Contacts of the helix formed by residues 36 - 47 (chain A) in PDB entry 2JI8
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 ILE 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL 3.6 10.1 - - - +
32A VAL* 3.6 30.3 - - + -
33A GLY 3.0 10.1 + - - +
35A PRO* 1.3 79.2 - - + +
37A THR* 1.3 64.6 + - - +
38A ASN 3.3 2.7 - - - -
39A LEU* 3.3 11.5 + - + +
40A ALA* 3.2 17.0 + - - +
77A LEU* 3.6 36.0 - - + +
78A THR 3.4 27.8 - - - +
79A VAL* 4.2 3.6 - - + +
106A GLY* 3.6 24.7 - - - +
168A LEU* 5.8 0.2 - - + -
173A PHE* 4.4 13.7 - - + -
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Residues in contact with THR 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 VAL* 4.0 25.3 - - + +
33A GLY* 2.9 34.0 + - - -
35A PRO 3.7 2.0 - - - -
36A ILE* 1.3 75.9 - - - +
38A ASN* 1.3 62.4 + - - +
40A ALA* 3.0 8.0 + - - +
41A ARG* 2.9 60.9 + - + +
483B TYR* 4.5 6.7 + - + -
497B CYS* 5.2 0.2 - - - -
498B THR* 4.4 6.5 - - + -
552B GLU* 4.3 7.5 + - - +
560B ASN* 4.5 7.1 + - - -
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Residues in contact with ASN 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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13A PHE* 4.2 13.7 - - + -
35A PRO 5.2 0.4 + - - -
36A ILE 3.3 0.2 - - - -
37A THR* 1.3 75.8 - - - +
39A LEU* 1.3 60.7 + - - +
41A ARG* 3.1 34.9 + - + +
42A MET* 3.1 40.6 + - + +
552B GLU* 5.5 0.8 + - - -
560B ASN* 5.0 8.5 + - - +
561B VAL 2.8 30.4 + - - +
562B VAL* 3.7 24.4 - - - +
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Residues in contact with LEU 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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13A PHE* 3.8 31.8 - - + +
16A LEU* 4.1 29.2 - - + -
17A ILE* 4.1 23.8 - - + -
20A LEU* 5.8 1.6 - - + -
28A MET* 4.5 12.8 - - + -
36A ILE* 3.3 13.5 + - + +
37A THR 3.3 0.6 - - - -
38A ASN* 1.3 75.4 - - - +
40A ALA* 1.3 58.8 + - - +
42A MET* 3.4 2.5 + - - +
43A TRP* 2.9 29.9 + - + +
77A LEU* 3.7 33.7 - - + -
104A LEU* 5.5 1.1 - - + -
168A LEU* 4.7 0.7 - - + -
173A PHE* 4.2 16.4 - - + -
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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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28A MET* 5.3 0.2 - - - -
32A VAL* 3.4 29.2 - - + -
36A ILE 3.2 5.6 + - - +
37A THR 3.0 11.1 + - - +
39A LEU* 1.3 80.0 - - - +
41A ARG* 1.3 63.7 + - - +
43A TRP* 3.4 8.9 - - - +
44A GLN* 3.4 22.7 + - - +
50A PHE* 4.2 23.1 - - + +
77A LEU* 4.4 4.2 - - + +
497B CYS* 3.9 9.2 - - - -
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Residues in contact with ARG 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 THR* 2.9 43.0 + - - +
38A ASN* 3.1 33.8 + - - +
39A LEU 3.3 0.2 - - - -
40A ALA* 1.3 75.3 - - - +
42A MET* 1.3 59.2 + - + +
44A GLN* 3.1 9.7 + - - +
45A ASP* 2.9 39.6 + - - +
483B TYR* 5.0 1.2 - - - -
487B GLU* 3.0 39.7 + - - +
497B CYS* 4.1 15.2 - - - -
498B THR* 4.0 7.9 - - - +
552B GLU* 3.4 32.9 + - - -
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Residues in contact with MET 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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11A ASP* 4.6 2.9 - - - +
13A PHE* 3.6 36.3 - - + -
14A HIS* 2.9 45.1 - - + +
17A ILE* 3.6 17.9 - - + +
38A ASN* 3.1 23.9 + - + +
39A LEU 4.0 1.3 - - - +
41A ARG* 1.3 74.4 - - + +
43A TRP* 1.3 66.1 + - - +
45A ASP* 3.7 15.1 - - + +
46A ASP* 2.9 26.7 + - - +
562B VAL 6.1 1.1 - - - -
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Residues in contact with TRP 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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17A ILE* 3.7 47.8 - - + +
20A LEU* 4.0 22.4 - - + -
21A LYS* 4.1 5.8 - - + -
25A ILE* 3.3 27.8 - - + -
26A ASP 3.6 22.9 - - - -
27A THR 3.8 3.1 - - - -
28A MET* 3.7 34.1 - - + +
39A LEU 2.9 15.3 + - - +
40A ALA* 3.4 10.8 - - - +
42A MET* 1.3 77.8 - - - +
44A GLN* 1.3 56.9 + - - +
46A ASP* 3.5 1.7 + - - +
47A GLY 3.4 4.0 + - - -
48A GLN* 3.1 49.5 + - + +
49A ARG 2.8 34.9 + - - +
50A PHE* 4.2 10.1 - + + -
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Residues in contact with GLN 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 3.5 11.6 - - - +
41A ARG* 3.1 8.5 + - - +
43A TRP* 1.3 75.0 - - - +
45A ASP* 1.3 64.7 - - - +
46A ASP 3.2 0.4 - - - -
47A GLY* 3.0 15.8 + - - -
48A GLN 3.5 13.7 + - - +
49A ARG* 5.5 0.4 - - - +
50A PHE* 3.7 39.4 + - + +
490B PRO* 3.6 26.5 - - + +
491B GLN* 3.5 14.2 - - - +
494B VAL* 3.9 13.2 - - + +
495B ILE 3.3 19.2 + - - -
496B SER* 3.7 1.0 - - - -
497B CYS* 3.3 31.5 + - - +
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Residues in contact with ASP 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 ARG* 2.9 27.5 + - - +
42A MET* 3.7 18.9 + - + +
44A GLN* 1.3 73.8 - - - +
46A ASP* 1.3 62.3 + - - +
47A GLY* 3.3 1.4 + - - -
490B PRO* 3.5 24.6 - - - +
491B GLN* 4.5 10.2 + - - -
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Residues in contact with ASP 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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14A HIS* 5.9 3.3 - - + -
17A ILE* 4.1 18.5 - - + +
18A ASP* 5.1 2.3 - - - +
21A LYS* 2.5 42.9 + - - +
42A MET 2.9 18.3 + - - +
43A TRP 3.6 6.5 - - - +
45A ASP* 1.3 75.8 - - - +
47A GLY* 1.3 57.0 + - - +
48A GLN* 3.7 8.1 + - + +
491B GLN* 5.2 0.2 - - - -
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Residues in contact with GLY 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 TRP 3.4 0.2 + - - -
44A GLN 3.0 13.5 + - - -
45A ASP 3.1 0.2 - - - -
46A ASP* 1.3 79.4 - - - +
48A GLN* 1.3 71.9 + - - +
49A ARG* 5.9 0.2 - - - +
491B GLN* 3.8 20.6 - - - -
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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