Contacts of the strand formed by residues 52 - 58 (chain O) in PDB entry 5EEY
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23O GLY* 4.0 4.7 - - - -
24O LEU 3.4 5.2 - - - +
26O ARG* 3.4 1.9 + - - -
33O HIS* 2.4 35.3 + - - -
47O GLN 4.6 1.8 - - - +
48O PHE* 3.6 5.6 - - + -
49O THR* 2.9 38.3 + - - +
51O HIS* 1.3 77.9 - - - +
53O SER* 1.3 59.3 + - - +
54O ALA 3.5 21.5 - - - +
55O ILE* 3.9 20.6 - - + -
101P TRP* 3.1 28.6 + - + +
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Residues in contact with SER 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N GLN* 3.0 36.5 + - - +
49N THR* 3.7 10.5 - - - -
24O LEU 3.2 4.6 + - - -
25O THR 3.7 0.7 + - - -
26O ARG* 3.3 38.6 - - - +
48O PHE* 3.8 7.1 - - - -
52O THR* 1.3 74.5 - - - +
54O ALA* 1.3 59.9 + - - +
101O TRP* 2.9 35.5 + - - +
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Residues in contact with ALA 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 4.4 5.2 - - + -
45N ILE 3.0 12.3 - - - +
46N ALA* 3.9 15.3 - - + -
24O LEU* 2.8 55.5 + - + +
48O PHE* 4.0 1.5 - - - -
52O THR* 3.5 6.1 - - - +
53O SER* 1.3 80.7 + - - +
55O ILE* 1.4 61.5 + - - +
101O TRP* 4.1 14.1 - - + -
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Residues in contact with ILE 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N VAL 3.7 1.6 - - - +
44N LEU* 3.5 4.4 - - - -
45N ILE* 2.7 45.9 + - + +
10O VAL* 3.9 23.6 - - + -
12O ILE* 4.7 3.6 - - + -
21O VAL* 3.7 29.6 - - + -
22O ILE 3.3 6.3 - - - +
46O ALA* 4.4 9.2 - - + +
47O GLN 4.5 3.6 - - - +
48O PHE* 3.8 25.4 - - + -
52O THR* 3.9 13.5 - - + -
54O ALA* 1.4 79.5 - - - +
56O LYS* 1.3 63.6 + - - +
57O VAL* 4.3 10.1 - - + -
101P TRP* 4.0 16.2 - - + -
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Residues in contact with LYS 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N GLU* 2.9 22.4 + - - +
37N LYS 4.0 2.4 + - - -
38N LEU* 4.2 15.3 - - + -
42N GLU* 3.7 20.6 - - + +
43N VAL 3.3 8.3 - - - +
44N LEU* 4.0 12.3 - - + -
20O ASN 3.6 1.9 - - - +
21O VAL* 3.7 0.9 - - - -
22O ILE* 2.7 46.4 + - + +
24O LEU* 3.9 11.3 - - + +
32O PHE* 4.1 7.3 - - + -
55O ILE* 1.3 73.9 - - - +
57O VAL* 1.3 68.6 + - - +
58O ARG* 3.1 30.6 - - + +
117W A 3.9 6.9 - - - +
118W G 2.8 31.7 + - - -
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Residues in contact with VAL 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N GLU* 3.8 8.5 - - - +
43N VAL* 2.8 35.5 + - + +
45N ILE* 4.8 7.2 - - + -
12O ILE* 4.2 26.2 - - + -
19O VAL* 4.2 10.1 - - + -
20O ASN 3.5 7.4 - - - +
21O VAL* 4.8 3.4 - - + -
55O ILE* 4.3 9.6 - - + -
56O LYS* 1.3 77.5 - - - +
58O ARG* 1.3 63.0 + - - +
61O ALA* 4.0 16.4 - - + -
63O ILE* 4.0 21.5 - - + -
72O SER* 3.5 24.4 - - - +
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Residues in contact with ARG 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N ASP* 5.8 0.2 + - - -
42N GLU* 2.9 31.2 + - + +
18O GLY 4.5 0.7 - - - +
19O VAL* 3.4 7.3 - - - +
20O ASN* 2.9 47.4 + - + +
22O ILE* 4.0 21.6 - - + +
32O PHE* 4.3 1.6 - - - -
56O LYS* 3.1 35.3 + - + +
57O VAL* 1.3 74.0 - - - +
59O GLY* 1.3 61.9 + - - +
116W G 5.0 7.7 - - - +
117W A 4.9 2.6 - - - +
118W G 3.5 10.1 + - - -
119W U 3.1 34.8 + - - +
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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