Contacts of the helix formed by residues 129 - 149 (chain A) in PDB entry 1WVV
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLY* 1.3 76.4 - - - +
130A ASP* 1.3 59.2 + - - +
131A GLU* 3.3 13.7 + - - +
132A VAL* 3.0 28.2 + - - +
133A LYS* 2.9 25.0 + - - +
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Residues in contact with ASP 130 (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* 5.3 7.0 - - + -
129A SER* 1.3 69.7 - - - +
131A GLU* 1.3 65.3 + - - +
133A LYS* 2.8 34.5 + - - +
134A LYS* 3.0 41.1 + - + +
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Residues in contact with GLU 131 (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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129A SER* 3.1 11.8 + - - +
130A ASP* 1.3 78.9 - - - +
132A VAL* 1.3 58.2 + - + +
134A LYS* 3.7 4.1 + - - +
135A ARG* 3.0 35.0 + - - +
285A GLY 3.9 6.2 - - - +
286A THR* 2.7 42.9 + - - +
287A THR* 3.4 29.7 + - - +
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Residues in contact with VAL 132 (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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127A THR 3.4 19.3 - - - +
128A GLY* 4.6 3.1 - - - -
129A SER* 3.0 25.2 + - - +
131A GLU* 1.3 77.0 - - + +
133A LYS* 1.3 59.6 + - - +
135A ARG* 3.2 23.8 + - - +
136A GLU* 2.9 28.7 + - + +
243A ILE* 4.0 23.5 - - + +
244A VAL* 4.2 17.0 - - + +
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Residues in contact with LYS 133 (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* 3.7 18.6 - - + +
125A ALA* 3.4 36.4 - - - +
126A LYS* 3.7 25.1 - - + +
127A THR 3.9 9.2 - - - +
128A GLY 2.5 29.0 + - - +
129A SER* 2.9 12.4 + - - +
130A ASP* 2.8 35.2 + - - +
132A VAL* 1.3 76.8 - - - +
134A LYS* 1.3 57.2 + - - +
136A GLU* 3.3 3.7 + - - +
137A ALA* 3.0 29.1 + - - +
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Residues in contact with LYS 134 (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* 3.9 30.0 - - + +
130A ASP* 3.0 30.0 + - + +
131A GLU* 4.6 3.8 + - - +
133A LYS* 1.3 75.8 - - - +
135A ARG* 1.3 59.9 + - - +
137A ALA 3.3 1.0 + - - -
138A ALA* 2.9 26.7 + - - +
284A LEU* 3.0 45.9 + - + +
285A GLY* 3.1 17.2 + - - +
286A THR* 3.7 24.2 - - + -
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Residues in contact with ARG 135 (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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131A GLU* 3.0 36.1 + - - +
132A VAL* 3.2 32.5 + - - +
134A LYS* 1.3 76.2 - - - +
136A GLU* 1.3 57.4 + - - +
138A ALA* 3.4 2.6 + - - -
139A ALA* 2.9 26.7 + - - +
243A ILE* 4.0 23.0 + - + +
246A ASN* 4.0 17.2 + - - -
249A PHE 6.2 0.2 - - - +
277A PHE* 3.6 20.8 - - + -
281A THR* 4.8 0.2 - - - -
286A THR* 3.7 8.5 + - + +
287A THR* 2.7 46.3 + - - +
288A THR 3.4 17.2 - - - -
289A GLY* 4.1 10.6 - - - +
290A PRO* 5.7 0.7 - - - -
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Residues in contact with GLU 136 (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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123A ALA 4.2 0.3 - - - +
124A PHE* 3.3 16.9 - - + -
125A ALA* 2.9 21.8 + - - -
126A LYS 4.6 0.3 + - - -
127A THR 5.2 2.3 + - - +
132A VAL* 2.9 17.8 + - + +
133A LYS* 3.8 5.2 - - - +
135A ARG* 1.3 73.8 - - - +
137A ALA* 1.3 61.4 + - - +
139A ALA* 3.2 3.0 + - - +
140A PHE* 2.9 28.8 + - - +
228A TRP* 2.9 28.7 + - + +
240A HIS* 2.6 41.5 + - - -
243A ILE* 3.6 20.6 - - + +
244A VAL* 4.1 5.8 - - + +
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Residues in contact with ALA 137 (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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91A PHE* 4.4 6.1 - - + -
92A VAL* 3.9 10.8 - - + -
93A VAL* 3.6 27.1 - - + -
124A PHE* 4.3 11.2 - - - -
125A ALA* 4.3 8.8 - - + +
133A LYS 3.0 17.0 + - - +
134A LYS 3.6 4.5 - - - +
136A GLU* 1.3 78.3 - - - +
138A ALA* 1.3 55.8 + - - +
140A PHE* 3.5 1.2 + - - +
141A LEU* 3.0 36.0 + - - +
284A LEU* 4.3 1.1 - - + -
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Residues in contact with ALA 138 (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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101A MET* 5.1 1.1 - - - -
134A LYS 2.9 17.6 + - - +
135A ARG 3.7 4.3 - - - +
137A ALA* 1.3 73.6 - - - +
139A ALA* 1.3 61.2 + - - +
141A LEU* 4.6 0.9 - - - +
142A ALA* 2.9 32.9 + - - +
277A PHE* 3.9 2.6 - - + -
280A PHE* 3.8 29.3 - - + +
281A THR* 3.9 25.1 - - + +
284A LEU* 4.1 8.6 - - + +
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Residues in contact with ALA 139 (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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135A ARG 2.9 18.6 + - - +
136A GLU 3.5 4.9 - - - +
138A ALA* 1.3 77.1 - - - +
140A PHE* 1.3 61.9 + - - +
142A ALA* 3.8 1.0 - - - +
143A ASN* 3.0 29.8 + - - -
228A TRP* 3.6 19.3 - - + -
243A ILE* 3.9 13.0 - - + -
249A PHE* 3.8 12.8 - - + -
277A PHE* 3.6 19.5 - - + -
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Residues in contact with PHE 140 (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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91A PHE* 6.5 0.4 - + - -
114A LEU* 4.3 14.1 - - + -
124A PHE* 3.7 26.9 - + + -
136A GLU 2.9 16.1 + - - +
137A ALA 3.8 1.3 - - - +
139A ALA* 1.3 77.6 - - - +
141A LEU* 1.3 82.4 + - + +
143A ASN* 3.3 4.2 + - - +
144A VAL* 2.9 50.1 + - + +
186A PRO* 5.3 0.2 - - + -
187A ILE* 4.9 4.3 - - + -
221A TRP* 4.4 9.9 - + - -
224A GLY* 3.6 33.4 - - - -
225A LEU* 3.8 21.1 - - + -
228A TRP* 3.5 36.9 - + + -
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Residues in contact with LEU 141 (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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91A PHE* 5.1 2.5 - - + -
93A VAL* 4.2 21.5 - - + -
98A PHE* 4.6 4.3 - - + -
101A MET* 3.8 22.7 - - + -
102A PHE* 3.4 27.5 - - + -
114A LEU* 4.0 25.4 - - + -
137A ALA 3.0 21.7 + - - +
140A PHE* 1.3 103.5 - - + +
142A ALA* 1.3 57.5 + - - +
144A VAL* 3.5 5.1 - - + +
145A SER* 2.9 23.9 + - - -
221A TRP* 4.6 7.4 - - + -
280A PHE* 3.6 16.8 - - + -
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Residues in contact with ALA 142 (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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138A ALA 2.9 20.1 + - - +
139A ALA 3.8 4.0 - - - +
141A LEU* 1.3 73.9 - - - +
143A ASN* 1.3 60.5 + - - +
145A SER* 3.2 4.0 + - - -
146A HIS* 2.9 27.6 + - - +
249A PHE* 4.6 2.9 - - + -
273A ARG* 4.5 4.8 - - - +
276A LYS* 4.0 11.8 - - + +
277A PHE* 3.5 37.2 - - + +
280A PHE* 3.5 11.2 - - + -
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Residues in contact with ASN 143 (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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139A ALA 3.0 22.3 + - - +
140A PHE 3.8 3.1 - - - +
142A ALA* 1.3 75.0 - - - +
144A VAL* 1.3 65.5 + - - +
146A HIS* 3.1 5.2 + - - +
147A GLN* 2.9 29.7 + - - +
187A ILE* 4.6 4.3 - - + -
228A TRP* 3.7 11.0 - - + -
249A PHE* 3.4 13.4 - - - -
252A THR* 3.1 26.1 + - - -
253A ILE* 4.7 2.1 - - - +
256A ILE* 3.4 26.1 - - + +
273A ARG* 3.0 33.6 + - - +
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Residues in contact with VAL 144 (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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102A PHE* 4.4 5.4 - - + -
140A PHE* 2.9 51.3 + - + +
141A LEU* 3.5 11.7 - - + +
142A ALA 3.3 0.2 - - - -
143A ASN* 1.3 76.7 - - - +
145A SER* 1.3 56.6 + - - +
147A GLN* 3.2 9.3 + - - -
148A THR* 2.8 24.4 + - - -
151A LEU* 3.4 33.7 - - + -
186A PRO* 3.5 33.2 - - + +
187A ILE* 4.2 6.1 - - + -
221A TRP* 4.8 4.5 - - + -
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Residues in contact with SER 145 (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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101A MET 5.0 0.9 + - - -
102A PHE* 3.6 19.9 - - - -
141A LEU 2.9 14.4 + - - -
142A ALA* 3.2 9.4 + - - -
144A VAL* 1.3 74.5 - - - +
146A HIS* 1.3 58.3 + - - +
148A THR* 4.0 0.9 - - - -
149A GLY 2.9 27.4 + - - -
150A GLY* 2.9 22.5 + - - +
276A LYS* 4.0 18.5 + - - +
280A PHE* 4.3 3.2 - - - -
501A CL 3.0 20.7 - - - +
279B GLN* 4.2 1.0 + - - -
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Residues in contact with HIS 146 (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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142A ALA 2.9 12.9 + - - +
143A ASN* 3.1 8.5 + - - +
145A SER* 1.3 78.4 - - - +
147A GLN* 1.3 63.1 + - - +
149A GLY* 3.9 0.5 + - - -
261A GLU* 4.5 2.4 + - - -
269A GLN* 3.3 33.7 + - - -
272A SER* 3.4 29.5 + - - -
273A ARG* 3.3 58.2 + - + +
276A LYS* 6.1 1.5 - - + +
501A CL 3.6 7.8 - - + +
269B GLN* 5.6 0.4 + - - -
272B SER* 3.8 12.8 + - - -
275B ASN* 3.1 16.8 + - - +
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Residues in contact with GLN 147 (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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143A ASN 2.9 22.3 + - - +
144A VAL 3.2 0.4 + - - -
146A HIS* 1.3 79.8 - - - +
148A THR* 1.3 58.1 + - - +
186A PRO 3.7 15.0 - - - +
187A ILE* 3.8 20.6 + - + +
188A GLN* 3.4 27.4 - - + +
256A ILE* 3.8 13.2 + - + +
257A ASN* 5.9 1.0 - - - +
273A ARG* 3.0 33.5 + - - +
401A GOL 2.8 26.5 + - - -
271B GLN* 4.4 7.1 - - - +
275B ASN* 3.2 11.9 + - - +
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Residues in contact with THR 148 (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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109A TYR* 3.9 4.5 - - - +
144A VAL 2.8 16.1 + - - -
145A SER 3.8 0.2 + - - -
147A GLN* 1.3 78.7 - - - +
149A GLY* 1.3 62.6 + - - +
151A LEU* 2.8 31.3 + - + +
152A PHE 3.2 0.5 + - - -
153A TYR* 3.0 49.6 + - - +
185A GLY 3.4 25.1 - - - +
186A PRO* 3.5 18.6 - - + +
188A GLN* 4.0 5.6 - - + +
275B ASN* 3.7 7.9 - - - +
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Residues in contact with GLY 149 (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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104A ASN* 5.8 1.6 - - - +
145A SER 2.9 6.6 + - - -
146A HIS 3.9 0.4 + - - -
148A THR* 1.3 77.4 - - - +
150A GLY* 1.3 62.4 + - - +
152A PHE* 3.3 19.2 + - - +
275B ASN* 3.3 34.8 - - - +
278B THR* 6.0 0.2 - - - -
279B GLN* 3.7 25.7 - - - +
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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