Contacts of the strand formed by residues 48 - 58 (chain A) in PDB entry 6YBX
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 GLY 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER 3.5 8.1 - - - -
19A LYS* 4.2 4.9 - - - -
24A LEU* 4.2 5.6 - - - -
45A THR* 4.3 3.2 - - - +
46A ASN 3.4 2.8 - - - -
47A GLY* 1.3 79.2 - - - +
49A LYS* 1.3 67.3 + - - +
89A GLU* 3.4 0.9 - - - +
90A PHE* 2.9 53.5 + - - -
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Residues in contact with LYS 49 (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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17A ALA* 3.4 4.0 - - - +
18A SER 2.9 32.1 + - - +
47A GLY* 4.2 7.1 + - - +
48A GLY* 1.3 79.5 + - - +
50A ILE* 1.3 64.9 + - - +
51A TRP* 3.7 12.1 - - + -
80A PHE* 3.6 46.4 - - + -
87A LEU* 4.1 24.5 - - + -
88A ALA 3.2 8.1 - - - +
89A GLU* 2.8 38.5 + - + +
90A PHE* 3.8 3.0 - - - -
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Residues in contact with ILE 50 (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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3A PHE* 3.6 33.4 - - + -
5A ILE* 4.1 28.9 - - + -
16A ALA 3.3 9.4 - - - +
17A ALA* 4.0 15.3 - - + -
39A ILE* 4.4 5.2 - - + -
49A LYS* 1.3 79.7 - - - +
51A TRP* 1.3 71.6 + - - +
87A LEU* 3.9 1.6 - - - +
88A ALA* 2.9 39.2 + - + +
90A PHE* 3.8 16.1 - - + -
112A MET* 3.9 2.0 - - - +
201A VAL* 4.2 27.6 - - + -
203A PHE* 4.4 7.0 - - + -
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Residues in contact with TRP 51 (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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15A ALA* 3.5 3.5 - - - -
16A ALA* 2.9 54.4 + - + +
18A SER* 3.9 19.3 - - - -
49A LYS* 3.7 23.1 - - + -
50A ILE* 1.3 82.6 - - - +
52A ALA* 1.3 80.8 + - - +
53A ARG* 3.7 8.3 - - + +
69A GLY* 3.0 20.2 + - - -
77A CYS* 4.0 10.1 - - + -
79A ARG 3.5 22.2 - - - -
80A PHE* 3.8 16.2 - + - -
81A GLY* 3.4 22.1 - - - -
85A THR* 3.7 19.1 - - + -
86A THR 3.5 19.1 - - - +
87A LEU* 4.0 11.7 - - + -
112A MET* 4.6 0.2 - - - -
203A PHE* 3.9 11.5 - - - -
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Residues in contact with ALA 52 (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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13A VAL* 4.1 17.0 - - + -
14A TRP 3.9 3.4 - - - -
15A ALA* 4.5 0.9 - - - +
51A TRP* 1.3 85.8 - - - +
53A ARG* 1.3 63.3 + - - +
68A THR 4.5 0.5 - - - +
85A THR* 4.6 0.2 - - - +
86A THR 4.8 2.0 + - - -
109A ASN* 2.8 24.2 + - - +
110A VAL* 4.1 23.6 - - + -
112A MET* 5.2 0.2 - - - +
203A PHE* 3.6 31.5 - - + -
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Residues in contact with ARG 53 (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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13A VAL* 3.4 8.5 - - - +
14A TRP* 2.9 57.5 + - - +
15A ALA 2.9 23.2 + - - -
16A ALA* 3.8 4.2 - - - +
28A GLY* 3.7 3.4 - - - -
29A ARG 4.1 2.0 - - - +
51A TRP* 3.7 11.2 - - + +
52A ALA* 1.3 77.7 - - - +
54A THR* 1.3 63.1 + - - +
56A CYS* 3.7 13.0 - - - -
58A PHE* 3.8 12.1 - - - -
66A CYS* 3.9 7.1 - - - -
68A THR* 3.3 14.4 - - - +
69A GLY 3.3 29.2 - - - +
70A ASP* 4.5 1.8 + - - +
71A CYS* 3.7 2.4 - - - +
74A LEU 2.8 28.1 + - - -
75A LEU* 2.8 24.4 + - - +
77A CYS* 3.4 14.5 - - - -
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Residues in contact with THR 54 (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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11A TYR* 4.3 17.7 - - + -
12A THR 5.0 2.5 - - - -
13A VAL* 4.5 3.4 - - + -
14A TRP* 4.6 1.6 - - - -
53A ARG* 1.3 79.2 - - - +
55A ASP* 1.3 78.5 + - - +
56A CYS* 3.4 2.8 + - - -
66A CYS* 3.7 2.3 - - - +
67A LYS* 3.0 22.3 + - - +
68A THR* 2.7 35.2 + - - +
109A ASN* 4.5 2.5 - - + +
110A VAL* 3.8 28.7 - - + -
142A GLY 5.0 1.6 + - - -
143A GLY* 5.9 0.3 - - - -
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Residues in contact with ASP 55 (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 THR 5.2 1.0 + - - -
14A TRP* 3.9 10.3 - - - -
54A THR* 1.3 83.5 + - - +
56A CYS* 1.3 61.2 - - - +
57A TYR* 4.1 17.6 + - + -
65A ILE* 4.1 1.7 - - - +
66A CYS* 3.6 1.7 - - - -
67A LYS* 3.4 43.9 + - + +
142A GLY 4.5 5.4 - - - +
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Residues in contact with CYS 56 (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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14A TRP* 3.5 55.3 - - + -
53A ARG* 3.7 10.8 - - - -
54A THR 4.0 1.3 - - - -
55A ASP* 1.3 77.2 - - - +
57A TYR* 1.3 72.9 + - - +
58A PHE* 3.5 15.5 - - + -
65A ILE 3.1 5.4 - - - -
66A CYS* 2.0 46.2 - - - -
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Residues in contact with TYR 57 (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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55A ASP* 4.1 18.4 + - + -
56A CYS* 1.3 80.1 - - - +
58A PHE* 1.3 61.2 + - - +
64A GLY* 3.0 5.7 - - - -
65A ILE* 2.8 44.6 + - + +
67A LYS* 5.9 5.4 - - - -
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Residues in contact with PHE 58 (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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14A TRP* 3.7 25.6 - + - -
53A ARG* 3.8 3.4 - - - -
56A CYS* 3.5 21.8 - - + -
57A TYR* 1.3 75.3 - - - +
59A ASP* 1.3 68.6 + - - +
62A GLY* 3.9 4.7 - - - -
63A SER 3.5 7.2 - - - +
64A GLY* 3.6 18.4 - - - -
65A ILE 4.3 4.0 - - - -
66A CYS* 3.6 20.6 - - - -
70A ASP* 5.2 0.7 - - - -
73A GLY* 4.0 8.5 - - - -
74A LEU 3.5 9.9 - - - -
75A LEU* 3.4 51.6 - - + -
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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