Contacts of the strand formed by residues 45 - 49 (chain F) in PDB entry 3AB0
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 LYS 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106E TRP* 5.2 0.4 - - - -
36F TYR* 3.3 11.1 - - - +
37F GLN* 2.8 42.0 + - - +
43F SER* 4.1 19.2 + - - +
44F PRO* 1.3 77.5 - - - +
46F PRO* 1.3 78.5 - - + +
47F TRP* 4.3 15.9 - - + -
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Residues in contact with PRO 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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102E TYR* 2.9 33.9 - - + +
103E PHE 4.6 2.5 - - - +
104E ASP* 3.2 34.8 - - + +
105E VAL* 5.5 0.2 - - - -
106E TRP* 5.1 0.4 - - + +
36F TYR* 3.8 10.5 - - + -
44F PRO 4.6 2.0 - - - +
45F LYS* 1.3 94.2 - - + +
47F TRP* 1.3 72.9 + - - +
55F ALA* 3.3 16.9 - - + +
56F SER* 5.1 6.5 - - - +
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Residues in contact with TRP 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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102E TYR* 4.6 1.4 + - - -
35F TRP* 3.0 20.9 + - + +
36F TYR* 4.0 7.2 - - - -
37F GLN* 3.4 51.1 - - + -
45F LYS* 4.3 13.0 - - + -
46F PRO* 1.3 95.4 - - - +
48F ILE* 1.3 70.3 + - + +
49F TYR 4.3 0.2 - - - -
54F LEU* 3.8 3.1 - - - -
55F ALA* 3.2 26.7 + - - +
58F VAL* 3.9 31.1 - - + +
59F PRO* 5.2 5.8 - - + -
62F PHE* 3.5 47.3 - + - -
73F LEU* 4.3 8.5 - - + -
82F ASP* 5.4 0.9 - - - -
86F TYR* 3.6 16.3 - + - -
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Residues in contact with ILE 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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102E TYR* 4.5 3.2 - - - -
33F MET 5.3 0.2 - - - +
34F TYR* 3.4 5.5 - - - +
35F TRP* 2.7 53.2 + - + +
47F TRP* 1.3 90.8 - - + +
49F TYR* 1.3 61.0 + - - +
51F THR* 3.8 17.9 - - - +
52F SER* 3.7 20.9 - - - +
53F ASN 3.3 16.4 - - - +
54F LEU* 5.5 7.2 - - + -
62F PHE* 5.3 2.7 - - + -
63F SER* 3.6 32.3 - - - +
64F GLY* 4.1 1.8 - - - +
73F LEU* 3.8 26.7 - - + -
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Residues in contact with TYR 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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103D ASP* 3.6 29.2 + - - -
102E TYR* 3.6 35.4 - + + -
33F MET 4.2 0.7 - - - -
34F TYR* 3.6 18.4 - - + -
48F ILE* 1.3 74.8 - - - +
50F ARG* 1.3 79.1 + - - +
51F THR 2.9 15.3 + - - -
52F SER 3.8 0.7 + - - -
53F ASN* 3.2 48.1 + - + +
54F LEU 3.3 28.6 + - - -
55F ALA* 4.6 4.9 - - - -
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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