Contacts of the strand formed by residues 54 - 61 (chain F) in PDB entry 5X11
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 ILE 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F LEU* 5.1 4.3 - - + -
12F LEU* 4.9 11.4 - - + -
45F LEU* 5.7 1.8 - - + +
48F LEU* 3.2 22.3 + - + +
49F THR* 3.5 27.4 - - - +
52F GLY* 3.3 2.6 - - - -
53F PHE* 1.3 80.2 - - + +
55F THR* 1.3 60.6 + - - +
70F TYR* 4.3 18.8 - - + -
71F THR 3.5 12.3 - - - +
72F LEU* 5.2 0.2 - - - -
73F THR* 4.0 4.0 - - - +
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Residues in contact with THR 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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49F THR* 4.7 3.8 - - - -
54F ILE* 1.3 74.6 - - - +
56F PHE* 1.3 62.8 + - - +
70F TYR* 3.4 6.0 - - - -
71F THR* 3.0 36.5 + - - -
73F THR* 3.8 16.2 - - - +
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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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49F THR* 4.1 21.9 - - + +
55F THR* 1.3 76.5 - - - +
57F ARG* 1.3 66.0 + - - +
58F THR* 4.2 12.3 - - - -
68F LYS* 3.7 42.8 - - + -
69F MET 3.2 13.2 - - - +
70F TYR* 3.5 36.3 - + + -
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Residues in contact with ARG 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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56F PHE* 1.3 78.5 - - - +
58F THR* 1.3 62.7 + - - +
59F THR* 3.7 19.6 + - - +
67F LYS 3.7 0.2 - - - +
68F LYS* 3.4 3.8 - - - -
69F MET* 2.9 55.8 + - + +
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Residues in contact with THR 58 (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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56F PHE* 4.2 12.0 - - + -
57F ARG* 1.3 75.5 - - - +
59F THR* 1.3 62.0 + - - +
60F ILE* 5.6 0.5 - - - +
66F GLU* 4.1 36.0 - - + +
67F LYS 3.4 13.0 - - - +
68F LYS* 4.5 11.2 - - + -
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Residues in contact with THR 59 (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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57F ARG* 3.7 19.7 + - - -
58F THR* 1.3 75.9 - - - +
60F ILE* 1.3 68.7 + - - +
61F GLN* 5.0 1.1 - - + +
66F GLU* 3.7 4.1 - - - +
67F LYS* 2.9 54.0 + - + +
69F MET* 3.9 30.1 - - + -
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Residues in contact with ILE 60 (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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58F THR 5.6 0.4 - - - +
59F THR* 1.3 82.0 + - - +
61F GLN* 1.3 64.1 + - - +
62F GLY 3.9 8.6 + - - +
63F THR 5.1 10.8 - - - +
64F LYS 5.5 0.9 - - - -
65F LEU 3.4 9.2 - - - +
66F GLU* 4.6 11.4 - - + +
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Residues in contact with GLN 61 (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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59F THR* 4.1 3.1 - - + +
60F ILE* 1.3 71.0 - - - +
62F GLY* 1.3 69.8 + - - +
64F LYS 3.9 0.2 + - - -
65F LEU* 2.9 49.8 + - + +
67F LYS* 3.5 37.0 + - - +
25M T 3.8 7.0 + - - -
26M T 3.4 24.2 + - - -
7N A 3.6 10.3 + - - +
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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