A PHE* 3.6 42.8 - + + -
197A TRP* 6.2 1.3 - + - -
301A RET 3.1 80.2 - - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 2.8 54.2 + - + +
96A ILE* 3.5 5.4 - - + +
98A TRP* 1.3 76.7 - - - +
100A LEU* 1.3 57.7 + - - +
101A THR 3.5 0.2 - - - -
102A VAL* 4.7 4.0 - - + -
103A PRO* 2.9 30.8 - - + +
130A GLY 5.8 0.9 - - - +
131A SER* 4.9 14.8 - - - +
134A MET* 4.3 24.5 - - + -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 6.5 0.7 - - + -
96A ILE* 2.7 30.6 + - + +
97A ASP* 3.7 5.4 - - - +
99A LEU* 1.3 79.9 - - - +
101A THR* 1.3 67.0 + - + +
102A VAL 3.6 0.2 - - - -
103A PRO* 3.9 5.0 - - - +
104A LEU* 2.9 53.7 + - + +
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Residues in contact with THR 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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68A VAL* 4.2 9.0 - - + +
71A ILE* 5.8 3.4 - - + -
72A ALA* 3.2 37.7 - - + +
97A ASP* 2.6 37.6 + - - +
98A TRP* 3.2 15.6 + - - -
100A LEU* 1.3 90.8 - - + +
102A VAL* 1.3 58.4 + - - +
103A PRO 3.5 0.4 - - - -
104A LEU* 3.7 5.2 - - + -
105A LEU* 2.7 43.8 + - - +
231A LYS* 4.7 3.5 - - - -
301A RET 5.1 0.2 - - - +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 2.8 53.9 + - + +
99A LEU* 4.7 5.2 - - + -
101A THR* 1.3 77.2 + - - +
103A PRO* 1.3 69.1 - - + +
105A LEU* 3.3 9.3 - - + +
106A ILE* 2.9 42.4 + - + +
126A LYS* 4.9 8.3 - - + +
127A LEU* 6.3 0.2 - - - -
130A GLY* 4.7 21.1 - - - +
197A TRP* 6.4 2.2 - - + -
301A RET 5.4 3.4 - - + -
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Residues in contact with PRO 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 LEU* 2.9 33.4 - - + +
100A LEU* 4.2 5.8 - - - +
101A THR 3.6 0.4 - - - -
102A VAL* 1.3 103.7 - - + +
104A LEU* 1.3 60.0 + - + +
106A ILE* 4.5 4.5 - - + -
107A CYS* 2.8 33.8 + - - +
123A LEU* 4.2 9.7 - - + +
126A LYS* 6.5 0.2 - - + -
127A LEU* 5.6 12.1 - - + -
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Residues in contact with LEU 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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68A VAL* 3.6 20.2 - - + -
100A LEU* 2.9 45.5 - - + +
101A THR* 3.8 0.7 - - + +
102A VAL 3.2 0.4 - - - -
103A PRO* 1.3 80.7 - - + +
105A LEU* 1.3 60.7 + - - +
107A CYS* 6.0 0.2 - - + -
108A GLU* 2.6 61.1 + - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER* 4.9 0.7 + - - -
68A VAL* 3.3 29.3 - - + +
69A THR* 4.6 10.1 - - - +
72A ALA* 5.9 0.4 - - + -
101A THR* 2.7 40.2 + - - +
102A VAL* 3.3 12.1 - - + +
104A LEU* 1.3 74.3 - - - +
106A ILE* 1.3 82.1 + - + +
108A GLU* 4.1 0.4 - - - +
109A PHE* 3.0 32.6 + - + +
193A ILE* 6.3 1.8 - - + -
230A ASN 5.9 2.2 - - - +
231A LYS* 5.8 4.7 - - + -
234A PHE* 4.3 25.8 - - + -
301A RET 5.3 15.9 - - + -
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 2.9 28.3 + - + +
103A PRO* 4.3 3.1 - - + +
105A LEU* 1.3 96.1 - - + +
107A CYS* 1.3 68.9 + - - +
109A PHE* 3.2 6.5 + - + +
110A TYR* 2.8 45.8 + - + -
123A LEU* 4.7 8.7 - - + -
126A LYS* 3.3 57.7 - - + -
189A MET* 6.4 1.3 - - - -
193A ILE* 5.8 7.9 - - + -
197A TRP* 6.4 2.0 - - + -
234A PHE* 6.0 0.9 - - + -
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Residues in contact with CYS 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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103A PRO 2.8 23.3 + - - +
104A LEU 4.1 0.2 - - - +
106A ILE* 1.3 77.4 - - - +
108A GLU* 1.3 65.7 + - - +
110A TYR* 3.6 4.0 - - - +
111A LEU* 2.7 44.8 + - - +
123A LEU* 3.4 38.8 - - + -
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Residues in contact with GLU 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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64A VAL* 3.6 43.5 - - + +
65A SER 4.8 0.4 - - - +
68A VAL* 5.3 2.0 - - + -
104A LEU* 2.6 54.9 + - + +
105A LEU* 4.1 2.5 - - - +
107A CYS* 1.3 88.1 - - - +
109A PHE* 1.3 67.7 + - - +
111A LEU* 2.9 27.6 + - + +
112A ILE* 3.0 18.0 + - - +
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Residues in contact with PHE 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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58A TRP* 4.5 11.0 - + - -
61A SER* 4.5 9.0 + - - -
64A VAL* 4.7 2.0 - - - +
65A SER* 4.4 23.5 + - - +
105A LEU 3.0 22.6 + - - +
106A ILE* 3.6 6.1 - - + +
108A GLU* 1.3 74.9 - - - +
110A TYR* 1.3 80.1 + + - +
112A ILE* 4.3 1.6 - - - +
113A LEU* 3.0 56.4 + - + +
185A ALA* 4.6 6.1 - - + -
186A TYR* 5.7 2.0 - + - -
189A MET* 3.8 29.8 - - + -
234A PHE* 4.6 7.9 - + + -
238A ILE* 3.5 40.8 - - + -
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Residues in contact with TYR 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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106A ILE* 2.8 40.7 + - + +
107A CYS* 3.9 4.3 - - - +
109A PHE* 1.3 88.0 - + - +
111A LEU* 1.3 56.5 + - - +
113A LEU* 4.0 18.6 - - + -
114A ALA* 2.7 39.0 + - - +
120A ALA* 3.6 22.9 - - + +
122A SER* 2.9 37.0 - - - -
123A LEU* 5.2 2.2 - - + +
126A LYS* 3.6 26.9 + - + -
166A LEU* 3.5 26.5 - - + +
186A TYR* 4.5 13.5 - + - -
189A MET* 5.7 3.2 - - + +
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Residues in contact with LEU 111 (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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64A VAL* 5.7 2.9 - - + -
107A CYS* 2.7 29.8 + - - +
108A GLU* 2.9 23.2 + - + +
110A TYR* 1.3 73.9 - - - +
112A ILE* 1.3 68.3 + - + +
114A ALA* 3.6 1.7 - - - +
115A ALA* 2.7 35.0 + - + +
118A ASN 4.8 1.6 - - - +
119A VAL* 4.7 19.0 - - + +
120A ALA 5.4 2.9 - - - +
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Residues in contact with ILE 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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57A LYS* 4.3 11.3 - - - +
60A THR* 3.8 27.1 - - + +
61A SER* 3.2 39.3 - - - +
64A VAL* 3.6 33.2 - - + -
108A GLU 3.0 5.8 + - - +
109A PHE 4.4 0.2 - - - +
111A LEU* 1.3 91.5 - - + +
113A LEU* 1.3 63.7 + - - +
115A ALA* 3.1 22.2 + - + +
116A ALA* 4.1 1.7 + - - +
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Residues in contact with LEU 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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58A TRP* 5.3 12.6 - - + -
61A SER* 4.2 4.6 + - - +
109A PHE* 3.0 54.1 + - + +
110A TYR* 3.8 17.3 - - + +
112A ILE* 1.3 80.1 - - - +
114A ALA* 1.3 61.9 + - + +
115A ALA 3.1 0.4 + - - -
116A ALA* 3.6 15.1 + - - +
182A VAL* 3.2 45.9 - - + +
185A ALA* 5.4 2.0 - - + -
186A TYR* 4.9 16.2 - - + +
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Residues in contact with ALA 114 (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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110A TYR 2.7 17.7 + - - +
111A LEU 4.1 0.2 - - - +
113A LEU* 1.3 71.8 - - + +
115A ALA* 1.3 49.6 + - - +
116A ALA 2.9 5.8 - - - -
117A THR* 2.8 21.7 + - + +
118A ASN 2.7 32.1 + - - -
119A VAL* 3.2 8.5 - - - +
120A ALA* 3.0 41.7 - - + +
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Residues in contact with ALA 115 (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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57A LYS* 5.6 3.2 - - - -
111A LEU* 2.7 16.4 + - + +
112A ILE* 3.1 26.9 - - + +
113A LEU 3.1 0.4 - - - -
114A ALA* 1.3 78.1 - - - +
116A ALA* 1.3 61.4 + - - +
117A THR 3.1 2.1 + - - -
118A ASN* 3.8 15.0 + - - -
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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