Contacts of the strand formed by residues 50 - 57 (chain F) in PDB entry 4OZH
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 LEU 50 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E PRO* 4.2 4.0 - - + -
116E LEU* 4.0 20.9 - - + +
117E ILE* 5.4 6.9 - - - +
118E PHE* 3.7 40.9 + - + +
42F TYR* 3.7 28.7 - - + -
43F ARG 3.8 2.5 - - - +
44F GLN* 3.9 13.5 - - + -
49F GLY* 1.3 70.0 - - - -
51F GLU* 1.3 59.4 + - - +
52F PHE* 3.9 2.7 + - - +
103F LEU* 3.8 26.0 - - + -
118F PHE* 3.6 34.3 - - + -
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Residues in contact with GLU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F TYR* 3.4 4.1 - - - -
43F ARG* 2.7 85.7 + - + +
49F GLY 3.7 2.2 + - - +
50F LEU* 1.3 70.9 - - - +
52F PHE* 1.3 68.0 + - - +
53F LEU* 4.1 10.1 - - + +
70F GLY 4.4 6.1 - - - +
72F PRO* 4.6 2.6 - - - +
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Residues in contact with PHE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E ASN* 5.2 1.6 - - - -
115E LYS* 4.0 36.3 - - + -
116E LEU 6.0 0.2 - - - +
40F TYR* 4.2 12.8 - + + -
41F TRP 4.3 2.9 - - - -
42F TYR* 3.8 30.2 - + + -
50F LEU 3.9 3.6 + - - -
51F GLU* 1.3 76.1 - - - +
53F LEU* 1.3 65.3 + - - +
54F ILE* 3.8 14.6 - - - -
55F TYR* 3.6 41.7 - + + -
67F ASP* 3.9 18.8 - - - -
69F SER 4.2 12.6 - - - -
70F GLY* 3.4 17.8 - - - +
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TRP* 3.1 18.6 + - + +
42F TYR 3.9 9.6 - - - +
43F ARG* 3.8 26.5 - - + +
51F GLU* 4.0 11.2 - - - +
52F PHE* 1.3 78.1 - - - +
54F ILE* 1.3 65.0 + - + +
69F SER 3.2 21.5 - - - +
70F GLY 3.4 24.8 - - - +
71F LEU* 3.4 14.4 + - + +
72F PRO* 3.9 22.7 - - + -
76F PHE* 5.1 2.2 - - + -
89F LEU* 4.3 12.8 - - + -
102F TYR* 3.7 33.0 - - + -
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Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TRP* 2.9 48.5 + - + +
52F PHE* 3.8 8.6 - - - -
53F LEU* 1.3 80.5 - - + +
55F TYR* 1.3 70.1 + - - +
56F PHE* 4.7 3.1 - - + -
65F ALA* 4.2 13.9 - - + -
67F ASP 3.9 20.0 - - - +
68F LYS* 4.2 15.0 - - + -
71F LEU* 3.8 28.9 - - + -
78F ALA* 3.7 33.2 - - + +
89F LEU* 4.3 7.9 - - + -
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Residues in contact with TYR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLN* 5.0 11.9 + - + +
61C THR* 4.3 8.3 + - - +
114E ASN* 3.3 29.7 + - - -
38F ALA* 5.0 0.4 - - + -
39F LEU 3.2 10.8 - - - +
40F TYR* 3.5 26.7 - + + -
52F PHE* 3.6 12.5 - + + -
54F ILE* 1.3 77.3 - - - +
56F PHE* 1.3 84.8 + - - +
57F GLN* 4.1 6.4 - - + +
65F ALA* 3.5 11.1 - - - +
66F PRO* 3.4 43.0 - - + +
67F ASP* 3.2 31.1 + - - +
110F SER* 3.1 27.8 + - - -
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Residues in contact with PHE 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ALA* 3.3 6.6 - - - -
39F LEU* 2.8 41.4 + - + +
41F TRP* 4.5 7.2 - + - -
54F ILE* 4.7 5.6 - - + -
55F TYR* 1.3 84.6 - - - +
57F GLN* 1.3 60.4 + - - +
58F GLY 3.9 1.8 - - - +
63F ASN 3.6 22.9 - - - -
64F SER 3.9 2.7 - - - -
65F ALA* 4.0 23.3 - - + -
78F ALA* 3.7 46.9 - - + -
79F GLU* 3.8 6.1 - - - -
80F ARG* 3.6 40.8 - - + +
87F SER* 3.7 18.8 - - - -
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Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR* 3.5 19.7 - - - +
64C ALA* 4.6 21.4 - - + +
65C VAL* 4.5 13.0 - - - +
37F THR* 3.2 28.7 + - - -
38F ALA* 3.9 3.6 - - - +
55F TYR* 4.1 14.6 - - + +
56F PHE* 1.3 71.0 - - - +
58F GLY* 1.3 61.2 + - - +
63F ASN 3.6 2.1 + - - -
64F SER* 3.1 22.6 + - - +
66F PRO* 4.4 8.8 - - + +
109F ARG* 3.8 6.5 - - - +
110F SER* 2.8 39.1 + - - -
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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