Contacts of the helix formed by residues 58 - 73 (chain A) in PDB entry 2BT4
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 HIS 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A SER* 3.0 14.1 + - - +
57A ASN* 1.3 86.7 - - + +
59A GLU* 1.3 67.8 + - - +
61A GLU* 3.1 26.6 + - + +
62A LEU* 3.1 15.0 + - - +
83A TYR* 4.0 2.5 - - - -
2401A PO4 2.3 40.3 + - - +
258B HIS* 5.1 1.1 - + + -
260B GLY* 3.6 4.5 - - - +
261B GLU* 3.3 27.1 - - + -
264B ASP* 2.9 25.6 + - - -
458C HIS* 5.1 0.9 - - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 1.3 71.2 - - - +
60A GLY* 1.3 63.9 + - - +
62A LEU* 3.2 7.2 + - - +
63A VAL* 3.1 24.3 + - + +
83A TYR* 3.5 30.0 + - + +
87A SER* 2.5 31.8 + - - +
88A VAL 4.8 0.2 + - - -
89A ALA* 3.9 4.9 + - + +
90A ILE* 4.1 8.2 - - + +
2401A PO4 3.7 4.3 + - - +
2405A TRS 2.7 48.0 + - - -
259B GLU* 4.0 2.3 - - + +
260B GLY 5.5 0.4 - - - +
459C GLU* 4.2 3.1 - - - +
483C TYR* 3.6 30.0 + - - +
486C THR* 5.1 0.2 + - - -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 1.3 78.1 - - - +
61A GLU* 1.3 61.7 + - - +
63A VAL* 3.4 5.2 + - - +
64A ASP* 3.0 27.5 + - - +
2401A PO4 3.1 10.0 + - - -
457C ASN* 3.3 25.5 + - - +
458C HIS* 3.3 20.5 + - - -
483C TYR* 4.4 0.8 + - - -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 2.6 26.2 + - - +
58A HIS* 3.1 24.3 + - + +
60A GLY* 1.3 74.1 - - - +
62A LEU* 1.3 66.8 + - - +
64A ASP* 3.1 10.9 + - + +
65A TRP* 2.9 60.2 + - + +
458C HIS* 3.4 12.5 - - + -
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Residues in contact with LEU 62 (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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12A LEU* 4.4 19.5 - - + +
13A ASN 3.9 18.8 - - - +
14A GLY* 4.0 16.8 - - - -
56A SER* 4.1 12.1 - - - +
58A HIS 3.1 11.5 + - - +
59A GLU 3.5 6.5 - - - +
61A GLU* 1.3 78.1 - - - +
63A VAL* 1.3 56.3 + - - +
65A TRP* 3.3 24.1 + - + +
66A ILE* 3.0 36.3 + - + +
78A ILE* 5.6 4.3 - - + -
80A PRO* 5.2 3.8 - - + +
83A TYR* 3.8 29.4 - - + -
90A ILE* 4.0 16.6 - - + -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.1 15.4 + - + +
60A GLY* 3.5 10.5 - - - +
61A GLU 3.2 0.2 - - - -
62A LEU* 1.3 73.1 - - - +
64A ASP* 1.3 67.5 + - - +
66A ILE* 3.1 9.9 + - - +
67A HIS* 3.0 26.6 + - + +
89A ALA* 3.9 29.8 - - + +
90A ILE* 3.9 15.5 - - + -
93A ALA* 4.2 1.3 - - + -
415C PRO* 4.7 1.1 - - + -
416C ASN* 3.6 24.2 - - - +
457C ASN* 3.6 30.7 - - + +
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Residues in contact with ASP 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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60A GLY 3.0 12.6 + - - +
61A GLU* 3.1 12.0 + - + +
63A VAL* 1.3 77.6 - - - +
65A TRP* 1.3 69.3 + - + +
67A HIS* 3.3 9.2 + - - +
68A GLU* 3.1 20.3 + - - +
457C ASN* 2.6 36.0 + - - +
458C HIS* 3.2 23.8 + - - -
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Residues in contact with TRP 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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10A MET* 3.4 9.0 - - + +
12A LEU* 3.8 23.8 - - + -
54A ARG* 3.2 61.0 - - + +
55A GLN 3.5 23.1 - - - -
56A SER* 3.6 23.8 - - - -
61A GLU* 2.9 46.0 + - + +
62A LEU* 3.7 15.5 - - + +
63A VAL 3.2 0.4 - - - -
64A ASP* 1.3 78.5 - - + +
66A ILE* 1.3 60.9 + - - +
68A GLU* 3.2 12.8 + - - +
69A ALA* 2.9 24.4 + - - +
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Residues in contact with ILE 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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12A LEU* 3.6 20.6 - - + -
62A LEU* 3.0 25.1 + - + +
63A VAL* 3.1 6.9 + - - +
65A TRP* 1.3 74.0 - - - +
67A HIS* 1.3 67.7 + - + +
69A ALA* 3.2 7.8 + - - +
70A ARG* 2.8 23.7 + - - +
76A ILE* 4.5 2.2 - - + -
78A ILE* 4.5 4.7 - - + -
90A ILE* 4.0 24.5 - - + -
93A ALA* 3.5 46.9 - - + +
94A LEU* 4.0 19.1 - - + +
97A CYS* 3.8 13.1 - - - -
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Residues in contact with HIS 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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63A VAL* 3.0 30.5 + - + +
64A ASP* 3.3 10.1 + - - +
66A ILE* 1.3 78.5 - - + +
68A GLU* 1.3 61.7 + - - +
70A ARG* 3.3 20.3 + - - +
71A LEU* 3.6 14.1 + - - +
93A ALA* 4.4 5.4 - - + -
96A THR* 4.3 8.3 + - - -
416C ASN* 2.7 31.5 + - - -
418C ASN* 3.3 37.9 + - - +
419C LEU* 3.8 26.2 - - + +
457C ASN* 3.7 11.7 + - - -
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 4.4 0.2 - - + -
54A ARG* 2.8 43.4 + - - -
64A ASP 3.1 12.2 + - - +
65A TRP* 3.3 16.0 - - - +
67A HIS* 1.3 75.4 - - - +
69A ALA* 1.3 61.8 + - - +
71A LEU* 3.1 6.7 + - - -
72A ASN* 3.0 41.5 + - - +
73A HIS* 4.2 10.0 - - + -
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Residues in contact with ALA 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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10A MET* 3.8 20.1 - - + +
12A LEU* 5.7 0.2 - - + -
65A TRP 2.9 14.0 + - - +
66A ILE* 3.5 8.1 - - - +
68A GLU* 1.3 75.4 - - - +
70A ARG* 1.3 64.6 + - - +
73A HIS* 3.0 41.2 + - + +
76A ILE* 3.9 29.4 - - + -
100A LEU* 4.1 4.8 - - + +
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Residues in contact with ARG 70 (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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66A ILE 2.8 12.4 + - - +
67A HIS* 3.3 14.1 + - - +
69A ALA* 1.3 76.5 - - - +
71A LEU* 1.3 83.8 - - + +
73A HIS 5.0 1.0 - - - +
96A THR* 2.8 46.7 + - - +
97A CYS* 3.8 17.7 - - - -
98A ASP* 5.1 3.4 + - - -
100A LEU* 4.2 12.2 - - - +
419C LEU* 3.7 24.1 - - - +
422C GLN* 3.1 49.0 + - - +
423C ARG* 5.3 2.2 - - - +
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Residues in contact with LEU 71 (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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2A ARG* 3.0 22.7 + - - -
67A HIS 4.0 11.2 - - - +
68A GLU* 3.1 8.5 + - - +
69A ALA 3.0 0.2 - - - -
70A ARG* 1.3 110.0 - - + +
72A ASN* 1.3 69.7 + - - +
73A HIS 3.9 0.9 - - - -
422C GLN* 5.6 1.3 - - - +
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Residues in contact with ASN 72 (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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2A ARG* 3.5 19.3 + - - +
7A ALA* 3.4 15.8 - - - +
8A PRO* 4.2 4.5 - - - +
68A GLU* 3.0 30.9 + - - +
71A LEU* 1.3 95.7 - - - +
73A HIS* 1.3 75.6 + - + +
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Residues in contact with HIS 73 (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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2A ARG* 3.9 12.8 - - - +
7A ALA* 4.0 1.1 - - - -
8A PRO* 3.2 34.4 - - + +
10A MET* 3.5 35.8 - - + +
52A ASP* 3.0 29.4 + - + +
68A GLU* 4.3 11.4 - - + -
69A ALA* 3.0 26.2 + - + +
70A ARG 5.0 1.2 - - - +
71A LEU 3.9 0.4 - - - -
72A ASN* 1.3 98.0 - - + +
74A CYS* 1.3 61.1 + - - +
75A GLY 3.4 11.7 - - - +
100A LEU* 3.3 18.8 - - - +
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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