Contacts of the strand formed by residues 46 - 51 (chain N) 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 GLU 46 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98M PHE* 5.3 0.2 - - - -
37N VAL* 3.5 5.4 - - - +
38N ARG* 2.5 86.5 + - + +
44N GLY 4.3 0.4 - - - -
45N LEU* 1.3 73.7 - - - +
47N TRP* 1.3 72.0 + - - +
48N VAL* 4.1 1.8 - - + +
61N ALA* 5.7 1.1 - - + -
63N SER* 3.8 18.7 + - - +
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Residues in contact with TRP 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M TRP* 4.2 8.5 - + - -
95M PRO* 3.8 26.9 - - + -
96M LEU* 3.6 42.8 + - + +
98M PHE* 4.6 11.9 - - + -
35N PHE* 3.3 29.3 - + - -
36N TRP 4.3 3.8 - - - -
37N VAL* 4.2 8.3 - - + -
45N LEU 4.0 1.8 + - - -
46N GLU* 1.3 83.1 - - - +
48N VAL* 1.3 63.1 + - - +
49N SER* 3.3 35.2 + - - -
50N TRP* 3.8 13.9 - - + -
59N LYS* 4.0 8.1 - - + -
60N TYR 3.3 42.6 - - - -
61N ALA* 3.6 16.7 - - + +
106N PHE* 4.2 6.7 - + - -
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Residues in contact with VAL 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N TRP* 3.3 14.8 + - + +
37N VAL 4.6 0.2 - - - -
38N ARG* 3.4 48.9 - - + +
46N GLU* 4.1 3.8 - - + +
47N TRP* 1.3 85.9 - - - +
49N SER* 1.3 70.4 + - - +
60N TYR* 3.4 4.0 - - - -
61N ALA* 2.8 32.6 + - + -
64N VAL* 4.1 10.9 - - + +
68N PHE* 4.0 27.4 - - + -
81N LEU* 4.5 8.1 - - + -
94N TYR* 4.5 3.8 - - + -
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Residues in contact with SER 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N PHE* 3.2 6.6 - - - -
36N TRP* 3.0 28.8 + - - -
47N TRP* 3.3 12.0 + - - -
48N VAL* 1.3 82.5 + - - +
50N TRP* 1.3 58.7 + - - +
59N LYS 3.6 4.1 + - - -
60N TYR* 3.5 24.6 - - - -
68N PHE* 5.4 0.3 - - - +
70N ILE* 3.7 22.3 - - - +
81N LEU* 3.5 23.3 - - - +
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Residues in contact with TRP 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H SER* 6.2 0.7 - - - -
33N PRO* 3.8 10.0 - - + +
34N MET 3.5 9.2 - - - -
35N PHE* 3.2 34.1 - + + -
47N TRP* 3.8 16.2 - - + -
49N SER* 1.3 75.0 - - - +
51N ILE* 1.3 71.0 + - - +
52N GLY* 3.7 26.7 - - - -
53N PRO* 5.6 0.4 - - + -
57N ILE* 3.7 39.0 - - + -
58N THR* 3.5 3.3 - - - -
59N LYS* 3.0 60.4 + - + +
70N ILE* 3.8 6.3 - - - +
99N GLU* 2.9 24.8 + - - -
104N TRP* 4.6 13.0 - + - -
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Residues in contact with ILE 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N PRO* 3.2 5.9 - - - +
34N MET* 3.0 39.6 + - + +
50N TRP* 1.3 85.1 - - - +
52N GLY* 1.3 69.6 + - - +
55N GLY* 3.8 21.3 - - - -
57N ILE 3.8 11.0 - - - +
58N THR* 4.0 12.8 - - + -
70N ILE* 4.0 17.7 - - + +
71N SER* 3.9 34.1 - - - +
72N ARG* 3.6 17.9 - - + +
79N LEU* 4.0 6.7 - - + -
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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