Contacts of the helix formed by residues 156 - 165 (chain A) in PDB entry 1V0B
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 LYS 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 3.3 31.9 + - - +
155A ARG* 1.3 77.7 - - - +
157A TYR* 1.3 68.5 + - - +
158A THR* 3.3 7.4 - - - +
159A HIS* 2.7 35.8 + - + +
160A GLU 3.0 2.9 + - - -
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Residues in contact with TYR 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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155A ARG 3.4 3.4 + - - -
156A LYS* 1.3 71.1 - - - +
158A THR* 1.3 80.5 - - + +
159A HIS 3.0 1.4 + - - -
160A GLU* 3.1 4.5 + - - +
161A VAL* 3.1 46.3 + - + +
204A VAL* 4.9 14.0 + - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LYS* 4.3 9.4 + - - +
157A TYR* 1.3 93.0 - - + +
159A HIS* 1.3 76.8 + - - +
161A VAL* 3.8 5.7 + - - +
162A VAL* 3.5 25.6 + - - +
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Residues in contact with HIS 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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12A GLU* 3.7 45.4 + - + +
13A GLY 4.9 4.2 + - - -
14A THR* 5.4 4.2 - - - -
127A LYS* 5.4 1.0 + - - +
129A GLN* 6.2 0.7 - - - -
155A ARG* 3.6 21.7 - - + +
156A LYS* 2.7 35.1 + - + +
158A THR* 1.3 85.6 + - - +
160A GLU* 1.3 62.3 + - - +
161A VAL 3.1 1.3 - - - -
162A VAL* 3.5 6.1 + - - +
163A THR* 2.8 28.3 + - - -
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Residues in contact with GLU 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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153A PRO 4.0 2.3 - - - +
154A VAL* 3.9 22.4 - - + +
155A ARG* 3.3 47.2 + - - +
156A LYS 3.0 4.8 + - - -
157A TYR* 3.1 7.6 + - - +
159A HIS* 1.3 76.3 - - - +
161A VAL* 1.3 64.5 + - + +
163A THR* 3.1 12.0 + - - -
164A LEU* 3.0 28.5 + - + +
167A ARG* 3.1 30.0 + - - -
206A GLU* 5.5 0.3 - - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.1 50.4 + - + +
158A THR* 3.9 7.6 - - - +
159A HIS 3.1 0.2 - - - -
160A GLU* 1.3 77.6 - - + +
162A VAL* 1.3 63.3 + - + +
164A LEU* 3.2 21.0 + - + +
165A TRP* 3.4 29.5 - - + +
203A GLY 3.8 16.4 - - - +
204A VAL* 4.2 21.3 - - + +
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Residues in contact with VAL 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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87A LYS* 5.2 19.1 - - + -
127A LYS* 4.8 12.1 - - + -
128A PRO* 5.8 1.3 - - + -
129A GLN* 6.4 0.9 - - + -
158A THR 3.5 15.0 + - - +
159A HIS* 3.5 9.3 + - + +
160A GLU 3.4 0.2 - - - -
161A VAL* 1.3 75.2 - - + +
163A THR* 1.3 64.0 + - - +
165A TRP* 3.2 58.0 - - + +
166A TYR* 3.2 17.3 - - + +
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Residues in contact with THR 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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124A ARG 6.1 0.7 - - - +
125A ASP* 3.7 9.4 - - - +
127A LYS* 3.6 14.9 + - + +
155A ARG* 3.1 40.3 + - - +
159A HIS 2.8 17.7 + - - -
160A GLU* 3.1 12.1 + - - +
162A VAL* 1.3 77.9 - - - +
164A LEU* 1.3 61.5 + - - +
166A TYR* 3.2 18.6 + - - +
167A ARG* 3.6 28.6 + - - +
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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 GLU* 3.0 37.4 + - + +
161A VAL* 3.4 13.0 - - - +
163A THR* 1.3 76.5 - - - +
165A TRP* 1.3 63.1 + - + +
166A TYR 2.9 2.1 + - - -
167A ARG* 3.0 45.6 + - - +
172A LEU* 4.8 1.3 - - + -
203A GLY 4.2 6.3 - - - +
204A VAL 3.8 7.2 - - - +
205A SER* 3.4 47.6 - - - +
206A GLU* 3.9 8.1 - - + +
209A GLN* 3.2 30.4 + - + +
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Residues in contact with TRP 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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87A LYS* 6.2 2.5 - - - -
161A VAL* 3.4 27.8 + - + +
162A VAL* 3.2 45.5 - - + +
163A THR 3.1 0.4 - - - -
164A LEU* 1.3 76.4 - - - +
166A TYR* 1.3 76.9 + - + +
167A ARG 3.6 0.4 + - - -
185A TRP* 5.1 0.3 + - - -
189A CYS* 3.7 16.8 - - - +
193A GLU* 5.6 0.7 - - - -
199A PRO* 3.8 32.5 - - + -
201A PHE* 3.5 21.1 + - - +
202A PRO* 3.4 32.1 - - + +
203A GLY 3.1 24.1 + - - -
209A GLN* 3.7 8.9 + - - +
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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