Contacts of the helix formed by residues 154 - 164 (chain A) in PDB entry 1ZSV
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 VAL 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A MET* 6.1 1.1 - - - -
125A PRO* 3.8 27.6 - - + +
128A THR* 3.9 13.7 - - + -
129A ALA* 3.5 18.5 - - - +
152A GLY 3.3 0.4 - - - -
153A ALA* 1.3 74.9 - - + +
155A GLY* 1.3 66.4 + - - +
157A VAL 3.1 5.4 + - - -
158A VAL* 3.0 21.8 + - + +
215A PHE* 3.6 36.6 - - + -
217A ASN* 4.1 12.3 - - - +
239A CYS* 4.2 2.2 - - - -
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Residues in contact with GLY 155 (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 VAL* 3.8 24.0 - - - +
149A ALA 3.6 19.9 + - - -
150A ALA* 3.5 7.7 - - - +
152A GLY 3.3 4.4 + - - -
154A VAL* 1.3 79.1 - - - +
156A SER* 1.3 55.2 + - - +
158A VAL* 3.4 4.9 + - - +
159A GLY 3.1 22.0 + - - -
187A PHE* 4.0 3.5 - - - -
217A ASN* 4.2 6.1 - - - +
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Residues in contact with SER 156 (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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150A ALA 3.2 16.9 + - - -
151A ALA* 4.3 7.6 + - - -
152A GLY 2.8 18.7 + - - -
153A ALA* 4.0 6.1 + - - -
155A GLY* 1.3 74.3 - - - +
157A VAL* 1.3 67.0 + - - +
159A GLY 4.0 0.7 - - - -
160A GLN* 3.0 36.6 + - - +
181A TYR* 4.9 5.5 - - - -
182A LEU* 4.6 2.5 - - - -
185A LEU* 4.5 17.0 - - - -
187A PHE* 4.0 6.3 - - - -
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Residues in contact with VAL 157 (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 THR* 4.3 25.8 - - + +
126A GLY* 4.1 19.7 - - - -
129A ALA* 3.7 10.5 - - + -
153A ALA 3.2 19.7 - - - +
154A VAL 3.1 6.2 + - - +
156A SER* 1.3 78.7 + - - +
158A VAL* 1.3 65.3 + - - +
160A GLN* 3.2 8.1 + - - +
161A ILE* 2.9 42.8 + - + +
287A LEU* 4.1 10.1 - - + -
296A ILE* 4.1 13.7 - - + -
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Residues in contact with VAL 158 (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 ALA* 3.3 26.6 - - + +
133A LEU* 3.1 40.3 - - + +
145A VAL* 4.8 3.6 - - + -
147A VAL* 4.2 11.7 - - + -
154A VAL 3.0 17.5 + - - +
155A GLY* 3.4 8.1 - - - +
157A VAL* 1.3 75.7 - - - +
159A GLY* 1.3 57.6 + - - +
161A ILE* 4.8 0.7 - - - -
162A ALA* 3.0 23.9 + - - +
215A PHE* 3.7 41.3 - - + -
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Residues in contact with GLY 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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147A VAL* 4.6 0.9 - - - +
155A GLY 3.1 8.1 + - - -
158A VAL* 1.3 80.6 - - - +
160A GLN* 1.3 57.0 + - - +
162A ALA* 3.4 0.9 + - - -
163A LYS* 3.0 33.4 + - - +
169A VAL* 3.7 21.3 - - - +
187A PHE* 3.4 26.0 - - - -
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Residues in contact with GLN 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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156A SER* 3.0 27.0 + - - +
157A VAL* 3.2 5.9 + - - +
159A GLY* 1.3 74.4 - - - +
161A ILE* 1.3 64.7 + - - +
163A LYS* 3.6 7.1 + - - +
164A LEU* 3.3 27.2 + - - +
185A LEU* 3.5 30.5 - - + +
187A PHE* 3.8 11.9 - - + -
295A LYS 4.0 14.4 - - - +
296A ILE* 3.6 17.3 - - + +
297A GLN* 2.8 54.5 + - - +
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Residues in contact with ILE 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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129A ALA* 4.4 2.9 - - + +
130A TYR* 3.7 35.4 - - + +
133A LEU* 3.7 18.4 - - + -
134A LEU* 3.8 26.9 - - + -
157A VAL* 2.9 34.9 + - + +
160A GLN* 1.3 72.9 - - - +
162A ALA* 1.3 64.5 + - - +
164A LEU* 3.5 8.8 + - + +
165A LYS* 3.1 26.7 + - + +
287A LEU* 4.2 3.8 - - + -
290A TRP* 4.0 20.2 - - + -
296A ILE* 3.9 16.8 - - + -
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Residues in contact with ALA 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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133A LEU* 3.6 13.4 - - + +
139A VAL* 5.4 0.4 - - - -
145A VAL* 4.2 11.9 - - + -
158A VAL 3.0 16.7 + - - +
159A GLY* 4.5 0.2 - - - -
161A ILE* 1.3 76.5 - - - +
163A LYS* 1.3 60.3 + - - +
165A LYS* 3.2 3.7 + - - +
166A GLY 3.1 5.5 + - - -
167A CYS* 3.0 43.9 + - + +
169A VAL* 3.5 23.8 - - + -
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Residues in contact with LYS 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 GLY 3.0 20.3 + - - +
160A GLN* 3.9 7.9 - - - +
161A ILE 3.2 0.2 - - - -
162A ALA* 1.3 77.0 - - - +
164A LEU* 1.3 56.7 + - - +
166A GLY* 3.0 20.4 + - - -
167A CYS 2.8 27.4 + - - +
168A LYS* 4.4 0.4 - - - +
169A VAL* 3.8 11.9 - - + -
185A LEU 5.0 4.0 - - - +
186A GLY* 3.6 28.0 - - - +
187A PHE* 4.8 1.8 - - + -
188A ASP* 2.9 29.2 + - - +
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Residues in contact with LEU 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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160A GLN 3.3 22.6 + - - +
161A ILE* 3.5 17.0 - - - +
163A LYS* 1.3 76.1 - - - +
165A LYS* 1.3 67.8 + - - +
166A GLY 3.4 0.2 - - - -
290A TRP* 3.5 52.3 - - + +
295A LYS* 4.1 39.3 - - + +
296A ILE* 4.3 5.2 - - + -
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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