Contacts of the helix formed by residues 143 - 161 (chain B) in PDB entry 1ZV0
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 LEU 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 5.0 0.2 - - - +
139B ARG* 3.9 44.0 - - + +
140B ARG 3.3 24.2 + - - +
141B THR* 4.1 10.1 - - + -
142B MET* 1.3 84.4 - - - +
144B VAL* 1.4 68.5 + - + +
145B ALA 3.5 2.8 - - - +
146B LYS* 3.6 4.9 + - - +
147B VAL* 3.5 25.8 + - - +
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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
----------------------------------------------------------
62B VAL* 4.8 1.1 - - + -
125B ASP* 4.3 2.2 - - - +
138B LEU* 4.1 22.2 - - + -
139B ARG 3.6 22.9 - - - +
140B ARG* 3.5 37.2 - - - +
143B LEU* 1.4 79.6 - - + +
145B ALA* 1.3 61.4 + - - +
147B VAL* 3.4 12.2 - - + +
148B THR* 3.1 32.0 + - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.4 38.6 - - + +
65B VAL* 3.5 11.5 - - + +
66B PHE* 3.2 33.9 - - + -
125B ASP* 3.9 2.0 - - - +
143B LEU 3.5 2.1 - - - +
144B VAL* 1.3 78.6 - - - +
146B LYS* 1.4 62.6 + - - +
148B THR* 3.2 17.1 + - - -
149B CYS* 3.3 10.4 + - - +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.0 22.6 - - + +
142B MET* 3.6 49.0 + - - +
143B LEU* 3.6 11.1 + - - +
144B VAL 3.5 0.6 - - - -
145B ALA* 1.4 77.0 - - - +
147B VAL* 1.4 59.4 + - + +
149B CYS* 3.4 6.7 + - - +
150B ILE* 3.1 40.1 + - + +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU 3.5 12.7 + - - +
144B VAL* 3.4 22.9 - - + +
146B LYS* 1.4 76.4 - - + +
148B THR* 1.4 64.7 + - + +
150B ILE* 3.5 12.3 + - + +
151B ILE* 3.2 27.6 + - - +
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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
----------------------------------------------------------
66B PHE* 3.3 15.5 - - - -
121B CYS* 4.4 14.1 - - + -
124B ILE* 6.5 0.9 - - + -
144B VAL* 3.1 22.6 + - + +
145B ALA* 3.2 11.4 + - - -
147B VAL* 1.4 76.9 - - + +
149B CYS* 1.4 58.3 + - - +
151B ILE* 3.6 9.8 - - + +
152B ILE* 3.4 30.9 + - - +
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Residues in contact with CYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.2 12.8 - - + +
66B PHE* 4.3 10.4 - - + -
69B ASN* 3.6 33.4 - - - -
118B LEU* 3.9 15.7 - - - -
145B ALA 3.3 15.7 + - - +
146B LYS* 3.6 6.5 - - - +
148B THR* 1.4 79.6 + - - +
150B ILE* 1.4 61.7 + - + +
152B ILE* 3.4 16.3 - - - +
153B TRP* 3.4 22.9 + - - -
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Residues in contact with ILE 150 (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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146B LYS* 3.1 28.9 + - + +
147B VAL* 3.5 13.0 + - + +
148B THR 3.4 0.2 - - - -
149B CYS* 1.4 75.2 - - + +
151B ILE* 1.4 65.0 + - - +
153B TRP* 3.3 55.8 + - + +
154B LEU 4.4 1.2 + - - -
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Residues in contact with ILE 151 (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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147B VAL 3.2 18.6 + - - +
148B THR* 3.6 14.6 - - + +
150B ILE* 1.4 76.2 - - - +
152B ILE* 1.4 66.3 + - + +
154B LEU* 3.3 41.0 + - + +
155B LEU* 3.5 14.3 - - + +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASN* 4.8 0.7 - - - +
114B ALA* 4.4 12.3 - - - +
117B PHE* 3.7 43.6 - - + +
118B LEU* 4.1 26.5 - - + -
120B THR* 6.3 1.6 - - + -
121B CYS* 5.7 3.1 - - + -
148B THR* 3.4 20.4 - - - +
149B CYS* 3.4 18.8 - - - +
151B ILE* 1.4 77.0 - - + +
153B TRP* 1.4 72.2 + - + +
155B LEU* 3.7 12.8 + - + +
156B ALA* 3.3 25.8 + - - +
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Residues in contact with TRP 153 (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 ASN* 3.0 42.1 + - + +
110B PHE* 3.9 26.3 - + + -
114B ALA* 5.3 4.3 - - + -
149B CYS* 3.4 23.9 + - - -
150B ILE* 3.4 45.5 - - + +
151B ILE 3.3 0.6 - - - -
152B ILE* 1.4 82.8 - - + +
154B LEU* 1.4 58.4 + - - +
156B ALA* 3.7 4.9 + - - -
157B GLY* 3.0 25.1 + - - -
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Residues in contact with LEU 154 (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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150B ILE 4.4 1.2 + - - +
151B ILE* 3.3 32.2 + - + +
153B TRP* 1.4 75.9 - - - +
155B LEU* 1.4 66.2 + - + +
157B GLY* 3.4 2.5 + - - -
158B LEU* 3.1 48.4 + - + +
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Residues in contact with LEU 155 (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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117B PHE* 3.6 32.4 - - + -
151B ILE* 3.5 27.8 - - + +
152B ILE* 3.7 9.8 + - + +
153B TRP 3.5 0.2 - - - -
154B LEU* 1.4 81.0 - - + +
156B ALA* 1.4 60.3 + - - +
158B LEU* 3.6 22.6 + - + +
159B ALA* 3.6 16.8 + - - +
202B LEU* 4.0 26.7 - - + -
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Residues in contact with ALA 156 (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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109B SER 5.5 0.4 - - - +
110B PHE* 3.6 46.7 - - + +
113B TYR* 4.9 3.1 - - - +
114B ALA* 4.5 12.6 - - + +
117B PHE* 3.9 9.0 - - + -
152B ILE 3.3 18.3 + - - +
153B TRP* 3.9 1.8 - - - +
155B LEU* 1.4 75.5 - - - +
157B GLY* 1.3 56.7 + - - +
159B ALA* 3.6 8.5 + - - +
160B SER* 3.3 23.9 + - - -
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Residues in contact with GLY 157 (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 PHE* 3.7 6.8 - - - -
153B TRP 3.0 16.3 + - - -
154B LEU* 3.4 4.7 + - - -
156B ALA* 1.3 72.5 - - - +
158B LEU* 1.4 58.9 + - - +
160B SER* 3.4 8.9 + - - -
161B LEU* 3.1 45.2 + - - +
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Residues in contact with LEU 158 (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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154B LEU* 3.1 38.9 + - + +
155B LEU* 3.8 22.9 - - + +
156B ALA 3.6 0.2 - - - -
157B GLY* 1.4 73.8 - - - +
159B ALA* 1.4 55.2 + - - +
162B PRO* 3.3 27.7 - - + +
195B LEU* 3.9 8.2 - - - +
202B LEU* 6.5 0.7 - - + -
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Residues in contact with ALA 159 (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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109B SER* 5.0 10.1 - - - -
113B TYR* 5.4 5.6 - - + -
155B LEU 3.6 8.6 + - - +
156B ALA* 3.6 12.7 + - - +
157B GLY 3.3 0.6 - - - -
158B LEU* 1.4 77.7 - - - +
160B SER* 1.3 62.3 + - - +
162B PRO* 4.0 0.3 - - - +
163B ALA* 3.4 22.2 + - - +
195B LEU* 4.2 15.9 - - - +
199B LYS* 4.2 30.5 + - + -
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Residues in contact with SER 160 (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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106B ALA* 3.9 37.6 - - - +
109B SER* 5.4 2.2 - - - -
110B PHE* 3.9 13.5 - - - -
156B ALA 3.3 11.6 + - - -
157B GLY* 3.4 13.2 + - - -
159B ALA* 1.3 76.7 - - - +
161B LEU* 1.3 73.4 + - - +
163B ALA* 3.5 15.4 + - - +
164B ILE* 3.7 13.9 - - - +
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Residues in contact with LEU 161 (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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157B GLY* 3.1 20.6 + - - +
160B SER* 1.3 82.3 + - - +
162B PRO* 1.4 67.3 - - + +
163B ALA 3.5 0.2 + - - -
164B ILE* 3.8 29.7 + - + +
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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