Contacts of the helix formed by residues 58 - 66 (chain F) in PDB entry 5YUS
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 PRO 58 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39F GLY 3.8 6.5 - - - +
40F VAL* 4.0 4.3 - - + -
56F ALA 3.7 6.1 - - - +
57F MET* 1.3 84.1 - - - +
59F THR* 1.3 61.1 + - - +
61F MET* 2.9 40.0 + - + +
62F ALA* 3.0 10.0 + - - +
837G T 3.1 22.9 - - + +
838G C 4.0 14.6 - - - +
839G T 3.7 37.9 - - + +
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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
----------------------------------------------------------
33F GLY 2.8 28.9 + - - +
34F SER 4.4 0.2 - - - -
35F ARG* 3.7 15.0 - - - +
39F GLY 2.9 24.3 + - - -
40F VAL 3.4 11.1 + - - -
41F ILE* 3.7 7.5 - - + +
57F MET 3.4 1.3 + - - -
58F PRO* 1.3 72.9 - - - +
60F GLY* 1.3 57.1 + - - +
62F ALA* 3.1 8.2 + - + +
63F LEU* 2.9 38.8 + - + +
69F LEU* 5.6 0.2 - - + -
71F LEU* 3.5 26.2 - - + -
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Residues in contact with GLY 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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35F ARG* 3.6 28.2 + - - +
58F PRO 3.2 1.0 - - - -
59F THR* 1.3 78.6 - - - +
61F MET* 1.3 59.5 + - - +
64F LYS* 3.2 17.0 + - - +
837G T 3.6 26.1 + - - -
838G C 3.7 17.8 - - - -
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Residues in contact with MET 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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57F MET* 3.4 34.8 - - + +
58F PRO* 2.9 24.7 + - + +
60F GLY* 1.3 73.5 - - - +
62F ALA* 1.3 66.0 + - - +
64F LYS* 3.3 3.6 + - + +
65F LEU* 3.1 31.2 + - + +
837G T 3.2 62.9 + - + +
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Residues in contact with ALA 62 (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 ILE* 3.8 24.0 - - + -
53F VAL* 4.0 3.5 - - + +
57F MET* 3.3 27.7 - - + +
58F PRO 3.0 6.5 + - - +
59F THR 3.1 8.2 + - - +
61F MET* 1.3 76.9 - - - +
63F LEU* 1.3 56.3 + - - +
65F LEU* 3.2 4.1 + - - +
66F CYS* 2.8 31.9 + - - +
69F LEU* 3.8 18.2 - - + -
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Residues in contact with LEU 63 (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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35F ARG* 4.0 40.6 - - + +
59F THR* 2.9 35.0 + - + +
60F GLY 4.1 3.8 - - - +
62F ALA* 1.3 73.4 - - - +
64F LYS* 1.3 65.0 + - - +
66F CYS 3.7 5.4 - - - +
67F PRO* 3.1 36.7 - - + +
69F LEU* 3.8 36.3 - - + +
71F LEU* 5.2 8.1 - - + -
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Residues in contact with LYS 64 (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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35F ARG* 5.0 2.8 - - - +
60F GLY 3.2 14.7 + - - +
61F MET* 3.3 5.6 + - + +
63F LEU* 1.3 78.4 - - - +
65F LEU* 1.3 61.7 + - + +
67F PRO* 4.1 8.8 - - - +
837G T 3.6 30.3 - - - +
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Residues in contact with LEU 65 (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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51F PHE* 3.4 40.9 - - + +
52F GLY* 3.9 17.0 - - - +
53F VAL* 4.9 1.8 - - + -
57F MET* 3.8 29.8 - - + -
61F MET* 3.1 20.3 + - + +
62F ALA* 3.7 5.8 - - - +
64F LYS* 1.3 78.3 - - + +
66F CYS* 1.3 58.6 + - + +
67F PRO* 3.6 4.8 - - - +
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Residues in contact with CYS 66 (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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28F PRO* 3.5 39.0 - - - -
51F PHE* 3.8 31.6 - - + -
53F VAL* 3.8 10.5 - - + -
62F ALA 2.8 12.0 + - - +
63F LEU* 3.3 7.7 - - - +
65F LEU* 1.3 79.6 - - - +
67F PRO* 1.3 67.2 - - - +
68F HIS* 3.2 5.2 - - - -
69F LEU* 2.9 32.5 + - + +
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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