Contacts of the strand formed by residues 55 - 68 (chain B) in PDB entry 5JTO
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 VAL 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN* 4.9 7.6 - - + +
50B GLN* 3.7 2.4 - - - +
51B LEU* 3.0 33.7 + - + -
52B ALA* 2.9 33.4 - - + +
53B ASP 3.1 11.0 - - - +
54B ASP* 1.3 77.9 - - + +
56B TYR* 1.3 61.7 + - - +
83B ILE* 3.6 25.6 - - + -
84B PHE 4.1 2.5 - - - -
85B SER* 3.8 17.0 - - - +
304E PRO* 5.8 1.8 - - + +
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 6.5 0.7 - - - -
49B SER 3.6 6.1 - - - +
50B GLN* 3.3 39.5 + - + -
51B LEU* 4.7 0.9 - - - -
54B ASP* 3.5 27.7 + - - -
55B VAL* 1.3 73.2 - - - +
57B GLU* 1.3 63.5 + - - +
58B VAL* 4.2 5.6 - - + -
83B ILE* 3.3 10.5 - - - +
84B PHE* 3.0 34.1 + - + +
86B ILE* 3.1 48.5 + - + -
87B ALA* 5.9 0.3 - - - -
89B ILE* 5.7 0.4 - - + -
277H LEU* 3.2 40.4 - - + +
278H LEU* 3.6 34.5 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 3.8 11.2 - - + +
17B TYR* 3.1 28.1 + - - +
19B LYS* 2.8 25.1 + - - +
48B SER* 3.3 5.8 - - - -
49B SER* 2.8 49.4 + - - +
51B LEU* 3.8 9.9 - - + -
56B TYR* 1.3 75.6 - - - +
58B VAL* 1.3 61.1 + - - +
59B VAL* 3.2 13.0 - - - +
81B GLY* 3.6 8.8 - - - -
82B GLY 3.2 26.7 + - - +
83B ILE* 3.8 12.6 - - + -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 3.9 2.7 - - - -
48B SER* 4.6 4.5 - - - +
56B TYR* 5.2 2.9 - - + -
57B GLU* 1.3 76.7 - - - +
59B VAL* 1.3 63.0 + - - +
60B LEU* 5.4 0.9 - - + -
82B GLY 2.8 39.3 + - - +
84B PHE* 4.2 19.7 - - + -
86B ILE* 5.0 9.2 - - + -
98B LEU* 4.0 29.4 - - + +
102B CYS* 4.7 6.7 - - + -
103B PRO* 5.1 4.7 - - + -
106B LEU* 3.3 19.3 - - + +
278H LEU* 6.4 0.9 - - + -
281H PHE* 3.6 31.0 - - + -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 3.7 21.1 - - + +
45B ASP 3.9 2.9 - - - +
46B THR* 4.1 1.9 - - - -
47B ALA* 2.9 52.4 + - + +
48B SER* 5.4 0.9 - - - -
57B GLU* 3.2 26.7 - - - +
58B VAL* 1.3 75.2 - - - +
60B LEU* 1.3 63.7 + - - +
61B ARG* 4.8 1.3 - - + +
79B GLN* 3.7 47.6 - - + +
80B GLN 3.8 2.9 - - - -
81B GLY* 3.9 4.0 - - - -
281H PHE* 4.7 0.5 - - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.9 21.3 - - + -
45B ASP 4.1 11.0 - - - +
46B THR* 4.4 16.2 - - + -
58B VAL* 4.1 2.3 + - + -
59B VAL* 1.3 72.0 - - - +
61B ARG* 1.3 68.4 + - - +
62B VAL* 3.6 29.4 + - + +
78B VAL 4.0 0.2 - - - +
79B GLN* 3.8 1.5 - - - -
80B GLN* 3.1 36.3 + - - +
103B PRO* 3.7 38.4 - - + +
106B LEU* 4.1 20.0 - - + -
107B PHE* 5.3 6.7 - - + -
110B ALA* 4.9 1.2 - - + +
133B PHE* 5.9 0.7 - - + -
281H PHE* 5.4 2.5 - - + -
286H MET* 6.4 2.2 - - + -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 5.1 1.6 - - - -
44B LEU* 3.1 29.6 - - - +
45B ASP* 3.0 53.4 + - + +
47B ALA* 5.6 3.0 - - - +
59B VAL* 4.0 1.9 - - + -
60B LEU* 1.3 72.7 - - - +
62B VAL* 1.3 63.2 + - - +
63B THR* 3.4 23.3 - - - +
77B GLU* 2.9 31.6 + - + -
78B VAL 3.3 12.8 - - - +
79B GLN* 3.1 32.1 + - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 5.3 1.8 - - + -
43B ASP 4.1 2.5 - - - -
44B LEU* 4.3 17.0 - - + -
60B LEU* 3.6 26.9 - - + +
61B ARG* 1.3 69.4 - - - +
63B THR* 1.3 60.4 + - - +
64B VAL* 4.4 7.4 - - + -
77B GLU* 3.6 1.9 - - - -
78B VAL 3.0 30.0 + - - +
107B PHE* 4.3 13.7 - - + -
110B ALA* 3.9 24.2 - - + -
111B ARG* 5.9 0.9 - - - +
114B ILE* 3.4 31.1 - - + +
128B LEU* 4.6 16.6 - - + -
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.4 5.2 - - - +
42B LEU* 3.5 3.5 - - - +
43B ASP* 3.0 50.5 + - + +
61B ARG* 3.4 16.6 - - - -
62B VAL* 1.3 72.4 - - - +
64B VAL* 1.3 65.2 + - - +
65B THR* 4.5 12.6 - - - +
76B CYS 3.5 12.8 - - - +
77B GLU* 3.1 30.5 + - + +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.9 21.1 - - + -
41B LYS 3.3 3.6 - - - +
42B LEU* 4.2 16.8 - - + -
62B VAL* 4.0 2.4 + - + -
63B THR* 1.3 74.6 - - - +
65B THR* 1.3 66.2 + - - +
74B PHE* 4.2 13.1 - - + +
75B LEU* 3.8 0.7 - - - -
76B CYS* 2.8 48.2 + - + +
114B ILE* 3.5 34.5 - - + -
126B LEU* 3.9 25.1 - - + -
128B LEU* 5.8 1.3 - - + -
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLU 3.5 1.6 - - - +
40B VAL* 3.2 5.9 - - - +
41B LYS* 2.8 56.2 + - + +
63B THR* 4.2 10.8 - - - +
64B VAL* 1.3 77.8 + - - +
66B ALA* 1.3 68.7 + - - +
67B SER* 5.0 7.4 - - - +
72B THR* 5.8 0.2 - - + -
74B PHE 3.9 2.7 - - - -
75B LEU* 3.7 24.0 - - + +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO* 4.0 11.2 - - + -
39B GLU 3.3 5.8 - - - +
40B VAL* 4.4 5.8 - - + -
65B THR* 1.3 79.7 - - - +
67B SER* 1.3 65.3 + - - +
72B THR* 3.5 6.4 - - - +
73B ALA* 2.9 23.2 + - + -
74B PHE* 3.0 53.5 + - + +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO* 3.7 1.0 - - - +
39B GLU* 2.9 46.3 + - - +
65B THR* 5.0 7.6 - - - +
66B ALA* 1.3 78.4 - - - +
68B LEU* 1.4 62.3 + - - +
69B GLY 4.4 3.6 + - - -
70B GLU 5.7 0.9 - - - -
71B GLU 3.3 19.1 - - - -
72B THR* 3.9 5.8 - - - -
73B ALA* 3.5 6.8 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 4.3 4.0 - - + -
34B LYS* 3.4 48.7 - - + +
35B ASP 4.1 0.9 - - - -
36B TRP* 3.2 38.6 - - + +
37B GLN 4.1 5.8 - - - +
38B PRO* 3.8 12.6 - - + -
67B SER* 1.4 72.4 - - - +
69B GLY* 1.3 63.2 + - - +
70B GLU 3.4 0.2 + - - -
71B GLU* 3.0 30.8 + - - +
72B THR 4.8 0.2 - - - +
73B ALA* 3.5 30.1 - - + -
297H TYR* 6.2 2.0 - - + -
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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