Contacts of the strand formed by residues 38 - 46 (chain B) in PDB entry 3K9L
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 ASP 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B GLU* 1.3 88.7 + - - +
39B SER* 1.3 82.0 + - - +
40B TYR* 3.7 30.8 + - - +
56B LEU* 3.8 1.7 - - - +
57B ASP* 2.9 32.1 + - - +
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ASP* 1.3 91.7 + - - +
40B TYR* 1.3 67.0 + - - +
54B ASP* 3.8 14.0 + - - -
55B ILE 3.5 4.5 - - - -
56B LEU* 3.9 18.7 - - - +
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 3.8 26.0 - - + -
21B ILE* 4.6 17.9 - - + +
24B ILE* 4.2 27.4 - - + -
25B GLN* 4.1 25.1 - - - -
35B THR* 5.8 3.5 - - - -
36B ILE 5.9 0.7 + - - -
37B GLU* 5.4 0.3 - - - -
38B ASP* 3.7 40.5 + - + +
39B SER* 1.3 78.2 - - - +
41B ARG* 1.3 61.1 + - - +
53B LEU 4.2 0.4 - - - -
54B ASP* 3.0 9.4 - - - +
55B ILE* 2.7 48.0 + - + +
57B ASP* 4.2 12.8 + - + -
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 3.2 43.4 + - - +
5B LYS* 4.8 3.6 - - - +
24B ILE* 5.0 4.2 - - - +
40B TYR* 1.3 77.9 - - - +
42B LYS* 1.3 67.8 + - - +
52B LEU* 3.8 36.3 - - + +
53B LEU 3.1 7.6 - - - +
54B ASP* 3.0 31.5 + - - +
167B CA 4.4 2.6 - - - -
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 2.7 30.3 + - + +
24B ILE* 3.1 47.4 + - + +
26B ASN* 4.3 8.5 + - - +
41B ARG* 1.3 79.6 - - - +
43B GLN* 1.3 72.3 + - - +
44B VAL* 3.7 20.8 + - + +
52B LEU* 4.4 4.3 - - - -
53B LEU* 2.8 40.7 + - + +
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Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 3.8 25.9 - - - +
42B LYS* 1.3 78.1 - - - +
44B VAL* 1.3 68.3 + - - +
50B THR* 3.6 23.5 - - + +
51B CYS 3.3 11.7 - - - +
52B LEU* 4.3 13.7 - - + +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B LYS* 3.7 31.2 - - + +
43B GLN* 1.3 83.0 - - - +
45B VAL* 1.3 64.9 + - - +
46B ILE* 3.7 21.3 - - + -
49B GLU 3.6 0.2 - - - +
50B THR* 3.4 6.3 - - - +
51B CYS* 2.8 40.6 + - - +
53B LEU* 3.6 33.4 - - + -
157B TYR* 4.8 9.6 - - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLN* 5.7 5.3 + - - +
44B VAL* 1.3 77.8 - - - +
46B ILE* 1.3 65.4 + - - +
48B GLY* 4.0 24.9 - - - +
49B GLU 3.2 8.3 - - - +
50B THR* 4.1 22.2 - - + +
157B TYR* 4.3 10.4 + - - -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.7 24.0 - - + -
45B VAL* 1.3 78.7 - - - +
47B ASP* 1.3 81.5 + - - +
48B GLY 3.2 0.4 - - - -
49B GLU* 3.0 15.1 + - - +
51B CYS* 4.2 5.2 - - - -
53B LEU* 4.2 7.0 - - + -
157B TYR* 3.8 52.3 - - + +
160B VAL* 4.0 28.5 - - + -
161B ARG* 4.7 2.0 - - - +
164B ARG* 3.0 33.3 + - - +
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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