Contacts of the strand formed by residues 52 - 58 (chain S) in PDB entry 5EF3
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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23S GLY* 3.8 16.8 - - - -
24S LEU 3.4 3.4 - - - +
26S ARG* 3.5 1.8 + - - -
33S HIS* 2.5 24.6 + - - -
47S GLN 4.5 1.3 - - - +
48S PHE* 3.5 5.7 - - + -
49S THR* 2.8 37.7 + - - +
51S HIS* 1.3 76.9 - - - +
53S SER* 1.3 56.7 + - - +
54S ALA 3.5 22.2 - - - +
55S ILE* 3.9 16.4 - - + -
101T TRP* 2.9 25.4 + - + +
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Residues in contact with SER 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R GLN* 3.0 40.3 + - - +
49R THR* 3.7 11.2 - - - -
24S LEU 3.3 4.0 + - - -
25S THR 3.9 0.3 + - - -
26S ARG* 3.3 36.8 + - - +
48S PHE* 3.8 6.9 - - - -
52S THR* 1.3 72.4 - - - +
54S ALA* 1.3 59.6 + - - +
101S TRP* 2.9 33.6 + - - +
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Residues in contact with ALA 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R LEU* 4.3 4.9 - - + -
45R ILE 3.1 12.8 - - - +
46R ALA* 4.0 14.6 - - + -
24S LEU* 2.8 52.1 + - + -
48S PHE* 4.0 1.5 - - - -
52S THR* 3.5 8.6 - - - +
53S SER* 1.3 79.3 + - - +
55S ILE* 1.3 62.9 + - - +
101S TRP* 4.2 13.9 - - + -
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Residues in contact with ILE 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R VAL 3.9 0.7 - - - +
44R LEU* 3.4 4.9 - - - +
45R ILE* 2.8 45.2 + - + +
10S VAL* 4.0 22.0 - - + -
12S ILE* 4.8 3.1 - - + -
21S VAL* 3.6 29.8 - - + -
22S ILE 3.3 5.4 - - - +
24S LEU* 4.7 0.2 - - - -
46S ALA* 4.3 9.9 - - + +
47S GLN 4.4 4.0 - - - +
48S PHE* 3.8 26.2 - - + -
52S THR* 3.9 11.9 - - + -
54S ALA* 1.3 80.8 - - - +
56S LYS* 1.4 64.1 + - - +
57S VAL* 4.5 7.6 - - + -
101T TRP* 3.9 17.7 - - + -
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Residues in contact with LYS 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R GLU* 2.7 29.9 + - + +
37R LYS 3.7 12.3 + - - -
38R LEU* 3.8 23.8 - - + -
42R GLU* 3.8 15.0 + - + -
43R VAL 3.3 10.1 - - - +
44R LEU* 4.2 6.1 - - + -
20S ASN 3.5 1.7 - - - +
21S VAL* 3.5 2.4 - - - -
22S ILE* 2.7 52.8 + - + +
24S LEU* 4.1 13.9 - - + +
32S PHE* 4.5 5.6 - - + -
55S ILE* 1.4 72.9 - - - +
57S VAL* 1.4 67.5 + - - +
58S ARG* 3.3 22.5 - - + +
136W G 6.0 0.2 - - - +
137W A 3.9 0.6 - - - +
138W G 3.0 19.8 + - - -
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Residues in contact with VAL 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R GLU* 3.8 9.7 - - - +
43R VAL 2.9 29.3 + - - +
45R ILE* 4.7 7.2 - - + -
12S ILE* 4.3 24.7 - - + -
19S VAL* 4.2 10.1 - - + -
20S ASN 3.3 6.7 - - - +
21S VAL* 4.7 4.7 - - + -
55S ILE* 4.5 8.5 - - + -
56S LYS* 1.4 77.4 - - - +
58S ARG* 1.4 61.3 + - - +
61S ALA* 4.0 17.3 - - + -
63S ILE* 3.9 23.1 - - + -
72S SER* 3.5 23.6 - - - +
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Residues in contact with ARG 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R GLU* 3.0 30.8 + - - +
18S GLY 4.4 1.1 - - - +
19S VAL* 3.3 7.3 - - - +
20S ASN* 2.8 47.1 + - + +
22S ILE* 3.6 26.0 - - + +
32S PHE* 4.2 2.2 - - - -
56S LYS* 3.3 30.2 - - + +
57S VAL* 1.4 73.7 - - - +
59S GLY* 1.3 62.5 + - - +
136W G 5.9 2.8 - - - +
137W A 5.3 1.4 - - - +
138W G 3.6 10.9 + - - -
139W U 3.4 35.3 + - - +
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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