Contacts of the strand formed by residues 56 - 67 (chain A) in PDB entry 2JK4
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 LYS 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.6 4.2 - - - +
51A ASN* 3.1 34.0 + - + +
52A THR* 3.0 10.7 + - + +
53A GLU 4.9 0.5 - - - +
54A THR* 3.1 5.6 + - - -
55A THR* 1.3 84.4 - - - +
57A VAL* 1.3 98.8 + - - +
58A THR* 3.3 22.9 - - + +
81A ASP* 4.7 9.3 + - - -
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Residues in contact with VAL 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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49A SER 4.3 5.2 - - - +
50A ALA* 4.7 7.2 - - + +
54A THR* 5.3 6.5 - - - +
56A LYS* 1.3 107.6 + - - +
58A THR* 1.3 66.2 + - - +
81A ASP* 4.9 2.4 - - - +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 3.8 1.2 - - - -
49A SER* 2.3 53.8 + - - +
51A ASN* 3.1 24.4 + - - +
56A LYS* 3.3 27.3 + - + +
57A VAL* 1.3 84.3 - - - +
59A GLY* 1.3 59.7 + - - +
60A SER* 5.0 3.7 + - - -
81A ASP* 5.2 8.3 - - - +
82A ASN* 6.0 4.3 - - - +
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 4.2 7.2 - - - -
48A GLY* 4.4 3.1 - - - -
58A THR* 1.3 76.0 - - - +
60A SER* 1.3 61.0 + - - -
61A LEU* 3.9 3.8 - - - -
79A ASN* 3.3 9.5 + - - -
80A THR* 2.4 32.9 + - - +
81A ASP* 5.3 1.2 + - - -
82A ASN* 3.3 4.9 + - - +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 2.8 44.4 + - - +
48A GLY* 4.6 0.6 - - - -
49A SER* 4.3 12.9 + - - -
58A THR* 4.3 4.4 + - - -
59A GLY* 1.3 76.1 + - - -
61A LEU* 1.3 60.8 + - - +
62A GLU* 4.3 1.5 + - - +
79A ASN* 3.2 23.6 + - - +
82A ASN* 4.5 0.3 + - - -
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Residues in contact with LEU 61 (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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45A THR 3.7 3.1 - - - +
46A SER* 3.6 27.1 - - - +
47A SER 2.8 28.0 - - - +
59A GLY* 3.9 6.3 - - - -
60A SER* 1.3 81.3 - - - +
62A GLU* 1.3 60.9 + - - +
78A TRP* 3.7 28.0 + - - +
79A ASN* 4.0 6.3 + - - +
80A THR* 4.3 21.2 + - + +
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Residues in contact with GLU 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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44A PHE* 4.4 0.7 - - - +
45A THR* 2.7 73.6 + - - +
47A SER* 5.5 4.1 + - - +
60A SER 5.6 0.9 - - - +
61A LEU* 1.3 75.2 - - - +
63A THR* 1.3 63.0 + - - +
64A LYS* 3.5 20.3 + - - +
75A THR* 3.9 2.4 - - - +
76A GLU 4.1 3.4 - - - -
77A LYS* 3.0 55.4 + - + +
78A TRP* 4.3 1.8 - - - +
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Residues in contact with THR 63 (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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42A LEU* 6.3 0.4 - - + -
43A GLU 4.1 9.9 - - - +
44A PHE* 4.2 21.2 - - + +
62A GLU* 1.3 76.5 + - - +
64A LYS* 1.3 75.3 + - - +
65A TYR* 5.7 2.2 - - + -
75A THR* 3.7 2.9 - - - +
76A GLU* 2.9 44.5 + - + +
78A TRP* 4.2 28.5 - - + -
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Residues in contact with LYS 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 LYS* 4.5 15.6 - - - +
42A LEU* 3.8 2.4 - - - +
43A GLU* 2.6 58.7 + - + +
44A PHE 4.9 0.9 - - - +
45A THR* 3.3 38.9 - - + +
62A GLU* 3.5 22.1 + - - +
63A THR* 1.3 83.7 - - - +
65A TYR* 1.3 61.5 + - - +
74A PHE 4.0 2.7 - - - -
75A THR* 4.4 14.4 - - + +
77A LYS* 5.4 2.0 - - - +
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Residues in contact with TYR 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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40A ASN 5.2 2.0 - - - -
41A GLY* 3.3 13.2 - - - -
42A LEU* 3.3 31.0 - - + -
43A GLU* 3.9 1.6 - - - -
63A THR* 5.7 3.1 - - + -
64A LYS* 1.3 76.0 - - - +
66A ARG* 1.3 79.2 + - - +
67A TRP* 2.8 46.9 + + + -
73A THR* 3.4 6.2 - - - +
74A PHE* 2.7 62.7 + + + +
75A THR* 5.2 0.4 + - - -
76A GLU* 5.0 2.5 - - - +
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Residues in contact with ARG 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 GLY* 3.6 8.2 - - - +
43A GLU* 3.3 27.7 + - - +
65A TYR* 1.3 91.3 + - - +
67A TRP* 1.3 79.6 + - - +
68A THR 2.3 42.1 + - - +
69A GLU* 2.8 41.5 + - - +
72A LEU 4.0 2.8 + - - -
73A THR* 3.1 22.9 - - + -
91A GLU* 5.4 2.2 + - - -
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Residues in contact with TRP 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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65A TYR* 2.8 43.7 + + + -
66A ARG* 1.3 72.7 - - - +
68A THR* 1.3 108.4 + - - +
70A TYR* 4.4 12.8 - + - -
71A GLY* 3.6 15.5 - - - -
72A LEU* 2.7 60.6 + - + +
73A THR* 3.9 0.6 - - - +
74A PHE* 4.9 7.6 - + + -
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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