Contacts of the strand formed by residues 42 - 47 (chain C) in PDB entry 3CQ3
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 ARG 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.8 2.3 - - - +
39C GLU* 2.8 68.9 + - + +
40C PRO* 3.2 1.4 - - - +
41C PRO* 1.3 87.0 - - + +
43C ALA* 1.3 64.3 + - - +
44C TYR* 6.5 0.4 - - + -
74C VAL* 4.3 2.8 - - - +
76C GLU* 3.1 28.5 - - + +
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Residues in contact with ALA 43 (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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37C VAL 3.5 6.1 - - - +
38C VAL* 4.2 13.9 - - + +
42C ARG* 1.3 77.6 - - - +
44C TYR* 1.3 61.4 + - - +
68C LEU* 4.7 8.5 - - + -
71C LEU* 4.7 5.4 - - + -
74C VAL* 3.6 26.5 - - + -
76C GLU 2.8 6.4 + - - +
77C VAL* 3.5 13.0 - - + +
78C GLU* 2.9 27.9 + - - +
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Residues in contact with TYR 44 (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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35C ASP* 3.4 28.0 - - - -
36C LEU* 3.3 7.6 - - - +
37C VAL* 2.6 59.8 + - + +
42C ARG* 6.6 0.2 - - - -
43C ALA* 1.3 75.4 - - - +
45C VAL* 1.3 64.3 + - - +
46C ARG* 3.1 43.3 + - + +
68C LEU* 5.3 0.7 - - - -
78C GLU* 3.5 31.0 - - + +
80C GLU* 3.7 24.8 - - + +
22D GLU* 5.3 2.0 - - - -
51D THR* 4.4 12.5 - - + +
52D PRO* 4.5 5.0 - - - +
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Residues in contact with VAL 45 (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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15C LEU* 4.9 2.0 - - + -
33C ILE* 3.8 30.3 - - + -
35C ASP 3.2 11.0 - - - +
36C LEU* 4.1 5.6 - - + -
44C TYR* 1.3 81.1 - - - +
46C ARG* 1.3 68.2 + - - +
47C MSE 4.1 3.1 - - + -
64C VAL* 3.9 9.6 - - + -
68C LEU* 3.9 22.2 - - + -
78C GLU 3.0 5.4 + - - +
79C VAL* 3.6 36.3 - - + -
80C GLU* 2.8 26.7 + - - +
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Residues in contact with ARG 46 (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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33C ILE 3.8 0.5 - - - -
34C TYR* 2.8 36.4 + - + +
35C ASP* 2.9 35.3 + - + +
44C TYR* 3.1 37.1 + - + +
45C VAL* 1.3 73.3 - - - +
47C MSE 1.3 65.9 - - - +
80C GLU* 3.2 16.2 - - + +
82C THR* 3.9 24.2 - - + +
84C GLU 5.1 3.4 + - - -
50D THR 2.9 29.4 + - - -
51D THR* 3.9 7.5 - - - +
52D PRO* 4.0 17.4 - - - +
87D TRP* 3.0 34.8 + - - -
88D THR* 4.5 0.2 - - - +
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Residues in contact with MSE 47 (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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27C VAL* 4.5 7.6 - - + -
32C LEU* 3.1 22.7 - - + +
33C ILE* 4.2 10.1 - - + -
34C TYR* 4.2 4.0 - - - +
45C VAL* 4.5 3.1 - - + -
46C ARG* 1.3 75.0 - - - +
48C THR* 1.3 77.4 + - - +
49C LEU* 4.7 4.0 - - + -
60C LEU* 3.9 25.1 - - + -
61C GLY* 4.1 8.3 - - - -
64C VAL* 3.6 36.8 - - + -
79C VAL* 3.9 22.0 - - + -
80C GLU 2.8 12.8 + - - +
81C VAL* 3.2 14.7 - - + -
82C THR* 2.8 31.0 + - - +
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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