Contacts of the helix formed by residues 35 - 44 (chain A) in PDB entry 1JUO
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 LEU 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 2.9 14.4 + - - +
34A PRO* 1.3 80.1 - - + +
36A TYR* 1.3 64.6 + - - +
37A GLY 3.3 0.7 + - - -
38A TYR* 3.5 31.9 + - + +
39A PHE* 3.5 8.7 + - - +
61A SER* 5.0 0.2 - - - -
92A PHE* 3.8 13.1 - - + -
95A PHE* 4.0 13.4 - - + -
96A LYS* 4.5 18.4 - - + +
99A TRP* 3.4 72.7 - - + +
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Residues in contact with TYR 36 (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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32A GLN* 3.8 22.4 - - - +
33A ASP* 3.2 17.4 + - + +
35A LEU* 1.3 78.0 - - - +
37A GLY* 1.3 59.2 + - - +
39A PHE* 3.1 19.1 + + - +
40A ALA* 2.8 50.0 + - + +
92A PHE* 3.4 43.2 - + + -
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Residues in contact with GLY 37 (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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32A GLN* 5.5 0.6 - - - +
33A ASP 4.6 0.8 + - - -
34A PRO 4.0 6.6 + - - -
35A LEU 3.3 1.0 - - - -
36A TYR* 1.3 80.9 - - - +
38A TYR* 1.3 64.0 + - - +
39A PHE 3.1 0.2 + - - -
40A ALA* 3.3 5.8 + - - +
41A ALA* 3.0 24.5 + - - +
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO 4.1 12.6 - - - -
35A LEU* 3.5 30.5 + - + +
36A TYR 3.4 0.4 - - - -
37A GLY* 1.3 75.7 - - - +
39A PHE* 1.3 63.7 + - - +
41A ALA* 3.4 16.0 + - - +
42A VAL* 3.9 2.1 + - - +
57A CYS* 3.5 31.0 - - + +
60A GLN* 3.5 30.7 + - + +
61A SER* 3.5 39.7 + - - -
95A PHE* 4.8 4.9 - + + -
99A TRP* 5.6 0.7 - + - -
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Residues in contact with PHE 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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35A LEU 3.5 4.6 + - - +
36A TYR* 3.1 16.7 + + - +
38A TYR* 1.3 78.3 - - - +
40A ALA* 1.3 68.6 + - - +
42A VAL* 3.0 10.0 + - - +
43A ALA* 2.9 36.9 + - + +
47A GLY* 3.3 25.6 - - - -
49A ILE* 3.5 41.1 - - + -
57A CYS* 4.7 3.8 - - - -
90A MET 3.7 4.5 - - - -
91A GLY 3.6 7.9 - - - -
92A PHE* 3.3 54.5 - + + -
95A PHE* 3.9 21.3 - + + -
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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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36A TYR* 2.8 48.2 + - + +
37A GLY* 3.9 4.9 - - - +
39A PHE* 1.3 78.6 - - - +
41A ALA* 1.3 61.6 + - - +
42A VAL 3.1 1.2 + - - -
43A ALA* 3.6 9.4 + - - +
44A GLY* 4.1 10.8 + - - +
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Residues in contact with ALA 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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37A GLY 3.0 13.0 + - - +
38A TYR* 3.5 14.6 - - - +
39A PHE 3.1 0.4 - - - -
40A ALA* 1.3 76.3 - - - +
42A VAL* 1.3 64.4 + - + +
44A GLY 5.2 0.4 - - - -
56A ARG* 5.3 0.7 + - - -
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Residues in contact with VAL 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 TYR 4.0 1.8 - - - +
39A PHE* 3.0 14.0 + - - +
41A ALA* 1.3 85.9 - - + +
43A ALA* 1.3 65.7 + - - +
44A GLY* 3.2 4.0 + - - -
49A ILE* 3.8 16.4 - - + -
53A GLU* 3.3 42.4 - - + +
56A ARG* 3.8 32.5 + - + +
57A CYS* 3.7 32.8 - - + +
60A GLN* 6.4 0.9 - - + -
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Residues in contact with ALA 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 PHE* 2.9 43.9 + - + +
40A ALA* 3.6 5.1 + - - -
42A VAL* 1.3 77.6 - - - +
44A GLY* 1.3 66.5 + - - +
45A GLN 3.4 0.2 + - - -
46A ASP* 3.0 23.7 - - - +
47A GLY* 3.7 13.4 + - - -
48A GLN 3.5 5.2 - - - +
49A ILE* 3.6 15.5 - - + -
53A GLU* 5.5 0.7 - - - -
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Residues in contact with GLY 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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40A ALA* 4.1 9.9 + - - +
41A ALA 5.2 0.2 - - - -
42A VAL* 3.2 5.8 + - - +
43A ALA* 1.3 81.1 - - - +
45A GLN* 1.3 74.4 + - - +
46A ASP 3.8 0.2 + - - -
47A GLY* 4.4 2.8 + - - -
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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