Contacts of the helix formed by residues 45 - 50 (chain F) in PDB entry 5YUY
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 ASN 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F CYS* 4.5 5.2 - - - -
14F ALA* 3.9 10.5 - - + +
18F MET* 3.6 31.4 - - + -
24F LEU 3.6 3.2 + - - -
25F ARG 4.1 0.2 + - - -
27F ILE 2.9 23.2 + - - -
28F PRO* 3.7 0.2 - - - +
29F ILE* 3.0 41.5 + - + +
44F ALA* 1.3 75.7 - - - +
46F TYR* 1.3 60.7 + - - +
47F PRO* 3.4 14.2 - - + +
48F ALA* 3.1 11.4 + - - +
49F ARG* 2.9 26.0 + - - +
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Residues in contact with TYR 46 (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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10F ASP* 5.5 0.9 - - + -
11F CYS* 3.5 20.2 - - - -
45F ASN* 1.3 72.7 - - - +
47F PRO* 1.3 72.9 - - + +
49F ARG* 3.6 35.5 + - + +
50F LYS* 2.9 24.8 + - - +
157F LYS* 4.0 14.7 + - - +
158F PRO* 3.5 47.6 - - + +
901H TTP 4.4 3.7 + - - -
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Residues in contact with PRO 47 (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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18F MET* 5.8 0.7 - - - -
25F ARG 4.2 9.4 - - - +
26F ASP* 4.1 15.9 - - - +
27F ILE 3.7 23.8 - - - +
28F PRO* 3.8 4.7 - - + -
45F ASN* 3.4 19.3 - - + +
46F TYR* 1.3 92.9 - - + +
48F ALA* 1.3 56.6 + - - +
50F LYS* 3.6 14.8 - - + +
51F PHE* 3.2 27.1 - - + -
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Residues in contact with ALA 48 (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* 3.6 10.5 - - + +
29F ILE 3.5 16.6 - - - +
44F ALA* 3.7 8.3 - - + -
45F ASN* 3.1 19.7 + - - +
47F PRO* 1.3 72.8 - - - +
49F ARG* 1.3 66.0 + - - +
50F LYS 3.1 2.2 - - - -
51F PHE* 3.0 15.5 + - - +
53F VAL* 3.4 22.5 + - + +
66F CYS* 4.7 0.7 - - - -
69F LEU* 3.6 22.9 - - + -
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Residues in contact with ARG 49 (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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11F CYS* 3.2 25.3 - - - +
43F THR* 3.0 26.1 + - - -
44F ALA* 3.0 16.9 + - + +
45F ASN 2.9 17.6 + - - +
46F TYR* 3.1 37.1 + - + +
48F ALA* 1.3 76.0 - - - +
50F LYS* 1.3 57.5 + - - +
52F GLY* 2.9 16.9 + - - -
53F VAL 3.5 20.0 - - - +
54F ARG* 2.9 30.3 + - - +
55F SER* 5.2 3.0 + - - -
157F LYS* 4.7 3.4 - - - +
901H TTP 3.2 35.2 + - - -
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Residues in contact with LYS 50 (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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46F TYR 2.9 11.2 + - - +
47F PRO* 3.6 15.1 - - + +
48F ALA 3.1 0.2 - - - -
49F ARG* 1.3 77.5 - - - +
51F PHE* 1.3 84.3 + - + +
52F GLY 3.4 0.5 + - - -
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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