Contacts of the strand formed by residues 52 - 58 (chain N) in PDB entry 5EEZ
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 THR 52 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23N GLY* 4.0 6.5 - - - -
24N LEU 3.4 5.2 - - - -
26N ARG* 3.4 1.8 + - - -
33N HIS* 2.3 31.2 + - - -
47N GLN 4.4 2.9 - - - +
48N PHE* 3.6 5.5 - - + +
49N THR* 3.0 33.9 + - - +
50N GLU 3.8 0.2 + - - -
51N HIS* 1.3 76.5 - - - +
53N SER* 1.3 58.5 + - - +
54N ALA 3.6 20.9 - - - +
55N ILE* 3.9 9.0 - - + -
101O TRP* 2.9 43.6 + - + +
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Residues in contact with SER 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M GLN* 3.1 38.0 + - - +
49M THR* 3.8 10.5 - - - -
24N LEU 3.3 4.2 + - - -
25N THR 3.8 0.7 + - - -
26N ARG* 3.5 34.9 - - - +
48N PHE* 3.9 6.7 - - - -
52N THR* 1.3 72.6 - - - +
54N ALA* 1.4 58.9 + - - +
101N TRP* 3.0 35.8 + - - +
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Residues in contact with ALA 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M LEU* 4.1 5.8 - - + -
45M ILE 3.1 13.5 - - - +
46M ALA* 4.0 14.6 - - + -
24N LEU* 2.8 56.3 + - + +
48N PHE* 3.9 1.9 - - - -
52N THR* 3.6 3.0 - - - +
53N SER* 1.4 77.9 + - - +
55N ILE* 1.3 64.3 + - - +
101N TRP* 4.2 13.9 - - + -
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Residues in contact with ILE 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M VAL 3.8 0.9 - - - +
44M LEU* 3.5 3.9 - - - -
45M ILE* 2.8 43.4 + - + +
10N VAL* 3.9 22.0 - - + -
12N ILE* 4.5 3.1 - - + -
21N VAL* 3.6 29.6 - - + -
22N ILE 3.3 6.3 - - - +
46N ALA* 4.4 10.1 - - + +
47N GLN 4.4 3.8 - - - +
48N PHE* 3.7 26.5 - - + -
52N THR* 3.9 11.2 - - + -
54N ALA* 1.3 80.4 - - - +
56N LYS* 1.4 63.8 + - - +
57N VAL* 4.3 10.3 - - + -
101O TRP* 4.0 18.6 - - + -
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Residues in contact with LYS 56 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M GLU* 2.9 30.0 + - + +
37M LYS 3.8 4.2 + - - -
38M LEU* 4.2 16.4 - - + -
42M GLU* 3.8 18.1 + - + -
43M VAL 3.2 10.1 - - - +
44M LEU* 4.1 9.6 - - + -
20N ASN 3.6 2.1 - - - +
21N VAL* 3.7 1.6 - - - -
22N ILE* 2.9 44.7 + - + +
24N LEU* 4.0 14.5 - - + +
32N PHE* 4.9 1.6 - - + -
55N ILE* 1.4 73.9 - - - +
57N VAL* 1.3 69.9 + - - +
58N ARG* 2.9 30.9 - - + +
112W A 3.7 8.7 - - - +
113W G 2.9 21.4 + - - -
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Residues in contact with VAL 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M GLU* 3.7 9.2 - - - +
43M VAL* 2.9 32.2 + - + +
45M ILE* 4.8 6.7 - - + -
12N ILE* 4.1 26.5 - - + -
19N VAL* 4.1 9.4 - - + -
20N ASN 3.5 7.9 - - - +
21N VAL* 4.6 2.9 - - + -
55N ILE* 4.3 8.7 - - + -
56N LYS* 1.3 78.1 - - - +
58N ARG* 1.3 63.4 + - - +
61N ALA* 4.0 16.8 - - + -
63N ILE* 3.9 22.4 - - + -
72N SER* 3.5 23.5 - - - +
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Residues in contact with ARG 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M GLU* 3.1 30.6 + - - +
18N GLY 4.6 0.7 - - - +
19N VAL* 3.5 6.2 - - - +
20N ASN* 3.0 44.6 + - + +
22N ILE* 3.8 30.7 - - + +
32N PHE* 4.0 1.2 - - - -
56N LYS* 2.9 21.8 - - + +
57N VAL* 1.3 74.7 - - - +
59N GLY* 1.3 63.6 + - - +
111W G 5.9 1.6 - - - +
112W A 4.7 3.2 + - - +
113W G 2.9 31.9 + - - -
114W U 3.2 29.1 + - - +
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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