Contacts of the strand formed by residues 63 - 69 (chain A) in PDB entry 2QBX
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 THR 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A SER* 3.9 25.6 - - - +
56A GLY 3.3 7.4 - - - +
57A TYR* 3.6 23.6 - - - -
61A MET 3.9 2.0 + - - -
62A ASN* 1.3 73.7 - - - +
64A ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 4.2 37.7 - - + +
55A SER* 3.2 7.2 - - - -
56A GLY 2.7 45.8 + - - +
58A ASP* 3.8 26.5 - - - +
62A ASN* 4.5 9.0 - - + +
63A THR* 1.3 80.7 - - - +
65A ARG* 1.3 65.2 + - - +
66A THR* 4.1 3.6 - - + -
196A ILE* 3.2 43.5 - - + +
197A ALA* 4.8 0.9 - - + -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A SER* 4.7 9.2 + - - +
37A ALA* 4.9 6.1 - - + +
39A ALA 4.1 18.2 - - - +
40A GLU* 4.4 15.0 - - - +
41A LEU* 3.3 34.8 - - + +
53A GLU* 2.8 41.8 + - - +
54A VAL 3.9 4.8 - - - -
55A SER* 3.4 22.2 - - - -
64A ILE* 1.3 77.7 - - - +
66A THR* 1.3 63.8 + - - +
196A ILE 3.7 10.2 - - - +
406A SO4 3.0 41.0 + - - -
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.8 0.9 - - - -
53A GLU* 3.2 8.7 - - - +
54A VAL* 2.8 50.9 + - - +
55A SER 4.3 2.6 + - - -
56A GLY* 4.0 22.4 - - - -
64A ILE* 4.1 8.5 - - + -
65A ARG* 1.3 80.1 - - - +
67A TYR* 1.3 65.2 + - - +
68A GLN* 5.0 2.6 + - - -
194A SER* 4.0 12.2 + - - +
195A LEU 3.4 12.6 - - - -
196A ILE* 3.7 28.3 - - + +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.7 21.5 - - + -
42A GLY* 3.5 1.6 + - - -
43A TRP* 3.0 62.1 + + + -
45A VAL* 4.0 12.6 - - + -
51A TRP* 3.5 20.6 - - + -
52A GLU 3.3 11.4 - - - -
53A GLU* 2.9 50.4 + - + -
66A THR* 1.3 75.5 - - - +
68A GLN* 1.3 59.9 + - - +
81A LEU* 3.6 24.2 - - + -
194A SER* 3.4 3.4 + - - -
195A LEU* 2.8 35.9 + - + +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP* 3.2 4.1 - - - -
52A GLU* 2.8 34.7 + - - +
54A VAL* 4.1 33.9 - - + +
55A SER 5.5 0.2 + - - -
66A THR* 5.0 2.2 + - - +
67A TYR* 1.3 75.8 - - - +
69A VAL* 1.3 64.4 + - - +
70A CYS* 5.7 0.2 - - + -
193A MET 3.4 12.6 - - - +
194A SER* 4.1 8.8 + - - -
4P TRP* 3.5 28.3 + - - -
5P ILE* 3.9 23.8 - - + +
6P GLN* 4.4 17.3 + - - +
8P ARG* 2.9 16.7 + - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLY* 3.5 29.6 - - - -
51A TRP* 3.7 17.5 - - + +
68A GLN* 1.3 76.0 - - - +
70A CYS* 1.3 66.1 + - - +
71A ASN* 4.6 4.0 - - - +
79A ASN* 4.1 8.1 - - + +
188A ASP* 3.6 44.4 - - + +
191A GLY 4.5 0.4 - - - +
192A CYS* 3.4 0.5 - - - -
193A MET* 2.9 47.8 + - + +
5P ILE* 4.6 0.2 - - - +
8P ARG* 3.3 6.7 - - - +
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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