Contacts of the strand formed by residues 40 - 46 (chain B) in PDB entry 1JAT
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 LYS 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.8 7.6 - - - +
31B ALA* 2.9 34.1 + - + +
32B ASP* 4.5 1.5 + - + -
35B ASP* 3.7 8.3 + - - +
39B THR* 1.3 81.2 - - + +
41B TRP* 1.3 67.5 + - - +
61B SER* 5.0 13.5 + - - +
62B ILE 3.5 3.8 - - - +
63B ASP* 2.9 35.4 + - - +
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Residues in contact with TRP 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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10B LEU* 3.9 20.8 - - + +
14B LEU* 3.8 38.6 - - + -
28B TYR* 3.7 30.7 - + + -
29B GLY* 3.3 28.3 - - - +
30B LEU* 3.6 20.9 - - + -
31B ALA* 4.0 1.5 - - - +
38B MET* 2.9 26.3 + - + -
39B THR 3.3 15.5 + - - -
40B LYS* 1.3 75.8 - - - +
42B ASN* 1.3 69.0 + - - +
61B SER* 3.4 7.4 + - - -
62B ILE* 2.8 43.2 + - + +
64B CYS* 4.0 12.0 - - - -
109B MET* 3.5 35.2 - - + -
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Residues in contact with ASN 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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28B TYR* 3.0 5.9 - - - +
29B GLY 2.7 34.0 + - - +
30B LEU 4.3 3.8 + - - -
31B ALA* 3.6 31.8 + - - +
41B TRP* 1.3 80.2 - - - +
43B GLY* 1.3 59.9 + - - +
44B THR* 5.5 2.7 - - + -
60B LEU 3.4 7.7 - - - +
61B SER* 5.0 4.7 + - - -
62B ILE* 5.4 0.9 - - - -
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Residues in contact with GLY 43 (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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27B SER 3.3 9.6 - - - -
28B TYR* 4.0 5.4 - - - -
41B TRP 4.1 0.2 + - - -
42B ASN* 1.3 75.4 - - - +
44B THR* 1.3 71.2 + - - +
59B SER* 3.4 2.3 - - - -
60B LEU* 2.8 42.8 + - - +
61B SER* 5.0 0.2 - - - +
62B ILE* 4.9 6.6 - - - +
113B LEU* 4.6 6.7 - - - -
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Residues in contact with THR 44 (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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26B CYS* 3.2 7.8 - - - +
27B SER* 2.5 55.3 + - - +
28B TYR* 6.2 0.2 - - - -
42B ASN* 5.5 2.5 - - + -
43B GLY* 1.3 80.8 - - - +
45B ILE* 1.3 64.9 + - - +
57B ILE* 3.9 18.6 - - + +
58B TYR 3.1 9.4 - - - +
59B SER* 4.6 10.1 - - - +
113B LEU* 4.5 1.5 - - - +
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Residues in contact with ILE 45 (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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25B SER 3.6 2.9 - - - -
26B CYS* 4.1 5.2 - - - -
44B THR* 1.3 78.5 - - - +
46B LEU* 1.3 73.8 + - - +
47B GLY 3.7 1.2 + - - -
57B ILE* 3.3 4.5 - - - +
58B TYR* 2.8 41.1 + - + +
60B LEU* 3.8 21.3 - - + -
77B PHE* 4.4 0.7 - - + -
113B LEU* 3.8 38.4 - - + +
116B LEU* 3.8 18.8 - - + -
117B ARG* 3.8 25.4 - - + -
120B MET* 3.8 25.1 - - + -
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Residues in contact with LEU 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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24B GLU 4.7 11.7 - - - +
25B SER* 2.8 24.0 + - - +
45B ILE* 1.3 74.3 - - - +
47B GLY* 1.3 69.1 + - - +
48B PRO 3.5 0.2 - - - -
55B ASN* 4.6 9.2 - - - +
56B ARG 3.5 22.9 - - - +
57B ILE* 3.9 14.2 - - + +
117B ARG* 2.8 41.3 + - - +
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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