Contacts of the strand formed by residues 46 - 51 (chain F) in PDB entry 1KXT
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 GLU 46 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270E SER 3.8 4.5 - - - -
271E GLY* 4.5 9.5 - - - -
273E LYS* 5.9 1.4 - - - -
37F TYR* 3.2 6.6 - - - -
38F ARG* 2.8 74.2 + - + +
44F GLU 4.4 4.5 - - - +
45F CYS* 1.3 78.5 - - - +
47F LEU* 1.3 76.2 + - - +
48F SER* 3.2 1.6 + - - +
60F ALA* 3.9 17.1 - - - +
62F SER* 4.4 5.4 + - - -
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Residues in contact with LEU 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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270E SER 3.1 19.8 + - - +
271E GLY* 3.9 9.6 - - - +
272E GLU* 3.9 12.6 - - - +
276E TYR* 4.2 14.8 + - + +
35F GLY* 4.9 0.7 - - - -
36F TRP 3.7 2.9 - - - +
37F TYR* 3.3 39.0 - - + +
46F GLU* 1.3 79.5 - - - +
48F SER* 1.3 61.9 + - - +
49F ALA 3.7 26.5 - - - +
50F ARG* 3.5 47.8 - - + +
58F ASN* 5.2 1.3 - - + +
60F ALA* 3.7 11.8 + - - +
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Residues in contact with SER 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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36F TRP* 2.7 27.9 + - - -
37F TYR* 4.8 1.3 - - - -
38F ARG* 4.8 8.8 - - - +
46F GLU* 3.2 8.4 + - - -
47F LEU* 1.3 72.2 - - - +
49F ALA* 1.3 60.2 + - - +
59F TYR* 3.5 1.6 - - - -
60F ALA* 2.9 30.9 + - - -
63F VAL* 3.6 10.0 - - - +
67F PHE* 3.7 28.9 - - - -
80F LEU* 4.5 3.1 - - - +
90F TYR* 4.5 14.5 - - - -
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Residues in contact with ALA 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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35F GLY* 3.3 1.6 - - - -
36F TRP* 2.9 27.8 + - + +
47F LEU* 3.6 7.3 - - - +
48F SER* 1.3 82.4 - - - +
50F ARG* 1.3 62.4 + - - +
58F ASN 3.3 8.1 - - - +
59F TYR* 3.5 30.1 - - + -
67F PHE* 5.7 0.4 - - + -
69F ILE* 4.0 17.7 - - + -
80F LEU* 4.2 13.2 - - + -
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Residues in contact with ARG 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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261E LYS* 6.0 1.6 - - - +
272E GLU* 2.9 40.2 + - - -
276E TYR* 3.3 12.5 - - - +
284E TRP* 3.6 27.7 - - - -
33F PRO* 4.3 12.1 - - + -
34F MET 3.4 13.7 - - - +
35F GLY* 4.0 1.8 - - - -
37F TYR* 4.6 6.6 + - - -
47F LEU* 3.5 20.7 - - + +
49F ALA* 1.3 79.2 - - - +
51F ILE* 1.3 69.9 + - - +
52F PHE* 3.6 18.9 - - + -
57F ALA* 3.1 10.9 - - - +
58F ASN* 3.0 56.9 + - + +
69F ILE* 3.9 4.0 - - - +
100F PRO* 6.1 5.3 - - - -
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Residues in contact with ILE 51 (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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32F TYR 4.3 0.7 - - - +
33F PRO* 3.2 2.4 - - - +
34F MET* 2.7 51.9 + - + +
50F ARG* 1.3 75.6 - - - +
52F PHE* 1.3 69.1 + - - +
55F GLY* 2.9 35.9 - - - +
56F SER 3.2 7.4 - - - +
57F ALA* 4.2 7.0 - - + -
69F ILE* 3.9 31.2 - - + +
70F SER* 5.2 5.6 - - - +
71F ARG* 4.3 30.0 + - + +
78F ALA* 5.7 2.9 - - + -
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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