Contacts of the strand formed by residues 68 - 73 (chain F) in PDB entry 3KYM
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 PHE 68 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ARG* 4.0 15.0 - - - -
48F VAL* 3.9 17.7 - - + -
60F TYR* 3.2 23.1 - - + -
64F VAL* 3.4 37.6 + - + +
66F GLY 4.3 9.4 + - - -
67F ARG* 1.3 107.7 - - + +
69F THR* 1.3 63.7 + - - +
81F LEU* 4.1 14.8 - - + -
82F GLN 3.0 4.3 - - - +
83F MET* 3.5 35.4 - - + -
84F ASN 4.2 2.5 - - - -
86F LEU* 4.1 12.8 - - + -
90F ASP* 3.9 19.1 - - - -
94F TYR* 4.2 7.4 - + - -
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Residues in contact with THR 69 (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* 6.2 1.1 - - + -
60F TYR* 3.1 11.9 - - + +
66F GLY 5.2 2.3 + - - -
67F ARG 4.7 0.7 + - - -
68F PHE* 1.3 75.9 - - - +
70F ILE* 1.3 66.2 + - - +
71F SER* 3.6 8.2 + - - -
81F LEU* 4.6 2.5 - - - -
82F GLN* 2.7 52.8 + - - +
84F ASN* 4.6 6.6 + - - -
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Residues in contact with ILE 70 (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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34F MET 4.1 15.9 - - - +
35F PHE 4.8 0.2 - - - -
36F TRP* 3.5 24.5 - - + -
49F SER* 2.8 33.7 - - - +
50F TRP 3.8 18.8 - - - +
51F ILE* 3.4 21.7 - - + +
58F THR* 3.6 16.8 - - + +
59F LYS 4.6 0.2 - - - +
60F TYR* 2.7 25.4 + - + +
69F THR* 1.3 73.4 - - - +
71F SER* 1.3 61.3 + - - +
79F LEU* 3.8 20.4 - - + -
80F TYR 3.7 12.6 - - - +
81F LEU* 4.2 3.1 - - + -
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Residues in contact with SER 71 (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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19F ARG* 5.2 2.9 + - - -
51F ILE* 4.2 5.4 - - - -
69F THR* 3.6 9.0 + - - -
70F ILE* 1.3 75.8 - - - +
72F ARG* 1.3 65.0 + - - +
79F LEU* 3.9 3.6 - - - +
80F TYR* 2.9 51.9 + - - +
82F GLN* 6.3 1.1 - - - -
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Residues in contact with ARG 72 (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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29F PHE* 3.2 41.8 + - + -
32F TYR 2.9 28.7 + - - -
33F PRO* 4.0 1.8 - - - +
34F MET* 4.0 2.9 - - - +
51F ILE* 3.3 22.5 - - + +
52F GLY 3.0 28.7 + - - -
53F PRO* 3.3 12.8 + - - +
54F SER 3.8 6.1 - - - +
55F GLY* 3.6 25.6 - - - +
71F SER* 1.3 81.5 + - - +
73F ASP* 1.3 67.7 + - - +
74F ASN* 2.8 19.1 + - - +
76F LYS* 5.3 0.2 + - - -
78F THR 3.9 8.7 - - - +
79F LEU* 4.5 9.4 - - + +
80F TYR* 4.6 1.8 - - - -
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Residues in contact with ASP 73 (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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29F PHE* 4.4 0.2 - - - -
72F ARG* 1.3 81.6 - - - +
74F ASN* 1.3 57.3 + - - +
76F LYS* 2.7 49.8 + - + +
77F ASN* 2.9 13.9 + - - -
78F THR* 3.0 22.6 + - + +
80F TYR* 3.6 30.0 + - + -
32I TYR* 2.7 19.4 + - - -
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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