Contacts of the helix formed by residues 142 - 150 (chain V) in PDB entry 4ADV
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 142 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1517A G 3.0 0.2 + - - -
1518A A 4.2 2.2 - - - -
140V LEU 3.4 2.0 + - - -
141V GLN* 1.3 69.9 - - - +
143V GLU* 1.3 76.3 + - - +
145V VAL* 3.1 4.9 + - - +
146V ASN* 3.0 35.8 + - - +
175V GLU* 3.5 44.1 + - + +
188V ASP* 2.9 55.6 + - + +
189V SER 3.9 4.0 - - - +
190V ALA* 4.0 13.5 - - + -
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Residues in contact with GLU 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516A G 5.6 2.9 - - - +
1517A G 5.8 0.2 - - - -
1518A A 2.3 39.6 + - - +
1519A A 5.1 6.3 - - - +
141V GLN 3.3 1.0 - - - -
142V LYS* 1.3 93.9 - - - +
144V VAL* 1.3 61.8 + - - +
146V ASN* 3.3 31.2 + - - +
147V ARG* 3.1 30.6 + - + +
156V ALA* 5.1 6.1 - - - +
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Residues in contact with VAL 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517A G 2.6 63.0 - - - +
119V SER* 5.0 3.1 - - - +
120V THR* 4.6 3.8 - - - +
123V MET* 4.1 15.5 - - + -
140V LEU* 3.9 25.1 - - + -
141V GLN* 2.9 10.5 + - + +
143V GLU* 1.3 75.4 - - - +
145V VAL* 1.3 65.0 + - - +
147V ARG* 3.2 9.9 + - - +
148V LEU* 3.0 23.0 + - + +
160V LEU* 4.3 11.2 - - + -
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Residues in contact with VAL 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140V LEU* 4.1 12.1 - - + -
141V GLN 3.2 7.7 + - - +
142V LYS 3.1 7.5 + - - +
144V VAL* 1.3 75.8 - - - +
146V ASN* 1.3 67.2 + - - +
148V LEU* 3.2 9.4 + - - +
149V VAL* 3.1 22.7 + - + +
170V VAL* 5.0 0.2 - - - +
172V PRO* 4.3 21.1 - - + -
190V ALA* 3.5 41.1 - - + +
191V VAL 4.6 1.1 - - - +
192V VAL* 3.9 34.3 - - + -
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Residues in contact with ASN 146 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142V LYS* 3.0 30.2 + - - +
143V GLU* 3.3 36.0 + - - +
144V VAL 3.3 0.2 - - - -
145V VAL* 1.3 81.3 - - - +
147V ARG* 1.3 56.3 + - - +
149V VAL* 3.6 10.8 - - - +
150V ALA* 3.0 29.3 + - - +
156V ALA* 3.7 11.4 - - + +
175V GLU* 4.6 9.9 + - - +
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Residues in contact with ARG 147 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516A G 4.1 22.3 + - - -
1517A G 1.6 51.0 + - - -
120V THR* 5.9 0.4 - - - +
143V GLU* 3.1 21.7 + - + +
144V VAL* 3.2 9.9 + - - +
146V ASN* 1.3 72.9 - - - +
148V LEU* 1.3 68.2 + - - +
149V VAL 3.2 0.7 + - - -
150V ALA 3.2 4.3 + - - -
155V LYS 5.9 0.2 - - - -
156V ALA* 3.2 33.4 - - + +
158V GLY* 5.7 4.6 - - - +
160V LEU* 3.8 39.9 - - + +
161V SER* 2.5 29.0 + - - +
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Residues in contact with LEU 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123V MET* 3.8 21.8 - - + -
127V PHE* 5.1 0.7 - - + -
140V LEU* 3.7 30.3 - - + -
144V VAL* 3.0 17.0 + - + +
145V VAL* 3.5 9.6 - - - +
147V ARG* 1.3 78.5 - - - +
149V VAL* 1.3 55.7 + - - +
160V LEU* 3.7 25.5 - - + +
161V SER* 3.8 9.5 - - - +
164V ALA* 3.6 25.2 - - + +
165V GLN* 3.0 19.6 + - - +
170V VAL* 3.6 22.8 - - + +
192V VAL* 3.9 16.4 - - + -
194V LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145V VAL 3.1 14.1 + - - +
146V ASN* 3.6 17.0 - - - +
148V LEU* 1.3 76.3 - - - +
150V ALA* 1.3 73.3 + - - +
151V GLY* 3.6 1.2 + - - -
165V GLN* 3.4 7.2 + - - +
170V VAL* 3.6 35.0 - - + +
172V PRO* 3.7 26.9 - - + -
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Residues in contact with ALA 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146V ASN 3.0 18.1 + - - +
147V ARG 3.2 6.7 + - - +
149V VAL* 1.3 78.4 - - - +
151V GLY* 1.3 59.2 + - - +
154V SER* 3.9 5.8 - - - +
156V ALA* 3.6 11.7 - - + -
157V TYR* 3.4 40.7 - - - +
161V SER* 3.8 1.2 - - - -
165V GLN* 2.9 21.0 + - - -
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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