Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 2WJ0
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 TYR 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 3.2 5.2 - - - +
42A GLY* 4.1 1.6 - - - -
44A GLY 4.1 9.9 + - - -
45A ARG 4.5 12.8 - - - -
46A THR* 1.3 84.5 - - - +
48A LEU* 1.3 66.2 + - - +
77A PHE* 4.6 3.8 - + + -
78A GLY 3.7 17.9 - - - +
79A ALA* 3.4 9.3 - - + -
80A GLU* 2.9 28.3 + - - +
47B TYR* 3.6 38.7 - + - -
77B PHE* 3.3 48.7 - + - -
78B GLY* 2.6 31.5 + - - -
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Residues in contact with LEU 48 (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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16A LEU* 4.4 11.2 - - + -
21A PHE* 3.9 26.2 - - + -
39A ILE 3.7 0.5 - - - +
40A VAL* 3.3 11.5 - - - +
41A ALA* 2.7 34.7 + - + +
46A THR* 3.3 28.5 - - + -
47A TYR* 1.3 76.3 - - - +
49A ALA* 1.3 59.2 + - - +
50A ILE* 3.9 28.6 - - + +
79A ALA* 3.7 4.4 - - - +
80A GLU* 3.8 4.7 - - - +
82A TYR* 3.8 28.7 - - + -
94A PHE* 6.0 1.8 - - + -
123A VAL* 3.8 21.8 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 4.8 2.5 - - + -
39A ILE 4.0 3.1 - - - -
40A VAL* 5.1 2.5 - - - +
48A LEU* 1.3 72.6 - - - +
50A ILE* 1.3 62.9 + - - +
70A LEU* 3.9 15.0 - - + -
73A PHE* 4.1 15.0 - - + -
74A ALA* 3.8 34.3 - - + -
79A ALA* 3.6 8.2 - - + +
80A GLU 3.1 8.0 + - - +
81A ALA* 4.3 0.4 - - - -
82A TYR 2.8 26.6 + - - -
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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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12A LEU* 4.7 2.7 - - + -
16A LEU* 4.2 21.5 - - + -
37A PRO* 3.2 6.9 - - - +
38A ASP* 3.0 25.3 + - - +
39A ILE* 3.1 27.6 + - + +
41A ALA* 5.3 0.7 - - + -
48A LEU* 3.9 32.8 - - + +
49A ALA* 1.3 80.6 - - - +
51A GLU* 1.3 74.0 + - - +
52A VAL* 4.0 13.9 - - + -
70A LEU* 4.0 2.1 - - - +
82A TYR* 3.2 17.0 - - + +
84A ALA* 4.1 15.7 - - + +
94A PHE* 4.7 13.7 - - + -
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Residues in contact with GLU 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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36A CYS 4.9 1.9 - - - +
37A PRO* 4.0 14.9 - - - +
38A ASP* 3.5 23.8 - - - +
50A ILE* 1.3 73.2 - - - +
52A VAL* 1.3 61.5 + - - +
53A LYS* 3.6 24.4 + - + -
62A LEU* 5.3 3.6 - - + -
66A GLU* 3.3 33.7 - - + +
70A LEU* 4.1 21.0 - - + +
82A TYR 2.8 12.8 + - - +
83A VAL* 3.3 14.3 - - + +
84A ALA 3.0 21.3 + - - -
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Residues in contact with VAL 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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5A GLY 5.5 0.4 - - - +
8A PHE* 4.7 2.9 - - + -
9A GLU* 4.4 20.2 - - + +
12A LEU* 4.0 11.4 - - + -
38A ASP* 2.8 34.7 + - + +
39A ILE* 3.7 29.8 - - + -
50A ILE* 4.0 7.2 - - + -
51A GLU* 1.3 72.5 - - - +
53A LYS* 1.3 82.1 + - - +
84A ALA* 3.7 3.1 - - - -
92A TRP* 3.6 33.0 - - + -
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Residues in contact with LYS 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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51A GLU* 3.6 20.8 + - - +
52A VAL* 1.3 93.7 + - - +
54A MET* 1.3 59.7 + - - +
55A ARG* 4.0 20.9 - - - +
60A LEU* 3.9 20.0 - - + -
61A TYR 5.6 0.4 + - - -
62A LEU* 3.8 20.0 - - + -
66A GLU* 2.7 31.4 + - - -
83A VAL* 4.4 7.9 - - + -
84A ALA 2.9 12.1 + - - +
85A LEU* 3.3 18.9 - - + +
86A LYS* 2.9 24.9 + - - +
92A TRP* 4.0 1.3 - - - -
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Residues in contact with MET 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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4A LYS* 6.0 0.2 - - + -
5A GLY* 6.0 3.1 - - - -
8A PHE* 3.8 55.4 - - + -
53A LYS* 1.3 74.8 - - - +
55A ARG* 1.3 121.1 + - - +
56A LYS* 4.3 13.9 - - + +
86A LYS* 3.5 15.9 - - + +
88A PRO* 4.6 10.1 - - + -
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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