Contacts of the helix formed by residues 37 - 48 (chain A) in PDB entry 1J3R
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.5 3.4 - - - +
36A ILE* 1.3 84.1 - - + +
38A GLU* 1.3 55.8 + - - +
39A GLU* 3.3 10.7 + - - +
40A ALA* 2.9 35.5 + - + +
41A TRP* 2.9 25.8 + - - +
79A VAL* 3.7 16.6 + - + +
80A GLY* 3.9 10.0 - - - -
81A ASN 5.6 0.2 - - - +
82A GLU* 4.5 0.6 + - - -
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE 4.6 6.5 - - - +
36A ILE 3.0 12.4 + - - +
37A ASP* 1.3 72.3 + - - +
39A GLU* 1.3 79.5 + - + +
41A TRP* 3.3 14.6 - - + +
42A LYS* 3.0 35.0 + - - +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 3.2 7.7 + - - +
38A GLU* 1.3 99.6 - - + +
40A ALA* 1.3 67.6 + - - +
42A LYS* 3.4 22.6 + - - +
43A LYS* 3.1 23.6 + - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 2.9 34.1 + - - +
39A GLU* 1.3 75.4 - - - +
41A TRP* 1.3 62.4 + - - +
43A LYS* 3.6 8.3 + - - +
44A MET* 3.1 32.4 + - + +
79A VAL* 4.0 2.7 - - + -
80A GLY* 3.7 23.6 - - - +
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Residues in contact with TRP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 2.9 50.0 + - + +
29A SER* 3.8 14.4 - - - -
31A MET 3.6 9.1 + - - -
32A LYS* 3.5 54.3 - - + -
33A GLY 5.6 0.2 - - - -
35A PHE* 3.9 23.3 - + + +
37A ASP 2.9 13.7 + - - +
38A GLU* 3.3 18.4 - - + +
40A ALA* 1.3 77.5 - - - +
42A LYS* 1.3 84.0 + - + +
44A MET* 3.3 3.8 + - - +
45A VAL* 3.1 41.6 + - + +
79A VAL* 3.7 10.5 - - + +
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.0 24.5 + - - +
39A GLU* 3.4 29.5 + - - +
41A TRP* 1.3 93.5 - - + +
43A LYS* 1.3 62.3 + - - +
45A VAL* 3.2 5.4 + - - +
46A GLU* 3.2 42.3 + - + +
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU 3.1 13.8 + - - +
40A ALA* 3.9 8.1 - - - +
42A LYS* 1.3 80.9 - - - +
44A MET* 1.3 59.6 + - + +
46A GLU* 3.5 6.5 + - - +
47A GLU* 2.9 65.6 + - + +
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Residues in contact with MET 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.5 23.8 - - + -
40A ALA* 3.1 20.3 + - + +
41A TRP 3.8 0.2 - - - +
43A LYS* 1.3 76.1 - - + +
45A VAL* 1.3 62.3 + - - +
47A GLU* 3.5 16.8 + - - +
48A GLY 3.3 7.1 + - - -
49A ASP 3.0 18.0 + - - -
50A PRO* 3.5 14.5 - - + +
78A LYS 3.3 26.9 - - - +
79A VAL* 4.0 13.2 - - - -
80A GLY 5.0 1.8 - - - -
84A PHE* 4.1 21.1 - - + -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.1 15.9 - - + -
29A SER* 4.2 8.7 - - - +
41A TRP* 3.1 49.4 + - + +
42A LYS* 3.2 8.5 + - - +
44A MET* 1.3 77.9 - - - +
46A GLU* 1.3 63.8 + - + +
48A GLY* 3.2 1.7 + - - -
49A ASP* 2.9 43.1 + - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 3.2 34.1 + - + +
43A LYS* 4.0 5.6 - - - +
45A VAL* 1.3 83.9 - - + +
47A GLU* 1.3 62.0 + - + +
48A GLY* 3.3 0.9 + - - -
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 2.9 62.0 + - + +
44A MET* 3.7 20.1 + - - +
45A VAL 3.2 0.4 - - - -
46A GLU* 1.3 77.7 - - + +
48A GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 48 (chain A).
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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27A ARG* 4.3 5.0 + - - -
44A MET 3.3 1.8 + - - -
45A VAL 3.2 1.3 + - - -
46A GLU 3.2 4.4 + - - -
47A GLU* 1.3 80.8 - - - +
49A ASP* 1.3 75.7 + - - +
50A PRO* 3.3 5.9 - - - +
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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