Contacts of the strand formed by residues 34 - 38 (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 TYR 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102E TYR* 3.5 33.9 - + + -
32F TYR* 4.0 18.9 - - + +
33F MET* 1.3 75.8 - - - +
35F TRP* 1.3 61.8 - - - +
36F TYR* 4.0 8.1 - - + +
48F ILE 3.4 4.5 - - - +
49F TYR* 3.6 7.4 - - + -
50F ARG* 3.2 51.2 + - - -
87F TYR 3.6 0.3 - - - +
88F CYS* 3.2 4.9 - - - -
89F GLN* 2.6 67.7 + - - +
90F GLN* 5.0 0.9 - - - -
91F TYR* 3.2 44.9 + + - -
92F HIS* 3.3 11.5 - + - -
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Residues in contact with TRP 35 (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* 5.0 0.3 - - - -
7F GLN* 3.2 26.9 - - - -
22F ILE* 3.4 34.3 - - + -
24F CYS* 3.9 22.2 - - + -
33F MET* 4.2 16.8 - - + +
34F TYR* 1.3 76.4 - - - +
36F TYR* 1.3 67.0 + - - +
47F TRP* 3.0 21.5 + - + -
48F ILE* 2.7 49.1 + - + +
51F THR 5.3 3.4 + - - -
64F GLY* 5.3 2.8 - - - -
65F SER 5.3 1.0 + - - -
71F TYR* 3.7 16.6 - - + +
72F SER* 3.6 10.4 + - - -
73F LEU* 3.3 47.7 - - + +
86F TYR* 4.9 0.2 - - + -
87F TYR 3.2 20.0 - - - -
88F CYS* 4.0 7.6 - - + -
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Residues in contact with TYR 36 (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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45E LEU* 5.8 1.8 - - + -
101E TRP 4.0 0.2 + - - -
102E TYR* 3.4 25.6 - + - -
103E PHE* 3.3 39.8 + + - -
106E TRP* 4.1 14.6 - + - -
34F TYR* 4.0 7.8 - - + +
35F TRP* 1.3 77.5 - - - +
37F GLN* 1.3 60.8 + - - +
38F GLN 4.2 0.4 - - - -
44F PRO* 4.8 10.8 - - + -
45F LYS 3.3 16.8 - - - +
46F PRO* 3.8 6.7 - - + -
47F TRP* 4.0 4.7 - - - -
86F TYR* 3.4 10.8 - - - -
87F TYR* 2.8 46.0 + - + +
89F GLN* 2.6 38.2 + - + -
98F PHE* 3.7 27.6 - + - -
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Residues in contact with GLN 37 (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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36F TYR* 1.3 73.5 - - - +
38F GLN* 1.3 62.8 + - - +
39F LYS* 3.8 34.8 + - - +
43F SER 4.6 0.5 - - - +
44F PRO* 3.5 0.8 - - - +
45F LYS* 2.8 43.7 + - - +
47F TRP* 3.4 51.2 - - + +
81F GLU 4.0 4.8 + - - -
82F ASP* 3.8 9.9 + - - +
84F ALA* 3.9 8.1 - - + -
85F THR 3.8 2.0 - - - -
86F TYR* 3.2 32.8 + - + -
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Residues in contact with GLN 38 (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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39E GLN* 2.8 45.1 + - - +
43E LYS* 3.7 12.3 + - - +
45E LEU* 5.1 2.0 - - - +
94E TYR* 3.9 3.5 + - - -
36F TYR* 4.2 0.4 - - + -
37F GLN* 1.3 74.7 - - - +
39F LYS* 1.3 66.5 + - - +
41F GLY 4.1 3.3 - - - -
42F SER 3.1 27.8 - - - +
43F SER 5.2 0.4 - - - -
44F PRO* 3.8 23.5 - - + +
84F ALA* 3.8 3.8 - - - -
85F THR* 2.7 47.8 + - - +
87F TYR* 3.3 24.0 + - + -
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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