Contacts of the strand formed by residues 34 - 39 (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 MET 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F LEU* 4.4 17.0 - - + -
22F CYS* 4.6 6.1 - - - +
24F ALA* 4.9 9.0 - - + -
28F THR* 6.4 0.7 - - - -
29F PHE 4.2 19.1 - - - +
30F SER* 4.7 13.2 - - - -
32F TYR* 3.4 7.4 + - + +
33F PRO* 1.3 74.8 - - - +
35F GLY* 1.3 59.7 + - - +
50F ARG* 3.4 4.3 - - - +
51F ILE* 2.7 48.7 + - + +
69F ILE* 4.8 1.1 - - + -
71F ARG* 5.3 4.5 - - - +
76F ASN 5.8 4.0 - - - +
77F THR 6.1 0.9 - - - -
78F ALA* 4.5 27.6 - - + +
92F CYS* 4.6 12.3 - - - -
93F ALA 3.3 6.1 - - - +
94F ALA* 3.1 27.1 - - + -
100F PRO* 5.8 1.1 - - - -
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Residues in contact with GLY 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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34F MET* 1.3 76.0 - - - +
36F TRP* 1.3 65.2 + - - -
37F TYR* 4.3 11.7 - - - -
47F LEU* 4.9 0.4 - - - -
49F ALA 3.3 11.7 - - - -
50F ARG* 4.0 5.6 - - - -
69F ILE* 4.5 4.0 - - - -
92F CYS* 3.6 4.3 - - - -
93F ALA* 2.7 44.3 + - - +
100F PRO* 5.4 2.2 - - - -
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Residues in contact with TRP 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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6F ALA* 4.6 8.7 - - + -
20F LEU* 3.6 34.8 - - + -
21F SER 3.5 24.2 - - - -
22F CYS* 3.7 11.7 - - + -
35F GLY* 1.3 77.2 - - - -
37F TYR* 1.3 57.4 + - - +
47F LEU* 3.7 2.8 - - - +
48F SER* 2.7 37.6 + - - -
49F ALA 2.9 13.0 + - - +
69F ILE* 3.5 25.3 - - + +
78F ALA* 3.7 27.3 - - + +
79F TYR 3.6 11.7 + - - +
80F LEU* 3.4 45.1 - - + +
90F TYR* 4.8 4.9 - - + -
91F TYR 3.3 19.5 - - - -
92F CYS* 3.8 16.6 - - + -
107F THR* 5.0 2.7 - - + -
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Residues in contact with TYR 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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270E SER 4.1 7.4 - - - -
272E GLU* 4.5 9.6 + - - -
35F GLY* 4.3 5.2 - - - -
36F TRP* 1.3 78.3 - - - +
38F ARG* 1.3 61.5 + - - +
45F CYS* 4.1 11.4 - - - -
46F GLU 3.2 4.9 - - - +
47F LEU* 3.3 46.8 - - + +
48F SER* 4.9 0.4 - - - -
50F ARG* 4.6 5.2 + - - -
90F TYR* 3.4 5.8 - - - +
91F TYR* 2.8 42.7 + - + +
93F ALA* 3.6 32.3 - - + -
100F LEU* 3.4 68.2 + + - -
103F TRP* 4.9 1.3 - + - -
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Residues in contact with ARG 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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37F TYR* 1.3 75.9 - - - +
39F GLN* 1.3 61.5 + - - +
40F ALA* 4.0 2.1 + - + +
44F GLU 4.1 1.7 - - - +
45F CYS* 3.7 1.8 - - - -
46F GLU* 2.8 68.1 + - + +
48F SER* 4.8 8.5 + - - -
62F SER* 3.5 22.8 + - - -
63F VAL* 4.1 15.9 - - - +
66F ARG* 5.5 0.2 - - - +
67F PHE* 4.4 1.4 - - - -
85F GLU* 4.6 8.6 + - - +
86F ASP* 2.9 37.1 + - - +
88F ALA* 4.4 7.4 - - + -
89F VAL 3.3 10.3 - - - +
90F TYR* 3.1 43.2 + - + -
91F TYR* 5.0 0.7 - - - -
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Residues in contact with GLN 39 (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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38F ARG* 1.3 70.7 - - - +
40F ALA* 1.3 76.5 + - - +
41F PRO* 3.8 1.7 - - - +
42F GLY 5.2 0.7 + - - -
43F LYS 2.5 30.2 + - - +
44F GLU 4.8 0.2 - - - -
45F CYS* 3.8 32.5 - - + +
88F ALA* 3.6 2.7 - - - -
89F VAL* 2.9 32.1 + - + +
91F TYR* 4.0 20.6 - - + -
100F VAL* 3.4 63.6 + - + +
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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