Contacts of the strand formed by residues 73 - 79 (chain C) 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 ALA 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS* 5.9 1.3 - - - +
47A ASP* 3.8 9.2 - - - +
4C PHE 3.1 6.5 + - - -
5C LEU* 3.2 8.8 - - + +
6C MET* 2.8 22.2 + - - -
46C LYS* 4.3 7.0 - - - +
62C PHE* 3.7 29.8 - - + -
66C THR* 4.4 11.2 - - + +
67C ALA* 3.8 18.0 - - + +
71C ALA 4.0 0.4 + - - -
72C PRO* 1.3 72.8 - - - +
74C THR* 1.3 62.0 + - - +
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 3.0 29.6 + - - +
48A ASP* 4.2 5.3 + - - +
6C MET* 3.2 31.4 - - - +
8C ARG* 4.1 17.8 - - + -
45C TYR 4.6 0.2 - - - +
46C LYS* 2.8 34.3 + - - +
62C PHE* 3.6 2.6 - - - -
73C ALA* 1.3 71.5 - - - +
75C VAL* 1.3 76.5 + - - +
76C GLY 4.3 1.6 - - - +
90C ILE* 4.4 11.7 - - + -
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.1 19.1 - - + -
6C MET 2.8 7.5 + - - +
7C ILE* 3.4 11.3 - - + +
8C ARG 2.8 26.9 + - - -
27C LEU* 4.1 21.1 - - + -
44C LEU* 4.1 29.6 - - + -
45C TYR 3.6 10.1 - - - +
51C LEU* 4.4 7.9 - - + -
62C PHE* 3.5 27.6 - - + -
74C THR* 1.3 76.9 - - - +
76C GLY* 1.3 70.7 + - - +
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ARG 3.6 6.1 - - - -
43C ARG 3.5 0.5 - - - +
44C LEU* 3.2 10.1 - - - +
45C TYR* 2.8 42.2 + - - -
74C THR* 4.2 2.0 - - - +
75C VAL* 1.3 73.3 - - - +
77C LEU* 1.3 60.2 + - - -
88C LEU* 3.8 20.2 - - - -
90C ILE* 4.0 10.3 - - - -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.1 12.3 - - + -
8C ARG 3.0 13.2 + - - +
9C ARG* 3.1 37.8 - - + +
14C ILE* 5.2 0.7 - - + -
31C VAL* 4.0 11.9 - - + -
35C LEU* 3.8 17.5 - - + -
42C GLN* 3.8 33.7 - - + +
43C ARG 3.4 1.3 - - - +
44C LEU* 3.7 22.2 - - + -
76C GLY* 1.3 74.2 - - - +
78C ALA* 1.3 64.6 + - - +
79C PHE* 3.7 28.3 - - + -
86C GLU* 5.5 0.2 - - - -
88C LEU* 3.7 10.2 - - - +
89C CYS 5.0 1.7 + - - +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLN* 3.6 2.4 - - - -
43C ARG* 2.8 40.7 + - + +
45C TYR* 4.1 22.0 - - + -
77C LEU* 1.3 75.9 - - - +
79C PHE* 1.3 63.7 + - - +
85C PHE* 3.5 5.8 - - + -
86C GLU* 3.6 30.3 - - + +
87C ALA 4.4 0.2 - - - +
88C LEU* 4.4 12.3 - - - +
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 3.3 42.0 - - - +
31C VAL* 4.4 2.0 - - + -
35C LEU* 3.7 31.9 - - + -
37C ARG* 3.6 50.7 - - + +
41C GLU 3.4 13.9 - - - -
42C GLN* 3.7 17.5 - - + -
77C LEU* 3.7 11.0 - - + -
78C ALA* 1.3 75.7 - - - +
80C ARG* 1.3 66.1 + - - +
81C ALA* 5.4 0.3 - - - +
85C PHE* 3.6 2.7 - - - -
86C GLU* 3.1 43.9 + - - +
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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