Contacts of the helix formed by residues 39 - 47 (chain A) in PDB entry 1JGN
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A HIS 3.2 3.3 + - - -
38A THR* 1.3 91.1 - - + +
40A ALA* 1.3 69.1 + - - +
41A GLY* 2.7 7.1 + - - +
42A LYS* 2.9 25.8 + - + +
43A ILE* 2.9 10.9 + - - +
76A LEU* 3.5 30.1 - - + -
79A HIS* 6.4 0.7 - - + -
80A GLN* 5.2 16.2 - - + +
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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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29A PHE* 4.0 17.4 - - + -
32A ILE* 3.1 39.0 - - + +
33A GLN* 4.0 2.2 - - - +
36A HIS* 3.8 18.8 + - + +
39A LEU* 1.3 72.6 - - - +
41A GLY* 1.3 64.2 + - - +
43A ILE* 3.0 23.8 + - - +
44A THR* 3.1 17.3 + - - +
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Residues in contact with GLY 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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29A PHE* 3.3 26.6 - - - -
39A LEU* 2.7 7.9 + - - -
40A ALA* 1.3 73.5 - - - +
42A LYS* 1.3 55.8 + - - +
44A THR* 2.9 23.7 - - - +
45A GLY* 3.8 1.7 + - - -
13B PHE* 5.1 2.8 - - - +
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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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39A LEU* 2.9 19.6 + - + +
41A GLY* 1.3 71.9 - - - -
43A ILE* 1.3 67.3 + - - +
45A GLY* 3.1 9.2 + - - -
46A MET* 3.3 34.6 - - + +
76A LEU* 3.6 22.9 - - + -
79A HIS* 3.8 26.3 + - + +
12B GLU* 3.1 50.3 + - + +
13B PHE 5.4 0.4 - - - +
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Residues in contact with ILE 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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32A ILE* 3.3 35.4 - - + -
38A THR* 4.3 1.3 - - - -
39A LEU 2.9 26.4 + - - +
40A ALA* 3.0 11.0 + - - +
42A LYS* 1.3 78.7 - - - +
44A THR* 1.3 65.2 + - - +
45A GLY 3.1 0.9 + - - -
46A MET* 3.3 0.7 + - - -
47A LEU* 2.9 29.1 + - + +
72A ALA* 3.2 43.5 - - + +
73A VAL* 3.9 19.1 - - + -
76A LEU* 3.3 24.8 - - + +
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Residues in contact with THR 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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24A LEU 4.3 1.7 + - - -
28A LEU* 3.0 35.5 - - - +
29A PHE* 3.4 34.6 + - + -
32A ILE* 3.5 1.2 - - - +
40A ALA 3.1 5.8 + - - +
41A GLY 2.9 26.9 - - - +
43A ILE* 1.3 77.6 - - - +
45A GLY* 1.3 52.4 + - - +
47A LEU 3.3 0.3 - - - -
48A LEU* 2.6 53.4 + - - +
13B PHE* 3.5 16.8 - - + -
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Residues in contact with GLY 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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41A GLY 4.6 0.9 - - - -
42A LYS* 3.1 9.7 + - - -
43A ILE 3.1 1.6 + - - -
44A THR* 1.3 82.6 - - - +
46A MET* 1.3 59.6 + - - +
48A LEU* 2.9 20.3 - - - +
11B LYS 2.5 18.2 - - - +
12B GLU* 3.8 1.8 - - - +
13B PHE* 3.4 32.5 - - - -
19B TYR* 4.9 0.3 - - - -
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Residues in contact with MET 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* 3.3 34.6 + - + +
43A ILE 3.3 4.0 + - - +
45A GLY* 1.3 73.4 - - - +
47A LEU* 1.3 66.6 + - + +
48A LEU 3.1 3.8 + - - -
49A GLU* 3.8 5.0 + - - +
75A VAL* 3.5 30.7 - - + +
76A LEU* 4.0 9.0 - - + -
79A HIS* 3.3 47.6 - - + +
2B VAL* 6.1 0.2 - - - -
4B SER* 6.2 0.2 - - - -
7B ASN* 4.1 3.5 - - - +
9B ASN 3.5 19.8 - - - +
10B ALA* 3.5 33.0 - - + +
11B LYS 3.0 14.1 + - - +
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Residues in contact with LEU 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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28A LEU* 3.1 30.9 - - + +
43A ILE* 2.9 27.8 + - + +
44A THR 3.3 1.8 - - - -
46A MET* 1.3 76.0 - - + +
48A LEU* 1.3 62.9 + - - +
49A GLU 3.0 3.8 + - - +
50A ILE* 3.2 17.5 + - + +
72A ALA* 3.7 22.2 - - + -
75A VAL* 4.0 16.6 - - + -
4B SER* 4.4 8.1 - - - +
6B LEU* 3.5 30.1 - - + -
7B ASN* 3.3 39.6 - - + +
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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