Contacts of the helix formed by residues 129 - 149 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLY* 1.3 75.4 - - - -
130B ASP* 1.3 61.0 + - - +
131B GLU* 3.5 11.0 + - - +
132B VAL* 3.0 32.2 + - - +
133B LYS* 2.8 26.3 + - - +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 5.2 4.2 - - + +
129B SER* 1.3 73.1 - - - +
131B GLU* 1.3 62.0 + - - +
133B LYS* 3.1 33.1 + - - +
134B LYS* 3.0 46.8 + - - +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 3.1 10.9 + - - +
130B ASP* 1.3 79.3 - - - +
132B VAL* 1.3 57.4 + - + +
134B LYS* 4.9 1.6 - - - -
135B ARG* 3.0 34.7 + - - +
286B THR* 2.8 38.1 + - - +
287B THR* 3.4 26.1 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR 3.6 16.4 - - - +
128B GLY* 4.5 3.4 - - - -
129B SER* 3.0 26.3 + - - +
131B GLU* 1.3 78.2 - - + +
133B LYS* 1.3 59.8 + - - +
135B ARG* 3.2 23.6 + - - +
136B GLU* 2.8 29.2 + - + +
243B ILE* 4.0 24.0 - - + +
244B VAL* 4.2 16.2 - - + +
246B ASN* 5.9 0.7 - - - +
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Residues in contact with LYS 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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92B VAL* 3.8 17.8 - - + +
125B ALA* 3.4 35.0 - - - +
126B LYS* 3.8 22.2 + - + +
127B THR 3.7 14.8 - - - +
128B GLY 3.3 19.3 - - - -
129B SER 2.8 14.5 + - - +
130B ASP* 3.1 30.6 + - - +
132B VAL* 1.3 76.0 - - - +
134B LYS* 1.3 62.2 + - - +
136B GLU* 3.4 3.9 + - - +
137B ALA* 3.1 23.4 + - - +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.8 38.4 - - + +
97B GLN* 6.3 0.7 - - - +
130B ASP* 3.0 32.9 + - - +
131B GLU* 5.1 0.9 - - - -
133B LYS* 1.3 73.9 - - - +
135B ARG* 1.3 61.7 + - - +
137B ALA 3.5 0.3 + - - -
138B ALA* 3.0 25.3 + - - +
284B LEU* 3.2 42.3 + - + +
285B GLY 4.8 4.7 + - - +
286B THR* 3.8 23.8 - - + -
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLU* 3.0 37.6 + - - +
132B VAL* 3.2 28.6 + - - +
134B LYS* 1.3 78.3 - - - +
136B GLU* 1.3 56.6 + - - +
138B ALA* 3.5 3.9 + - - +
139B ALA* 2.9 26.9 + - - +
243B ILE* 4.1 22.9 + - + -
246B ASN* 3.8 20.2 + - - -
277B PHE* 3.6 19.7 - - + -
281B THR* 4.6 0.2 - - + -
286B THR* 3.8 7.8 - - - +
287B THR* 2.8 44.4 + - - +
288B THR 3.5 15.9 - - - -
289B GLY* 3.7 14.6 - - - -
290B PRO* 5.0 0.6 - - - +
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Residues in contact with GLU 136 (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 4.1 0.5 - - - +
124B PHE* 3.3 16.5 - - + -
125B ALA* 2.9 22.3 + - - -
127B THR 5.2 2.1 + - - +
132B VAL 2.8 16.0 + - - +
133B LYS* 3.7 5.3 - - - +
134B LYS 3.3 0.4 - - - -
135B ARG* 1.3 74.9 - - - +
137B ALA* 1.3 58.8 + - - +
139B ALA* 3.1 4.3 + - - +
140B PHE* 2.9 29.3 + - - +
228B TRP* 2.9 31.6 + - + +
240B HIS* 2.5 40.1 + - - -
243B ILE* 3.7 18.5 - - + +
244B VAL* 4.0 9.9 - - + +
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Residues in contact with ALA 137 (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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91B PHE* 4.4 6.3 - - + -
92B VAL* 4.0 11.0 - - + -
93B VAL* 3.6 28.3 - - + -
124B PHE* 4.2 12.1 - - - -
125B ALA* 4.3 8.4 - - + +
133B LYS 3.1 16.3 + - - +
134B LYS 3.8 4.0 - - - +
136B GLU* 1.3 75.2 - - - +
138B ALA* 1.3 58.2 + - - +
140B PHE* 3.8 0.7 - - - +
141B LEU* 2.9 37.6 + - + +
284B LEU* 4.3 0.7 - - + -
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Residues in contact with ALA 138 (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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101B MET* 5.0 1.3 - - - -
134B LYS 3.0 18.1 + - - +
135B ARG 3.7 4.5 - - - +
137B ALA* 1.3 76.4 - - - +
139B ALA* 1.3 57.4 + - - +
141B LEU* 4.8 0.4 - - - -
142B ALA* 2.9 33.3 + - - +
277B PHE* 3.9 3.1 - - + -
280B PHE* 3.8 24.2 - - + -
281B THR* 3.8 27.6 - - + +
284B LEU* 4.0 10.2 - - + +
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Residues in contact with ALA 139 (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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135B ARG 2.9 18.2 + - - +
136B GLU 3.1 4.9 + - - +
138B ALA* 1.3 74.7 - - - +
140B PHE* 1.3 64.6 + - - +
142B ALA* 3.6 1.1 + - - +
143B ASN* 3.0 30.5 + - - -
228B TRP* 3.5 19.5 - - + -
243B ILE* 4.0 12.3 - - + -
249B PHE* 3.9 13.7 - - + -
277B PHE* 3.7 19.3 - - + -
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Residues in contact with PHE 140 (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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91B PHE* 6.4 0.2 - + - -
114B LEU* 4.3 5.6 - - + -
124B PHE* 3.7 27.6 - + + -
136B GLU 2.9 15.7 + - - +
137B ALA 3.8 1.8 - - - +
139B ALA* 1.3 78.4 - - - +
141B LEU* 1.3 70.9 + - + +
143B ASN* 3.3 2.6 + - - +
144B VAL* 3.0 49.6 + - + +
187B ILE* 4.9 2.7 - - + -
221B TRP* 3.8 32.1 - + - -
224B GLY* 3.5 33.2 - - - -
225B LEU* 3.6 22.0 - - + -
228B TRP* 3.4 34.7 - + + -
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Residues in contact with LEU 141 (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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91B PHE* 4.9 3.4 - - + -
93B VAL* 4.1 24.0 - - + -
98B PHE* 4.8 1.6 - - + -
101B MET* 3.7 22.4 - - + -
102B PHE* 3.5 15.0 - - + -
114B LEU* 4.0 18.2 - - + -
137B ALA* 2.9 21.2 + - - +
138B ALA* 4.8 0.2 - - - -
140B PHE* 1.3 94.4 - - + +
142B ALA* 1.3 52.7 + - - +
144B VAL* 3.4 4.5 + - + +
145B SER* 2.7 35.2 + - - -
221B TRP* 3.7 30.1 - - + -
280B PHE* 3.5 18.4 - - + -
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Residues in contact with ALA 142 (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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138B ALA 2.9 20.0 + - - +
139B ALA 3.9 3.4 - - - +
141B LEU* 1.3 74.2 - - - +
143B ASN* 1.3 61.4 + - - +
145B SER* 3.3 2.8 + - - -
146B HIS* 2.9 27.4 + - - +
249B PHE* 4.9 2.0 - - + -
273B ARG* 4.7 4.2 - - - +
276B LYS* 3.9 9.5 - - + +
277B PHE* 3.5 38.4 - - + +
280B PHE* 3.5 14.5 - - + -
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Residues in contact with ASN 143 (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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139B ALA 3.0 23.3 + - - +
140B PHE 3.8 3.1 - - - +
142B ALA* 1.3 74.6 - - - +
144B VAL* 1.3 63.2 + - + +
146B HIS* 3.2 6.3 + - - +
147B GLN* 3.0 24.3 + - - +
187B ILE* 6.4 0.2 - - - -
228B TRP* 3.7 12.8 - - + -
249B PHE* 3.5 16.0 - - - -
252B THR* 3.2 24.9 + - - -
253B ILE* 4.9 0.9 - - - +
256B ILE* 3.5 24.2 - - + +
273B ARG* 2.9 38.0 + - - +
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Residues in contact with VAL 144 (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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102B PHE* 4.6 2.0 - - + -
140B PHE* 3.0 49.9 + - + +
141B LEU* 3.5 9.9 - - - +
143B ASN* 1.3 73.2 - - + +
145B SER* 1.3 61.0 + - - +
147B GLN* 3.1 3.1 + - - +
148B THR* 2.7 32.7 + - - +
151B LEU* 3.4 31.0 - - + -
186B PRO* 3.6 34.1 - - + +
187B ILE* 4.4 5.8 - - + -
221B TRP* 4.1 10.1 - - + -
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Residues in contact with SER 145 (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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269A GLN* 5.6 0.2 - - - +
272A SER* 6.0 0.3 - - - -
101B MET 5.2 0.7 + - - -
102B PHE* 3.6 20.8 - - - -
141B LEU 2.7 20.7 + - - -
142B ALA 3.5 6.3 - - - -
143B ASN 3.3 0.2 - - - -
144B VAL* 1.3 71.9 - - - +
146B HIS* 1.3 63.4 + - - +
148B THR* 3.9 3.4 - - - -
149B GLY* 3.0 8.8 + - - -
150B GLY* 3.0 37.7 + - - +
276B LYS* 3.8 29.4 + - - +
280B PHE* 4.1 4.1 - - - -
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Residues in contact with HIS 146 (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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266A ASN* 4.6 8.2 + - - +
268A ALA* 3.4 17.3 - - - +
269A GLN* 3.7 27.9 + - - +
142B ALA 2.9 14.3 + - - +
143B ASN* 3.4 11.9 - - - +
144B VAL 3.2 0.2 - - - -
145B SER* 1.3 78.6 - - - +
147B GLN* 1.3 64.6 + - + +
149B GLY 4.1 0.2 + - - -
261B GLU* 4.4 4.4 + - - -
269B GLN* 2.9 34.5 + - + +
272B SER* 4.2 5.0 + - - -
273B ARG* 3.4 61.0 + - + +
276B LYS* 5.7 4.8 - - + +
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Residues in contact with GLN 147 (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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268A ALA* 3.5 11.6 - - - +
143B ASN 3.0 15.6 + - - +
144B VAL* 3.1 6.0 + - - +
146B HIS* 1.3 80.3 - - - +
148B THR* 1.3 57.9 + - - +
153B TYR* 5.8 0.2 - - - -
186B PRO 3.8 7.6 - - - +
187B ILE* 3.8 22.7 + - + +
188B GLN* 3.7 37.9 - - + +
256B ILE* 4.4 17.7 - - - +
273B ARG* 4.8 8.1 + - - -
402B GOL 4.3 13.2 + - - -
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Residues in contact with THR 148 (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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268A ALA* 4.2 3.6 - - - -
109B TYR* 3.9 2.5 - - - +
144B VAL 2.7 16.4 + - - +
145B SER 3.7 0.3 + - - -
147B GLN* 1.3 80.7 - - + +
149B GLY* 1.3 61.0 + - - +
151B LEU* 2.9 30.2 + - + +
152B PHE 3.1 0.9 + - - -
153B TYR* 3.0 53.7 + - - +
185B GLY 3.5 25.1 - - - +
186B PRO* 3.6 20.9 - - + +
188B GLN* 4.4 5.4 - - + +
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Residues in contact with GLY 149 (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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268A ALA* 3.3 33.8 - - - +
269A GLN* 5.9 0.4 - - - -
271A GLN* 4.4 4.4 - - - +
272A SER* 4.4 9.9 - - - -
275A ASN* 2.9 25.0 + - - -
145B SER 3.0 5.8 + - - -
146B HIS 5.0 0.2 - - - -
148B THR* 1.3 78.7 - - - +
150B GLY* 1.3 61.2 + - - +
152B PHE* 3.2 10.7 - - - +
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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
------------------------------------------------------------
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