Contacts of the helix formed by residues 111 - 133 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D THR 4.4 0.2 + - - -
110D LEU* 1.3 78.2 - - - +
112D GLU* 1.3 63.5 + - - +
113D ASP* 3.4 10.6 + - - +
114D THR* 3.2 27.0 + - - -
115D ILE* 3.0 20.7 + - - +
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Residues in contact with GLU 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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111D SER* 1.3 75.0 - - - +
113D ASP* 1.3 59.2 + - - +
114D THR 3.4 0.2 - - - -
115D ILE* 4.2 7.9 - - - -
116D ARG* 2.9 35.4 + - - +
215D LEU* 4.8 9.1 - - + +
246D GLU 4.5 1.0 - - - +
247D THR* 3.5 11.8 - - - +
248D SER* 2.5 51.7 + - - -
251D LEU* 3.5 25.3 - - + +
277D PHE* 3.5 12.9 - - + -
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SER* 3.2 8.7 + - - +
112D GLU* 1.3 76.5 - - - +
114D THR* 1.3 60.3 + - - +
116D ARG* 3.0 26.8 + - - +
117D LEU* 3.1 26.0 + - - +
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Residues in contact with THR 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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103D TYR* 5.2 2.0 - - + +
110D LEU* 4.2 21.3 - - + -
111D SER* 3.2 20.4 + - - -
113D ASP* 1.3 75.3 - - - +
115D ILE* 1.3 68.2 + - - +
117D LEU* 3.1 7.2 + - + +
118D PHE* 2.9 56.0 + - + -
156D PRO* 4.6 19.7 - - + +
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU* 3.6 22.0 - - + +
111D SER 3.0 23.7 + - - +
112D GLU* 3.7 8.1 - - - +
114D THR* 1.3 76.2 - - - +
116D ARG* 1.3 57.3 + - - +
118D PHE* 3.3 5.5 + - - +
119D LEU* 2.8 34.8 + - + +
211D VAL* 3.8 31.0 - - + +
214D CYS* 4.0 17.3 - - + -
215D LEU* 3.9 37.9 - - + +
251D LEU* 4.6 5.4 - - + -
277D PHE* 4.0 15.9 - - + -
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Residues in contact with ARG 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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112D GLU* 2.9 16.4 + - - +
113D ASP* 3.0 36.7 + - - +
114D THR 3.2 0.2 - - - -
115D ILE* 1.3 77.0 - - - +
117D LEU* 1.3 56.2 + - - +
119D LEU* 3.4 1.6 + - - +
120D GLN* 2.9 53.2 + - + +
276D PRO 5.4 0.2 + - - -
277D PHE* 2.8 59.5 + - + +
278D LEU* 4.4 1.1 - - - +
279D ASP 3.6 19.3 + - - -
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Residues in contact with LEU 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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113D ASP 3.1 15.0 + - - +
114D THR* 3.1 9.6 + - - +
116D ARG* 1.3 78.5 - - - +
118D PHE* 1.3 69.8 + - + +
120D GLN* 3.6 16.7 + - - +
121D GLN* 3.3 30.2 + - + +
156D PRO 3.1 28.7 - - - +
157D ASN* 4.0 21.1 - - - +
159D ILE 4.0 15.0 - - - +
160D ARG* 4.9 8.1 - - - +
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Residues in contact with PHE 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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100D LEU* 4.1 18.8 - - + -
103D TYR* 4.0 20.6 - + - -
110D LEU* 3.9 30.1 - - + -
114D THR* 2.9 33.3 + - + +
115D ILE* 3.8 4.5 - - - +
117D LEU* 1.3 91.0 - - + +
119D LEU* 1.3 59.1 + - - +
121D GLN* 3.3 6.9 + - - +
122D ILE* 3.0 37.2 + - + +
146D LEU* 4.9 1.8 - - + -
156D PRO 4.4 1.8 - - - -
159D ILE* 3.9 38.1 - - + -
161D VAL* 3.7 26.9 - - + +
214D CYS* 5.2 4.5 - - - -
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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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115D ILE* 2.8 20.0 + - + +
116D ARG* 3.9 0.9 - - - +
118D PHE* 1.3 74.8 - - - +
120D GLN* 1.3 60.5 + - - +
122D ILE* 4.4 13.5 - - + -
123D ALA* 2.8 28.6 + - - +
207D ILE* 3.7 29.6 - - + -
211D VAL* 4.0 20.4 - - + -
254D LEU* 3.5 32.5 - - + -
258D LEU* 5.7 0.2 - - + -
272D PHE* 3.8 17.3 - - + -
277D PHE* 4.2 7.9 - - + -
278D LEU* 3.6 21.1 - - + -
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Residues in contact with GLN 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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116D ARG* 2.9 32.4 + - + +
117D LEU* 3.8 21.4 - - - +
119D LEU* 1.3 76.0 - - - +
121D GLN* 1.3 59.9 + - + +
123D ALA* 3.5 7.4 + - - +
124D GLY* 3.1 21.8 + - - -
278D LEU* 2.9 41.8 + - + +
279D ASP 3.7 2.4 + - - -
280D ALA* 3.4 21.1 - - + +
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Residues in contact with GLN 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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74D ASN* 3.0 39.4 + - - +
117D LEU* 3.3 33.3 + - + +
118D PHE* 3.3 12.3 + - - +
119D LEU 3.1 0.4 - - - -
120D GLN* 1.3 77.4 - - + +
122D ILE* 1.3 66.1 + - - +
124D GLY* 3.2 2.3 + - - -
125D ALA 3.1 17.0 + - - -
159D ILE 3.3 19.6 + - - -
160D ARG* 3.2 31.4 + - - +
161D VAL* 3.0 32.1 + - + +
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Residues in contact with ILE 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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74D ASN* 5.3 0.7 - - - -
100D LEU* 5.8 2.0 - - + -
118D PHE* 3.0 28.3 + - + +
119D LEU* 3.8 18.4 - - + +
121D GLN* 1.3 77.3 - - - +
123D ALA* 1.3 56.9 + - - +
125D ALA* 3.2 7.6 + - - +
126D MET* 2.9 41.2 + - + +
139D LEU* 5.9 1.3 - - + -
144D ILE* 4.4 28.5 - - + -
161D VAL* 4.2 14.1 - - + -
162D LYS 6.6 0.2 - - - -
163D ILE* 4.6 13.0 - - + -
207D ILE* 4.1 21.1 - - + -
210D ILE* 5.0 16.4 - - + -
211D VAL* 6.4 0.4 - - + -
272D PHE* 5.2 0.2 - - + -
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Residues in contact with ALA 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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119D LEU 2.8 18.6 + - - +
120D GLN* 3.6 6.3 - - - +
122D ILE* 1.3 77.5 - - - +
124D GLY* 1.3 56.3 + - - +
126D MET* 3.2 0.8 + - - -
127D ARG* 2.8 26.4 + - - +
272D PHE* 3.9 23.3 - - + -
273D PHE* 3.5 17.6 - - + +
278D LEU* 3.7 23.6 - - + -
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Residues in contact with GLY 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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72D HIS* 3.4 22.0 + - - -
74D ASN* 5.2 0.2 - - - -
120D GLN 3.1 14.9 + - - -
121D GLN* 3.2 4.2 + - - -
123D ALA* 1.3 75.8 - - - +
125D ALA* 1.3 63.2 + - - +
127D ARG* 3.3 19.1 + - - +
128D LEU 3.4 8.3 + - - -
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Residues in contact with ALA 125 (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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72D HIS* 3.7 12.6 - - - +
74D ASN* 3.6 32.8 - - + +
75D ILE* 4.0 11.2 - - + +
121D GLN 3.1 7.1 + - - +
122D ILE* 3.2 7.8 + - - +
124D GLY* 1.3 77.7 - - - +
126D MET* 1.3 62.2 + - - +
128D LEU* 3.2 5.2 + - - +
129D LEU* 3.1 27.6 + - - +
163D ILE* 3.7 15.9 - - + -
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Residues in contact with MET 126 (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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122D ILE* 2.9 24.3 + - + +
123D ALA* 3.2 6.7 + - - +
125D ALA* 1.3 73.4 - - - +
127D ARG* 1.3 60.5 + - - +
129D LEU* 3.8 20.9 - - + +
130D HIS* 2.9 33.0 + - - +
134D ILE 5.6 0.7 - - - +
139D LEU* 4.1 11.7 - - - -
163D ILE* 4.1 15.3 - - - -
203D ASP* 3.8 35.0 - - + +
207D ILE* 3.7 27.6 - - + -
269D PHE* 4.1 20.4 - - + -
272D PHE* 4.6 3.1 - - + -
273D PHE* 3.8 13.2 - - + -
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Residues in contact with ARG 127 (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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123D ALA 2.8 13.5 + - - +
124D GLY* 3.5 13.1 - - - +
125D ALA 3.2 0.4 - - - -
126D MET* 1.3 78.7 - - - +
128D LEU* 1.3 56.9 + - - +
130D HIS* 3.9 1.6 - - - +
131D SER* 3.0 29.4 + - - -
273D PHE* 3.4 56.7 + - + +
274D HIS* 4.3 16.2 + - - -
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Residues in contact with LEU 128 (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 LEU* 4.1 21.8 - - + -
71D LYS 3.7 16.8 - - - +
72D HIS* 3.7 37.0 - - + -
75D ILE* 4.1 7.0 - - + -
124D GLY 3.4 7.8 + - - +
125D ALA 3.2 8.6 + - - +
127D ARG* 1.3 76.9 - - - +
129D LEU* 1.3 66.1 + - - +
131D SER* 2.8 25.1 + - - +
132D LYS* 3.0 34.7 + - - +
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Residues in contact with LEU 129 (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 LEU* 4.5 6.3 - - + -
75D ILE* 3.6 25.8 - - + -
125D ALA* 3.1 28.1 + - + +
126D MET* 3.8 26.9 - - + +
128D LEU* 1.3 77.5 - - - +
130D HIS* 1.3 65.0 + - - +
132D LYS* 2.9 6.2 + - - +
133D GLY 2.9 19.1 + - - -
134D ILE* 3.0 41.4 + - + +
136D HIS* 3.9 31.9 - - + +
163D ILE* 5.1 2.5 - - + -
166D PHE* 4.1 19.3 - - + -
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Residues in contact with HIS 130 (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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126D MET* 2.9 18.8 + - - +
127D ARG 3.9 3.6 - - - +
129D LEU* 1.3 75.4 - - - +
131D SER* 1.3 64.6 + - - +
133D GLY* 3.2 13.0 + - - +
134D ILE 4.3 4.7 + - - +
269D PHE* 3.4 59.5 - + + +
273D PHE* 4.4 9.6 - + + -
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Residues in contact with SER 131 (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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127D ARG* 3.0 17.1 + - - -
128D LEU* 2.8 29.6 + - - +
130D HIS* 1.3 81.0 - - - +
132D LYS* 1.3 62.5 + - - +
133D GLY 3.3 0.4 + - - -
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Residues in contact with LYS 132 (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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69D GLU* 3.1 29.0 + - + +
70D LEU* 4.1 8.7 - - + +
71D LYS 5.6 0.6 - - - +
128D LEU* 3.0 40.9 + - + +
129D LEU* 2.9 6.4 + - - +
131D SER* 1.3 80.5 + - - +
133D GLY* 1.3 60.9 + - - +
134D ILE* 3.9 17.7 - - + -
171D TYR* 3.5 23.3 - - + +
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Residues in contact with GLY 133 (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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129D LEU 2.9 3.7 + - - -
130D HIS* 3.2 12.5 + - - -
131D SER 3.3 1.0 + - - -
132D LYS* 1.3 80.2 - - - +
134D ILE* 1.3 60.3 + - - +
135D ILE* 5.5 1.1 - - - -
171D TYR* 3.3 5.4 - - - +
172D LEU* 2.8 40.5 + - - +
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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