Contacts of the helix formed by residues 102 - 124 (chain D) in PDB entry 2OCP
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 GLU 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D MET* 2.9 13.6 + - - +
99D MET 3.7 2.2 - - - -
101D ARG* 1.3 86.5 - - + +
103D PRO* 1.3 61.2 - - - +
104D ALA 3.2 2.5 - - - -
105D ARG* 2.8 34.5 + - + +
106D TRP* 2.9 27.6 + - + -
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Residues in contact with PRO 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D MET* 3.1 21.7 - - + +
100D TYR 3.6 10.8 - - - +
101D ARG 3.5 9.0 - - - +
102D GLU* 1.3 87.3 - - - +
104D ALA* 1.3 64.0 + - + +
105D ARG 3.0 0.2 - - - -
107D SER* 2.4 37.0 + - - +
155D LEU* 5.3 0.4 - - + -
160D SER* 3.2 23.1 - - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ARG* 3.0 19.6 + - - -
102D GLU 3.2 1.4 + - - -
103D PRO* 1.3 83.6 - - + +
105D ARG* 1.3 57.7 + - - +
107D SER 4.9 0.2 - - - -
159D GLY 4.8 9.9 - - - +
160D SER* 3.5 18.1 - - - +
165D GLU* 4.6 2.6 - - - +
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Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA 3.1 25.3 + - - -
105C ARG* 3.0 52.1 + - - +
165C GLU* 3.4 13.5 + - - -
102D GLU* 2.8 28.5 + - + +
104D ALA* 1.3 81.3 - - - +
106D TRP* 1.3 116.0 + - - +
107D SER 3.8 0.7 - - - -
108D TYR* 5.4 1.1 + - - +
109D THR* 4.3 5.9 + - - -
165D GLU* 5.1 1.5 - - - +
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Residues in contact with TRP 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C SER* 4.4 9.2 - - - -
164C ILE* 5.7 5.6 - - + -
165C GLU* 3.8 23.3 - - + -
95D LEU* 4.5 7.9 - - + -
98D MET* 3.8 42.6 - - + +
99D MET* 3.9 21.8 - - - +
102D GLU* 2.9 22.2 + - + -
105D ARG* 1.3 134.0 - - + +
107D SER* 1.3 60.2 + - - +
108D TYR 3.4 2.0 - - - -
109D THR* 3.4 35.2 + - + -
110D PHE* 2.8 32.0 + - - +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D MET* 3.9 7.4 - - - +
103D PRO* 2.4 34.0 + - - +
104D ALA 4.9 0.2 - - - -
105D ARG 3.8 0.8 - - - -
106D TRP* 1.3 75.9 - - - +
108D TYR* 1.3 65.9 + - - +
110D PHE* 3.1 7.3 + - - +
111D GLN* 2.9 27.5 + - - +
155D LEU* 3.8 23.4 - - - +
160D SER* 3.4 23.4 - - - -
161D LEU* 3.9 7.0 - - - -
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Residues in contact with TYR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C TYR* 4.2 9.0 - + - -
109C THR* 3.6 30.1 - - + -
112C THR* 2.7 31.6 + - - -
105D ARG 5.4 1.1 + - - +
106D TRP 3.4 0.4 - - - -
107D SER* 1.3 77.0 - - - +
109D THR* 1.3 69.9 + - - +
111D GLN* 3.0 14.5 + - - +
112D THR* 3.0 39.2 + - + +
161D LEU* 3.2 15.8 - - + +
165D GLU* 3.3 58.3 + - + +
168D ILE* 3.0 17.8 - - + +
169D TYR* 3.9 21.1 - + + -
172D TRP* 4.3 4.9 - - - -
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Residues in contact with THR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C TYR* 3.8 23.8 - - + -
109C THR* 5.7 0.2 + - - -
164C ILE* 4.9 3.1 - - + -
165C GLU* 4.6 4.1 + - + -
168C ILE* 3.7 25.6 - - + -
95D LEU* 4.4 7.9 - - + -
105D ARG* 4.3 6.6 + - - -
106D TRP* 3.4 42.6 + - + +
107D SER 3.3 0.4 - - - -
108D TYR* 1.3 83.1 - - - +
110D PHE* 1.3 62.3 + - - +
112D THR* 2.8 24.7 + - - -
113D PHE* 3.2 7.4 + - - +
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Residues in contact with PHE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D TRP* 4.1 38.4 - + + -
95D LEU* 3.8 35.8 - - + +
96D LEU* 3.7 31.0 - - + -
99D MET* 4.0 14.8 - - + -
106D TRP 2.8 21.4 + - - +
107D SER* 3.4 5.2 - - - +
109D THR* 1.3 72.7 - - - +
111D GLN* 1.3 66.4 + - - +
113D PHE* 2.9 14.8 + + - +
114D SER* 2.9 20.2 + - - -
301D DTP 3.3 51.8 - + - -
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Residues in contact with GLN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D SER 2.9 11.8 + - - +
108D TYR* 3.5 11.4 - - + +
110D PHE* 1.3 77.7 - - - +
112D THR* 1.3 58.1 + - - +
114D SER* 3.1 8.9 + - - -
115D PHE* 2.8 33.7 + - - +
147D ASP* 3.4 9.2 - - - +
151D PHE* 3.8 0.3 - - - +
152D ALA* 3.7 31.9 - - + -
155D LEU* 3.1 31.8 - - + +
161D LEU* 5.1 4.7 - - + -
169D TYR* 3.7 20.0 - - + -
301D DTP 2.8 43.9 + - - -
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C TYR* 2.8 26.8 + - + +
112C THR* 5.3 2.5 - - + -
168C ILE* 3.9 2.4 - - - +
172C TRP* 3.2 28.7 + - - +
108D TYR* 3.0 52.4 + - + +
109D THR* 2.8 14.7 + - - -
110D PHE 3.2 0.2 - - - -
111D GLN* 1.3 77.7 - - + +
113D PHE* 1.3 61.0 + - - +
115D PHE* 4.6 4.3 - - - -
116D LEU* 3.3 13.7 + - - +
169D TYR* 5.2 5.2 - - + -
172D TRP* 6.3 0.9 - - + -
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C HIS* 5.0 13.7 - + - -
168C ILE* 3.8 33.0 - - + -
171C ASP* 5.3 9.0 - - - -
71D PRO* 5.8 0.2 - - + -
74D THR* 3.9 25.8 - - + -
75D TRP* 3.1 39.0 - + - -
78D ILE* 4.5 12.8 - - + -
95D LEU* 3.9 25.4 - - + -
109D THR 3.2 3.6 + - - +
110D PHE* 2.9 9.6 + + - +
112D THR* 1.3 82.0 + - - +
114D SER* 1.3 62.4 - - - +
116D LEU* 3.9 9.9 - - + +
117D SER* 3.2 25.2 + - - -
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Residues in contact with SER 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D TRP* 4.3 17.9 - - - +
110D PHE* 2.9 28.7 + - - -
111D GLN* 3.1 19.2 + - - -
113D PHE* 1.3 75.9 - - - +
115D PHE* 1.3 62.0 + - - +
117D SER* 3.3 6.2 + - - -
118D ARG* 2.9 43.6 + - - +
147D ASP* 2.5 25.4 + - - -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C TRP* 3.8 27.4 - + - -
111D GLN 2.8 19.0 + - - +
112D THR* 4.2 3.1 - - - +
114D SER* 1.3 77.9 + - - +
116D LEU* 1.3 62.2 + - - +
118D ARG* 3.3 2.1 + - - -
119D LEU* 2.9 31.5 + - + +
144D VAL* 3.7 29.4 - - + -
147D ASP* 3.5 19.5 - - + +
169D TYR* 4.3 9.2 - + + -
172D TRP* 4.6 4.7 - - + -
173D HIS* 3.3 56.8 - + - -
176D LEU* 4.2 11.4 - - + -
177D LEU* 4.2 14.1 - - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ILE* 5.5 0.4 - - + -
171C ASP* 3.4 33.0 - - + +
172C TRP* 3.5 52.0 - - + +
175C PHE* 3.8 33.4 - - + -
112D THR 3.3 16.7 + - - +
113D PHE* 3.9 14.8 - - + +
115D PHE* 1.3 78.1 - - - +
117D SER* 1.3 58.4 + - - +
119D LEU* 3.2 5.5 + - + +
120D LYS* 2.8 40.7 + - + +
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 5.2 0.2 + - - -
71D PRO* 3.0 37.5 - - - +
75D TRP* 4.7 4.9 - - - -
113D PHE* 3.2 22.8 + - - -
114D SER* 3.5 7.0 - - - -
116D LEU* 1.3 81.8 - - - +
118D ARG* 1.3 63.4 + - - +
120D LYS* 3.2 11.4 + - - +
121D VAL* 3.2 22.9 + - - +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 3.0 40.5 + - - +
75D TRP* 3.9 11.6 - - + -
114D SER* 2.9 25.4 + - - +
115D PHE* 3.8 3.6 - - - +
117D SER* 1.3 74.6 - - - +
119D LEU* 1.3 60.7 + - - +
121D VAL* 3.0 27.6 - - + +
122D GLN* 3.2 14.1 + - - +
142D ARG* 3.8 22.3 - - - +
143D SER* 3.4 24.7 + - - +
144D VAL* 3.9 17.3 - - + +
147D ASP* 2.8 38.7 + - - +
151D PHE* 4.8 0.2 - - - -
301D DTP 2.8 47.9 + - - -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C TRP* 5.1 3.6 - - + -
175C PHE* 4.5 12.1 - - + -
115D PHE* 2.9 24.9 + - + +
116D LEU* 3.6 4.9 - - + +
118D ARG* 1.3 75.4 - - - +
120D LYS* 1.3 67.0 + - - +
122D GLN* 3.2 2.4 + - - -
123D LEU* 3.1 40.2 + - + +
144D VAL* 3.6 18.1 - - + +
176D LEU* 4.0 23.8 - - + -
177D LEU* 4.2 9.2 - - + -
180D PHE* 4.0 28.3 - - + -
184D ILE* 3.9 26.7 - - + -
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ASP* 2.7 32.0 + - - -
175C PHE* 4.0 48.7 - - + +
116D LEU* 2.8 29.2 + - + +
117D SER* 3.5 8.7 - - - +
119D LEU* 1.3 76.2 - - - +
121D VAL* 1.3 63.4 + - - +
123D LEU* 2.9 14.5 + - - +
124D GLU* 3.1 20.4 + - + +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ALA* 3.6 29.4 - - + -
69D THR* 4.8 11.7 - - + +
70D GLU* 6.1 0.9 - - - +
71D PRO* 6.4 1.8 - - + -
117D SER 3.2 7.4 + - - +
118D ARG* 3.0 24.7 - - + +
120D LYS* 1.3 79.6 - - - +
122D GLN* 1.3 66.3 + - + +
123D LEU 3.4 0.7 + - - -
124D GLU* 3.5 34.5 + - - +
138D GLN* 5.6 1.9 + - - -
140D PHE* 3.6 22.2 - - + -
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 2.9 34.9 + - - +
118D ARG* 3.5 14.3 - - - +
119D LEU* 3.2 6.8 + - - +
120D LYS 3.2 0.8 - - - -
121D VAL* 1.3 81.5 - - - +
123D LEU* 1.3 60.4 + - - +
124D GLU 3.5 3.1 - - - +
140D PHE* 3.8 24.9 - - + -
142D ARG 4.9 0.5 - - - +
143D SER* 4.1 5.6 - - - -
144D VAL* 3.4 35.8 + - - +
145D TYR* 4.5 3.6 - - - -
183D ARG 3.3 9.0 - - - +
184D ILE* 3.2 35.6 + - + +
186D LEU* 3.8 25.2 - - + +
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 3.9 27.8 - - + -
179C GLU* 4.7 3.1 - - - +
119D LEU* 3.1 19.9 + - + +
120D LYS* 2.9 8.7 + - - +
122D GLN* 1.3 77.6 - - - +
124D GLU* 1.3 66.9 + - - +
125D PRO* 3.7 4.3 - - - +
180D PHE* 3.9 39.0 - - + -
183D ARG* 3.7 52.4 + - + +
184D ILE* 3.6 27.4 - - + -
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 5.5 1.2 + - - -
120D LYS* 3.1 15.6 + - + +
121D VAL* 3.5 39.0 + - + +
122D GLN 4.3 4.3 - - - +
123D LEU* 1.3 81.0 - - - +
125D PRO* 1.3 79.3 - - + +
126D PHE* 4.0 5.9 + - - -
138D GLN* 5.4 3.1 + - - +
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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