Contacts of the helix formed by residues 144 - 155 (chain F) in PDB entry 3DCG
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 SER 144 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.2 7.4 - - - -
80B LYS* 5.4 3.8 - - - +
112B CYS* 3.6 13.5 + - - -
142F VAL 3.7 1.6 + - - -
143F GLY* 1.3 74.2 - - - +
145F LEU* 1.3 65.1 + - - +
146F GLN* 3.4 17.9 + - - +
147F TYR* 3.1 17.2 + - - +
148F LEU* 3.0 18.5 + - - +
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Residues in contact with LEU 145 (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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72B LYS 5.4 0.2 - - - +
73B VAL* 4.1 15.3 - - + -
76B TYR* 3.2 47.6 + - + -
93B PHE* 3.7 23.6 - - + -
95B ILE* 4.4 2.9 - - + -
103B LEU* 3.8 33.7 - - + +
107B ALA* 3.8 22.2 - - + -
112B CYS* 3.0 23.5 + - - +
144F SER* 1.3 72.3 - - - +
146F GLN* 1.3 57.3 + - - +
148F LEU* 4.3 3.4 - - + -
149F ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 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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104B LEU* 3.9 22.0 - - + +
107B ALA* 3.4 15.5 + - + -
108B ASN* 3.6 44.2 + - + +
111B ASP* 4.3 9.1 + - - +
112B CYS 3.2 24.7 + - - +
144F SER* 3.2 8.4 + - - +
145F LEU* 1.3 77.4 - - - +
147F TYR* 1.3 57.4 + - - +
149F ALA* 3.4 2.8 + - - +
150F LEU* 3.0 29.3 + - - +
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Residues in contact with TYR 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 GLY* 4.2 13.2 - - - -
144F SER* 3.1 19.0 + - - +
146F GLN* 1.3 79.7 - - - +
148F LEU* 1.3 79.7 + - + +
150F LEU* 3.3 8.6 + - + +
151F ALA* 2.9 40.0 + - + +
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Residues in contact with LEU 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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76B TYR* 3.8 18.6 - - + -
79B TYR* 4.6 7.0 - - + +
93B PHE* 4.0 31.4 - - + +
95B ILE* 3.7 16.2 - - + +
142F VAL* 5.0 0.4 - - + -
143F GLY* 3.7 22.9 - - - +
144F SER 3.0 15.6 + - - +
145F LEU* 3.8 4.3 - - - +
147F TYR* 1.3 97.8 - - + +
149F ALA* 1.3 57.3 + - - +
151F ALA* 3.4 7.3 + - + +
152F ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 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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95B ILE* 3.9 8.9 - - - +
100B ALA* 3.4 36.0 - - - +
103B LEU* 4.2 13.7 - - + -
104B LEU* 3.7 20.2 - - - +
145F LEU 2.9 18.7 + - - +
146F GLN 3.8 3.6 - - - +
148F LEU* 1.3 75.6 - - - +
150F LEU* 1.3 62.2 + - - +
152F ALA* 3.3 3.3 + - - -
153F LEU* 3.3 17.3 + - - +
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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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104B LEU* 4.5 17.9 - - + +
146F GLN 3.0 17.1 + - - +
147F TYR* 3.7 8.1 - - + +
149F ALA* 1.3 73.0 - - - +
151F ALA* 1.3 65.7 + - - +
153F LEU* 3.0 28.9 + - + +
154F ILE* 3.1 30.9 + - + +
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Residues in contact with ALA 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 TYR* 2.9 31.6 + - + +
148F LEU* 3.6 10.1 - - + +
150F LEU* 1.3 76.7 - - - +
152F ALA* 1.3 61.3 + - - +
154F ILE* 3.3 17.6 + - - +
155F LYS* 3.3 36.0 + - - +
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Residues in contact with ALA 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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95B ILE* 3.8 40.2 - - + +
97B PRO* 3.9 17.0 - - + +
100B ALA* 4.0 6.1 - - + -
148F LEU 3.0 13.9 + - - +
149F ALA 3.5 10.3 - - - +
150F LEU 3.1 0.4 - - - -
151F ALA* 1.3 77.3 - - - +
153F LEU* 1.3 57.1 + - - +
155F LYS* 3.6 22.4 + - - +
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Residues in contact with LEU 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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99A LEU* 5.5 6.7 - - + -
97B PRO* 4.0 13.5 - - + +
100B ALA* 3.7 22.7 - - + -
101B LEU* 4.0 40.2 - - + +
104B LEU* 4.6 6.1 - - + -
149F ALA 3.3 8.3 + - - +
150F LEU* 3.0 26.4 + - + +
152F ALA* 1.3 72.8 - - - +
154F ILE* 1.3 65.8 + - + +
155F LYS 3.2 5.4 - - - +
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Residues in contact with ILE 154 (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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150F LEU* 3.1 38.5 + - + +
151F ALA* 3.3 15.0 + - - +
153F LEU* 1.3 78.7 - - + +
155F LYS* 1.3 73.6 + - + +
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Residues in contact with LYS 155 (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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97B PRO* 4.8 13.0 - - + -
151F ALA* 3.3 31.6 + - - +
152F ALA* 3.6 17.7 + - - +
153F LEU 3.2 4.8 - - - +
154F ILE* 1.3 94.6 - - + +
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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