Contacts of the helix formed by residues 111 - 133 (chain B) in PDB entry 4WNP
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 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B THR 4.3 0.2 + - - -
110B LEU* 1.3 76.4 - - - +
112B GLU* 1.3 60.0 + - - +
113B ASP* 3.5 8.7 + - - +
114B THR* 3.0 27.1 + - - -
115B ILE* 2.9 24.8 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU 3.8 0.2 + - - -
111B SER* 1.3 73.6 - - - +
113B ASP* 1.3 59.4 + - - +
115B ILE* 3.7 9.3 - - - +
116B ARG* 2.9 36.7 + - - +
215B LEU* 4.2 11.4 - - + +
246B GLU 4.3 1.6 - - - +
247B THR* 3.5 15.9 - - - +
248B SER* 2.7 47.7 + - - -
251B LEU* 3.5 24.3 - - + +
277B PHE* 3.8 11.1 - - + -
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 3.2 8.4 + - - +
112B GLU* 1.3 81.6 - - - +
114B THR* 1.3 57.3 - - - +
116B ARG* 2.8 27.8 + - - +
117B LEU* 3.0 26.3 + - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 5.6 2.9 - - + +
110B LEU* 4.0 17.3 - - + -
111B SER* 3.0 24.7 + - - -
113B ASP* 1.3 76.2 - - - +
115B ILE* 1.3 67.5 + - - +
117B LEU* 3.3 7.2 + - + +
118B PHE* 3.0 57.1 + - + -
156B PRO* 6.2 0.2 - - - +
157B ASN* 5.4 5.7 + - - -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 3.5 32.8 - - + +
111B SER 2.9 17.2 + - - +
112B GLU* 3.7 10.1 - - - +
114B THR* 1.3 77.6 - - - +
116B ARG* 1.3 56.9 + - - +
118B PHE* 3.8 5.6 - - - +
119B LEU* 2.8 28.7 + - + +
211B VAL* 3.7 33.7 - - + +
214B CYS* 3.9 10.1 - - + -
215B LEU* 3.7 41.3 - - + +
251B LEU* 4.5 4.7 - - + -
277B PHE* 4.3 12.6 - - + -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 2.9 20.9 + - - +
113B ASP* 2.8 35.5 + - - +
115B ILE* 1.3 75.1 - - - +
117B LEU* 1.3 67.1 + - - +
119B LEU* 4.5 0.9 - - - -
120B GLN* 2.8 52.9 + - + +
248B SER* 5.3 1.2 + - - -
250B PRO* 5.7 2.6 - - - +
277B PHE* 2.8 63.5 + - + +
278B LEU* 4.4 1.6 - - - -
279B ASP 4.1 11.3 + - - -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ASP 3.0 15.3 + - - +
114B THR* 3.3 12.1 + - + +
116B ARG* 1.3 78.5 - - - +
118B PHE* 1.3 75.5 + - + +
120B GLN* 3.6 15.0 + - - +
121B GLN* 3.1 43.2 + - + +
156B PRO 4.3 2.0 - - - +
157B ASN* 3.6 34.5 - - + +
159B ILE 4.0 11.2 - - - +
160B ARG* 4.3 11.7 - - - +
238D THR* 4.4 18.4 - - + +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 4.1 23.6 - - + -
103B TYR* 4.5 8.5 - + - -
110B LEU* 4.0 23.6 - - + -
114B THR* 3.0 40.0 + - + +
115B ILE* 3.8 4.3 - - - +
117B LEU* 1.3 95.5 - - + +
119B LEU* 1.3 56.4 + - - +
121B GLN* 3.2 8.0 + - - +
122B ILE* 3.0 36.6 + - + +
144B ILE* 6.1 0.7 - - + -
146B LEU* 4.5 10.5 - - + -
156B PRO 5.0 1.6 - - - -
159B ILE* 4.0 33.9 - - + -
161B VAL* 3.5 26.6 - - + +
214B CYS* 5.8 1.1 - - - -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 2.8 23.1 + - + +
116B ARG* 3.9 2.7 - - - +
118B PHE* 1.3 69.3 - - - +
120B GLN* 1.3 60.2 + - - +
121B GLN 3.1 1.6 - - - -
122B ILE* 4.2 16.6 - - + -
123B ALA* 2.8 32.6 + - - +
207B ILE* 3.7 28.9 - - + -
211B VAL* 3.7 26.9 - - + -
254B LEU* 3.8 27.6 - - + -
258B LEU* 5.7 0.7 - - + -
272B PHE* 4.0 14.6 - - + -
277B PHE* 4.1 13.2 - - + -
278B LEU* 3.9 13.2 - - + -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG* 2.8 37.0 + - + +
117B LEU* 3.8 17.5 - - - +
119B LEU* 1.3 76.6 - - - +
121B GLN* 1.3 60.7 + - + +
123B ALA* 3.5 4.7 + - - +
124B GLY* 3.1 22.0 + - - -
278B LEU* 2.5 46.9 + - + +
280B ALA* 3.8 15.4 - - + +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN* 3.0 40.5 + - - +
117B LEU* 3.1 36.0 + - + +
118B PHE* 3.2 8.0 + - - +
119B LEU 3.1 0.2 - - - -
120B GLN* 1.3 76.7 - - + +
122B ILE* 1.3 65.6 + - - +
124B GLY* 3.1 1.9 + - - -
125B ALA 3.1 17.5 + - - -
159B ILE 3.3 21.2 + - - -
160B ARG* 3.2 30.1 - - - +
161B VAL* 3.0 33.9 + - + +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN* 5.4 0.4 - - - -
100B LEU* 5.7 2.2 - - + -
118B PHE* 3.0 24.9 + - + +
119B LEU* 3.8 21.5 - - + +
121B GLN* 1.3 74.7 - - - +
123B ALA* 1.3 59.2 + - - +
125B ALA* 3.1 8.1 + - - +
126B MET* 2.8 40.9 + - + +
139B LEU* 6.0 1.3 - - + -
144B ILE* 4.3 30.1 - - + -
161B VAL* 4.3 9.4 - - + +
163B ILE* 4.3 15.5 - - + -
207B ILE* 4.6 19.1 - - + -
210B ILE* 5.2 14.1 - - + -
211B VAL* 6.3 0.7 - - + -
272B PHE* 5.3 0.2 - - + -
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU 2.8 21.5 + - - +
120B GLN 3.7 5.2 - - - +
122B ILE* 1.3 73.6 - - - +
124B GLY* 1.3 57.7 + - - +
126B MET* 3.3 0.4 + - - -
127B ARG* 2.9 31.6 + - - +
272B PHE* 3.6 32.9 - - + -
273B PHE* 3.7 11.2 - - + +
278B LEU* 3.9 19.3 - - + -
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS* 3.5 21.2 + - - -
74B ASN* 5.2 0.2 - - - -
120B GLN 3.1 14.9 + - - -
121B GLN* 3.1 5.5 + - - -
123B ALA* 1.3 76.1 - - - +
125B ALA* 1.3 60.4 + - - +
127B ARG* 3.2 19.5 + - - +
128B LEU* 3.3 9.2 + - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS* 3.8 13.0 - - - -
74B ASN* 3.6 26.9 - - + +
75B ILE* 3.9 11.7 - - + -
121B GLN 3.1 9.5 + - - +
122B ILE 3.1 8.9 + - - +
124B GLY* 1.3 76.6 - - - +
126B MET* 1.3 61.0 + - - +
128B LEU* 3.1 5.6 + - - +
129B LEU* 3.0 28.4 + - + +
163B ILE* 3.7 16.8 - - + -
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 2.8 29.6 + - + +
123B ALA* 3.8 5.8 - - - +
124B GLY 3.3 0.2 - - - -
125B ALA* 1.3 73.1 - - - +
127B ARG* 1.3 57.4 + - - +
129B LEU* 3.8 25.1 - - + +
130B HIS* 2.9 32.4 + - - +
134B ILE 5.7 0.9 - - - +
139B LEU* 4.1 17.3 - - - -
163B ILE* 4.2 12.1 - - - -
203B ASP* 3.9 33.4 - - + +
207B ILE* 3.7 22.9 - - + -
269B PHE* 4.4 18.2 - - + -
272B PHE* 4.4 4.9 - - + -
273B PHE* 3.8 12.6 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ALA* 2.9 15.6 + - - +
124B GLY* 3.4 14.1 - - - +
125B ALA 3.2 0.2 - - - -
126B MET* 1.3 78.1 - - - +
128B LEU* 1.3 60.5 + - - +
130B HIS* 3.9 1.4 - - - +
131B SER* 3.0 26.0 + - - -
273B PHE* 3.3 58.1 + - + +
274B HIS* 3.9 29.3 + - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU 5.0 0.2 - - - +
70B LEU* 4.0 23.6 - - + -
71B LYS 3.6 27.4 - - - +
72B HIS* 3.8 28.3 - - + -
75B ILE* 4.2 4.3 - - + -
124B GLY 3.3 2.4 + - - +
125B ALA* 3.1 9.2 + - - +
127B ARG* 1.3 77.8 - - - +
129B LEU* 1.3 65.9 + - - +
131B SER* 2.9 25.8 + - - +
132B LYS* 3.0 24.6 + - - +
245D ARG* 3.7 33.2 - - - +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 4.5 6.7 - - + -
75B ILE* 3.6 27.1 - - + -
125B ALA* 3.0 28.2 + - + +
126B MET* 3.8 27.4 - - + +
128B LEU* 1.3 75.4 - - - +
130B HIS* 1.3 63.0 + - - +
132B LYS* 3.0 6.8 + - - +
133B GLY 3.0 5.0 + - - -
134B ILE* 2.9 51.7 + - + +
136B HIS* 3.9 31.2 - - + +
163B ILE* 5.4 2.0 - - + -
166B PHE* 3.9 22.4 - - + -
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Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 5.6 7.9 + - - -
302A GOL 4.1 10.4 + - - -
126B MET* 2.9 19.3 + - + +
127B ARG 3.9 2.7 - - - +
129B LEU* 1.3 77.2 - - - +
131B SER* 1.3 63.7 + - - +
133B GLY* 3.1 13.5 + - - +
134B ILE 4.7 4.7 - - - +
269B PHE* 3.3 56.8 - + + +
273B PHE* 4.1 15.5 - + + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS* 6.2 1.4 - - - -
174A SER* 4.7 2.3 - - - -
302A GOL 3.5 20.5 + - - -
127B ARG* 3.0 15.4 + - - -
128B LEU* 2.9 27.2 + - - +
130B HIS* 1.3 78.7 - - - +
132B LYS* 1.3 62.2 + - - +
133B GLY 3.3 0.2 - - - -
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN* 5.5 0.2 - - - +
174A SER* 2.8 44.1 + - - +
302A GOL 3.8 6.0 + - - -
69B GLU* 3.3 35.9 + - + +
70B LEU* 4.1 11.9 - - + -
128B LEU* 3.0 34.1 + - + +
129B LEU 3.0 9.9 + - - +
131B SER* 1.3 82.6 - - - +
133B GLY* 1.3 58.4 + - - +
134B ILE* 3.8 17.3 - - + -
171B TYR* 3.6 10.5 - - - +
245D ARG* 4.2 14.1 - - - +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A GOL 3.6 23.3 - - - -
129B LEU 3.0 2.8 + - - -
130B HIS* 3.1 10.1 + - - -
131B SER 3.3 1.0 + - - -
132B LYS* 1.3 78.6 - - - +
134B ILE* 1.3 60.3 + - - +
135B ILE* 5.4 1.6 - - - -
171B TYR* 3.3 6.4 - - - +
172B LEU* 2.9 37.5 + - - +
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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