Contacts of the helix formed by residues 142 - 153 (chain F) in PDB entry 6V3O
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 ASP 142 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208E ASP* 5.4 3.8 - - - +
122F ARG* 3.6 23.7 + - - +
140F GLU* 4.0 1.6 + - - -
141F SER* 1.3 72.5 - - - +
143F ILE* 1.3 64.9 + - - +
144F GLU* 3.0 11.6 + - - +
145F GLU* 2.7 47.9 + - - +
146F THR* 3.0 25.4 + - - -
692F GLN* 3.2 26.5 - - - +
696F ALA* 4.9 0.7 - - - -
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ASP* 1.3 75.8 - - + +
144F GLU* 1.3 60.8 + - + +
146F THR* 3.4 5.3 + - - -
147F LEU* 3.0 52.2 + - + +
165F LEU* 5.2 3.8 - - + -
259F PHE* 4.6 6.1 - - + -
262F ARG* 3.9 27.6 - - + +
263F VAL* 4.6 14.1 - - + -
266F ALA* 4.1 15.0 - - + -
692F GLN* 3.1 26.9 + - + +
695F THR* 4.3 17.9 - - + -
696F ALA* 4.1 25.4 - - + +
699F LEU* 4.6 7.2 - - + -
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Residues in contact with GLU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E ASP* 2.8 39.7 - - - +
142F ASP* 3.0 9.9 + - - +
143F ILE* 1.3 80.2 - - + +
145F GLU* 1.3 61.7 + - + +
147F LEU* 3.2 3.9 + - + +
148F LYS* 2.9 66.6 + - + +
262F ARG* 5.2 1.2 - - - -
265F THR* 4.7 0.2 - - - +
266F ALA* 4.1 32.4 + - + +
269F ASN* 4.1 19.5 - - + +
270F ILE* 5.7 0.4 - - + -
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Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG* 2.7 33.7 + - - -
127F LYS* 3.5 16.2 + - - -
141F SER* 3.2 16.5 - - - -
142F ASP* 2.7 36.6 + - - +
144F GLU* 1.3 73.2 - - + +
146F THR* 1.3 57.3 + - - +
148F LYS* 3.8 9.1 - - + +
149F ARG* 2.9 33.8 + - - +
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Residues in contact with THR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F SER* 3.7 12.5 - - - -
142F ASP 3.0 18.1 + - - -
143F ILE* 3.6 6.5 - - + +
145F GLU* 1.3 76.8 - - - +
147F LEU* 1.3 63.5 + - - +
149F ARG* 3.3 11.8 + - - +
150F LEU* 3.0 39.6 + - + +
653F HIS* 4.8 1.7 + - - -
696F ALA* 3.6 36.0 - - + +
699F LEU* 5.0 9.2 - - + -
700F GLU* 4.0 22.0 + - + +
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ILE* 3.0 29.9 + - + +
144F GLU* 3.2 5.1 + - - +
146F THR* 1.3 76.3 - - - +
148F LYS* 1.3 61.3 + - - +
150F LEU* 3.2 6.5 + - + +
151F VAL* 3.1 28.6 + - - +
161F VAL* 3.6 24.0 - - + -
165F LEU* 4.6 4.7 - - + -
263F VAL* 6.0 0.4 - - + -
266F ALA* 3.7 32.5 - - + -
267F LEU* 4.1 13.2 - - + +
270F ILE* 3.8 30.3 - - + -
699F LEU* 3.6 22.4 - - + -
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Residues in contact with LYS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLU* 2.9 53.0 + - - +
145F GLU* 3.8 8.3 - - + +
147F LEU* 1.3 75.0 - - - +
149F ARG* 1.3 58.4 + - - +
151F VAL* 3.4 2.9 + - - +
152F SER* 2.9 36.7 + - - -
269F ASN* 4.2 19.0 + - - +
270F ILE* 4.2 14.4 - - + -
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Residues in contact with ARG 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU* 3.2 11.4 + - - -
141F SER* 2.6 34.4 + - - -
145F GLU* 2.9 21.9 + - - +
146F THR* 3.7 15.5 + - - +
148F LYS* 1.3 76.1 - - - +
150F LEU* 1.3 59.1 + - + +
153F GLU* 2.9 57.5 + - + +
154F VAL* 3.0 14.3 + - + -
700F GLU* 2.7 45.8 + - - -
704F HIS* 4.6 11.9 - - - -
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F THR* 3.0 38.9 + - + +
147F LEU* 3.2 11.0 + - - +
149F ARG* 1.3 82.4 - - + +
151F VAL* 1.3 58.1 + - - +
154F VAL* 3.5 17.5 - - + +
155F GLY 3.1 9.0 + - - -
156F LYS* 2.9 28.6 + - + +
161F VAL* 4.3 14.1 - - + -
699F LEU* 5.6 2.0 - - + -
700F GLU* 4.2 30.1 - - + +
703F MET* 3.6 51.6 - - + -
704F HIS* 5.0 0.2 - - + -
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Residues in contact with VAL 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU 3.1 16.4 + - - +
148F LYS* 4.2 3.1 - - - +
150F LEU* 1.3 79.5 - - - +
152F SER* 1.3 63.0 + - - +
155F GLY* 3.5 15.8 - - - -
156F LYS 3.1 20.1 - - - +
158F PRO* 3.8 26.2 - - + -
161F VAL* 4.1 16.6 - - + -
270F ILE* 4.4 20.4 - - + +
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Residues in contact with SER 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F LYS* 2.9 19.7 + - - -
151F VAL* 1.3 81.2 - - - +
153F GLU* 1.3 66.6 + - - +
155F GLY* 4.5 1.1 + - - -
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Residues in contact with GLU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ARG* 2.9 40.1 + - + +
152F SER* 1.3 88.4 - - - +
154F VAL* 1.3 66.6 + - + +
155F GLY* 3.2 1.4 + - - -
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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