Contacts of the helix formed by residues 36 - 48 (chain j) in PDB entry 5JPQ
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 36 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29j VAL* 4.5 6.2 - - + +
30j VAL 3.8 31.6 - - - +
31j GLY* 3.8 11.9 - - - +
32j ASP 3.1 4.0 + - - +
35j LYS* 1.3 81.6 - - - +
37j ALA* 1.3 63.3 + - - +
40j HIS* 2.8 35.0 - - + +
202j ILE 5.4 1.1 - - - +
203j ASP 5.6 0.4 - - - -
204j ASP* 4.4 11.0 - - + +
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Residues in contact with ALA 37 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29j VAL* 4.8 9.4 - - + +
31j GLY 5.2 0.2 - - - -
32j ASP 3.2 6.7 + - - +
33j HIS* 2.8 24.2 - - + +
35j LYS 3.2 0.4 - - - -
36j GLU* 1.3 85.8 - - - +
38j ILE* 1.3 63.5 + - - +
40j HIS* 4.1 0.3 - - - +
41j LEU* 3.1 20.7 + - - +
128j PHE* 5.8 4.5 - - + -
152j LEU* 4.5 21.1 - - + -
153j LEU 5.3 7.0 - - - +
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Residues in contact with ILE 38 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33j HIS 3.0 8.6 + - - +
34j ALA* 3.1 13.3 + - + +
37j ALA* 1.3 80.0 - - + +
39j VAL* 1.3 65.4 + - - +
41j LEU* 3.1 8.0 + - - +
42j TYR* 3.1 19.8 + - - +
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Residues in contact with VAL 39 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34j ALA 3.3 7.7 + - - +
35j LYS* 3.8 11.7 - - - +
37j ALA 3.5 0.2 - - - -
38j ILE* 1.3 78.1 - - - +
40j HIS* 1.3 64.6 + - - +
42j TYR* 3.0 10.1 + - - +
43j TYR* 3.0 21.2 + - - +
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Residues in contact with HIS 40 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29j VAL* 5.3 8.1 - - + -
35j LYS 4.0 1.2 + - - +
36j GLU* 2.8 27.4 + - + +
37j ALA 4.1 0.2 - - - +
38j ILE 3.2 0.2 - - - -
39j VAL* 1.3 79.3 - - - +
41j LEU* 1.3 51.5 + - - +
43j TYR* 3.0 8.5 + - - +
44j ILE* 2.7 37.6 + - - +
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Residues in contact with LEU 41 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37j ALA 3.1 17.5 + - - +
38j ILE* 3.1 8.3 + - - +
40j HIS* 1.3 75.9 - - - +
42j TYR* 1.3 63.2 + - - +
44j ILE* 3.8 6.1 - - - +
45j MET* 3.0 24.3 + - - +
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Residues in contact with TYR 42 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38j ILE 3.1 10.3 + - - +
39j VAL* 3.0 12.4 + - - +
41j LEU* 1.3 77.9 - - - +
43j TYR* 1.3 62.0 + - - +
45j MET* 3.2 15.0 + - - +
46j SER* 3.3 12.8 + - - -
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Residues in contact with TYR 43 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39j VAL 3.0 11.9 + - - +
40j HIS* 3.5 10.3 - - - +
42j TYR* 1.3 74.3 - - - +
44j ILE* 1.3 59.8 + - - +
46j SER* 3.2 6.7 + - - -
47j SER* 2.9 31.5 + - - -
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Residues in contact with ILE 44 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40j HIS 2.7 20.9 + - - +
41j LEU* 3.8 6.7 - - - +
43j TYR* 1.3 73.3 - - - +
45j MET* 1.3 57.1 + - - +
47j SER* 4.4 5.2 - - - -
48j MET* 2.6 41.7 + - + +
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Residues in contact with MET 45 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41j LEU 3.0 14.5 + - - +
42j TYR* 3.6 9.9 - - - +
43j TYR 3.2 0.2 - - - -
44j ILE* 1.3 78.7 - - - +
46j SER* 1.3 65.9 + - - +
48j MET 3.5 12.5 - - - +
53j ASN* 3.8 15.7 - - + +
54j LYS 5.0 0.4 + - - +
56j VAL* 5.2 14.4 - - + -
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Residues in contact with SER 46 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42j TYR 3.3 8.0 + - - -
43j TYR* 3.2 9.4 + - - -
45j MET* 1.3 81.6 - - - +
47j SER* 1.3 64.7 + - - +
48j MET 4.5 1.2 - - - -
49j ASP* 4.8 5.0 - - - +
53j ASN* 5.0 3.9 - - - +
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Residues in contact with SER 47 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12j PRO* 4.3 17.2 - - - +
43j TYR* 2.9 18.7 + - - -
44j ILE* 3.9 4.0 - - - -
46j SER* 1.3 81.0 - - - +
48j MET* 1.3 57.2 - - - +
49j ASP* 3.1 12.0 + - - +
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Residues in contact with MET 48 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11j ILE* 6.3 2.9 - - + -
12j PRO* 5.2 8.5 - - + -
15j ILE* 5.5 9.4 - - + -
44j ILE* 2.6 25.6 + - + +
45j MET* 3.5 6.3 - - - +
47j SER* 1.3 71.0 - - - +
49j ASP* 1.3 59.5 + - - +
50j VAL 4.0 1.3 + - - -
53j ASN* 3.2 19.2 - - - -
54j LYS* 4.1 4.5 + - - +
148j LEU* 6.1 4.7 - - + -
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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