Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 1V72
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 THR 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LYS* 5.0 1.6 - - - +
156A ILE* 4.6 5.2 - - + +
157A TYR* 1.3 75.9 - - - +
159A LEU* 1.3 63.9 + - - +
160A ASP* 3.4 10.9 + - - +
161A GLU* 2.7 43.8 + - - +
162A ILE* 3.0 22.8 + - - +
190A LEU* 4.6 13.2 - - + -
293A GLU* 6.0 1.6 - - - +
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Residues in contact with LEU 159 (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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158A THR* 1.3 73.9 - - - +
160A ASP* 1.3 60.5 + - - +
162A ILE* 3.5 6.7 + - + +
163A GLU* 3.1 30.8 + - - +
190A LEU* 4.1 17.5 - - + +
192A CYS* 3.9 30.7 - - + -
196A GLU* 3.6 35.4 - - + +
197A MET* 3.8 17.3 - - + -
201A ALA* 4.6 3.1 - - + +
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Residues in contact with ASP 160 (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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158A THR* 3.1 8.8 + - - +
159A LEU* 1.3 80.1 - - - +
161A GLU* 1.3 60.4 + - + +
163A GLU* 3.5 7.0 + - - +
164A ALA* 2.9 30.9 + - - +
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Residues in contact with GLU 161 (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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120A LYS* 2.8 38.3 + - - -
157A TYR* 3.3 10.9 - - + -
158A THR* 2.7 48.4 + - - +
160A ASP* 1.3 74.7 - - + +
162A ILE* 1.3 65.9 + - - +
164A ALA* 3.4 6.2 + - - +
165A ILE* 3.1 29.7 + - + +
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Residues in contact with ILE 162 (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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147A ILE* 4.1 23.1 - - + -
149A GLN* 3.5 26.2 - - - +
157A TYR* 3.6 16.2 - - + +
158A THR 3.0 18.4 + - - +
159A LEU* 3.8 8.3 - - + +
161A GLU* 1.3 73.5 - - - +
163A GLU* 1.3 66.0 + - - +
165A ILE* 3.0 11.5 + - - +
166A GLY* 2.9 18.4 + - - -
176A LEU* 4.5 2.8 - - + +
178A MET* 4.0 5.6 - - + -
197A MET* 3.8 24.2 - - + +
201A ALA* 3.7 21.2 - - + +
203A VAL* 4.3 16.2 - - + -
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Residues in contact with GLU 163 (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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159A LEU 3.1 15.4 + - - +
160A ASP* 3.9 7.1 - - - +
162A ILE* 1.3 79.3 - - - +
164A ALA* 1.3 58.9 + - - +
166A GLY* 2.9 15.4 + - - -
167A ASP* 3.0 19.6 + - - +
200A LYS 4.9 3.8 - - - +
201A ALA* 3.3 30.5 - - + +
401A ZN 2.2 35.8 - - - -
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Residues in contact with ALA 164 (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 ILE* 3.7 17.3 - - + +
127A ARG* 5.2 6.9 + - - +
160A ASP 2.9 18.8 + - - +
161A GLU* 3.5 9.6 - - - +
163A GLU* 1.3 80.3 + - - +
165A ILE* 1.3 60.6 + - - +
167A ASP* 3.2 27.3 + - - +
168A VAL* 3.4 11.6 + - - +
401A ZN 4.2 0.2 - - - -
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Residues in contact with ILE 165 (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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121A LEU* 4.9 12.8 - - + +
123A ILE* 4.0 19.7 - - + -
126A LEU* 3.8 18.6 - - + -
145A VAL* 4.1 10.8 - - + -
147A ILE* 3.7 26.2 - - + -
157A TYR* 3.8 23.1 - - + -
161A GLU* 3.2 15.7 - - + +
162A ILE* 3.0 7.9 + - - +
164A ALA* 1.3 76.3 - - - +
166A GLY* 1.3 63.7 + - - +
168A VAL* 3.3 6.0 + - - +
169A CYS* 3.0 22.5 + - - -
176A LEU* 4.0 24.7 - - + -
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Residues in contact with GLY 166 (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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162A ILE 2.9 12.3 + - - -
163A GLU 2.9 6.4 + - - -
165A ILE* 1.3 79.1 - - - +
167A ASP* 1.3 55.9 + - - +
169A CYS* 3.3 4.0 + - - +
170A LYS* 2.9 37.2 + - - +
176A LEU* 4.0 16.8 - - - +
201A ALA 4.1 8.1 - - - -
202A GLY* 4.8 6.3 - - - -
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Residues in contact with ASP 167 (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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163A GLU* 3.0 18.5 + - - +
164A ALA* 3.2 12.2 + - - +
166A GLY* 1.3 74.3 - - - +
168A VAL* 1.3 57.1 + - + +
170A LYS* 3.8 5.4 - - - +
171A SER* 2.8 37.5 + - - -
401A ZN 2.1 36.5 - - - -
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Residues in contact with VAL 168 (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 ILE* 3.7 20.6 - - + -
126A LEU* 4.4 15.0 - - + -
127A ARG* 3.8 29.6 - - + +
130A THR* 3.6 28.0 - - + +
145A VAL* 6.1 0.2 - - + -
164A ALA 3.5 15.5 - - - +
165A ILE* 3.3 6.7 + - - +
167A ASP* 1.3 76.3 - - + +
169A CYS* 1.3 59.6 + - - +
171A SER* 3.2 8.2 + - - -
172A SER* 2.9 31.0 + - - +
174A LEU* 5.1 0.7 - - + -
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Residues in contact with CYS 169 (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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145A VAL* 3.5 38.4 - - - -
165A ILE* 3.0 19.2 + - - +
166A GLY* 3.6 9.9 - - - +
167A ASP 3.2 0.2 - - - -
168A VAL* 1.3 77.2 - - - +
170A LYS* 1.3 58.9 + - + +
172A SER 3.2 1.7 + - - -
173A SER 2.9 9.5 + - - -
174A LEU* 2.7 49.2 + - - +
175A GLY 3.9 5.2 - - - -
176A LEU* 3.9 24.9 - - + -
202A GLY 5.9 0.2 - - - +
204A ASP* 5.7 0.2 - - - +
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Residues in contact with LYS 170 (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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166A GLY 2.9 21.9 + - - +
167A ASP* 4.0 4.5 - - - +
169A CYS* 1.3 73.7 - - + +
171A SER* 1.3 65.5 + - - +
173A SER* 3.2 14.2 + - - +
174A LEU 4.3 1.8 + - - +
202A GLY* 5.1 18.2 - - - +
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Residues in contact with SER 171 (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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167A ASP 2.8 19.8 + - - -
168A VAL* 3.2 10.8 - - - -
170A LYS* 1.3 79.5 - - - +
172A SER* 1.3 62.2 + - - +
173A SER* 3.7 1.7 + - - -
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Residues in contact with SER 172 (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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130A THR* 4.2 21.0 + - - -
131A ARG* 5.6 2.9 - - - +
142A PRO* 5.7 0.4 - - - -
168A VAL* 2.9 14.4 + - - +
171A SER* 1.3 79.0 + - - +
173A SER* 1.3 73.9 + - - +
174A LEU* 3.2 31.0 + - - +
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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