Contacts of the helix formed by residues 34 - 46 (chain A) in PDB entry 1OLN
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 ASN 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 3.3 15.6 + - - -
33A VAL* 1.3 75.9 - - - +
35A ILE* 1.3 69.0 - - - +
36A MET* 3.4 2.5 - - + -
37A GLU* 3.0 41.3 + - + +
38A PHE 3.6 2.1 + - - -
64A LYS* 3.7 19.0 + - - +
65A SER* 5.2 1.7 - - - -
66A PHE* 3.5 12.2 - - - -
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Residues in contact with ILE 35 (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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19A THR* 4.4 13.7 - - + +
24A VAL* 4.8 5.6 - - + -
25A GLY* 3.6 34.1 - - - +
28A LEU* 4.5 7.2 - - + -
29A GLY* 3.5 32.1 - - - +
33A VAL* 3.6 5.1 - - - +
34A ASN* 1.3 68.2 - - - +
36A MET* 1.3 55.5 + - - +
38A PHE* 2.6 35.9 + - + +
39A CYS* 3.0 29.6 + - - -
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Residues in contact with MET 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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19A THR* 5.7 3.5 - - - +
34A ASN* 3.2 2.4 + - + +
35A ILE* 1.3 76.9 - - - +
37A GLU* 1.3 83.1 + - + +
39A CYS* 3.5 8.7 + - - +
40A LYS* 3.3 56.4 + - + +
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Residues in contact with GLU 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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34A ASN* 3.0 32.7 + - + +
35A ILE 2.9 1.4 + - - -
36A MET* 1.3 93.8 - - + +
38A PHE* 1.3 58.2 + - - +
40A LYS* 4.4 2.3 - - - +
41A ARG* 2.9 67.2 + - + +
65A SER* 5.7 1.4 + - - -
66A PHE* 3.8 7.7 - - + -
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Residues in contact with PHE 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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11A LEU* 4.2 4.5 - - + -
13A LEU* 3.4 34.3 - - + -
18A ALA* 6.2 0.9 - - + -
24A VAL* 4.6 10.3 - - + -
28A LEU* 3.6 24.5 - - + -
33A VAL* 4.9 2.2 - - + -
34A ASN 4.5 0.4 - - - +
35A ILE* 2.6 19.2 + - + +
37A GLU* 1.3 73.4 - - - +
39A CYS* 1.3 60.7 + - - +
41A ARG* 4.1 1.1 - - - -
42A PHE* 2.5 53.9 + + + +
56A VAL* 3.8 8.7 - - + -
58A ILE* 3.3 39.3 - - + -
66A PHE* 3.6 17.6 - + + -
68A PHE* 3.5 26.7 - + - -
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Residues in contact with CYS 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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18A ALA* 3.5 15.5 - - + -
19A THR* 2.8 54.5 - - - +
24A VAL* 5.6 2.0 - - - -
35A ILE* 3.0 34.1 + - - -
36A MET* 3.7 7.6 - - - +
38A PHE* 1.3 77.2 - - - +
40A LYS* 1.3 61.2 + - + +
42A PHE* 4.6 0.4 - - - -
43A ASN* 2.9 39.8 + - - +
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Residues in contact with LYS 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 MET* 3.3 48.6 + - + +
37A GLU* 4.4 2.2 - - - +
39A CYS* 1.3 75.5 - - + +
41A ARG* 1.3 60.4 + - - +
43A ASN* 3.7 4.8 - - - +
44A ALA* 3.0 28.9 + - - +
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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 GLU* 2.9 53.0 + - + +
38A PHE 3.0 2.6 + - - +
40A LYS* 1.3 74.5 - - - +
42A PHE* 1.3 62.6 + - - +
44A ALA* 2.9 19.5 - - - +
45A GLU* 2.5 22.4 - - - +
65A SER* 5.3 1.8 + - - -
66A PHE* 3.0 62.2 + - - +
67A THR* 4.2 5.9 - - - +
68A PHE* 3.8 25.6 - - + -
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Residues in contact with PHE 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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13A LEU* 3.4 43.5 - - + -
14A PRO 3.0 23.3 - - - -
15A ALA 3.2 7.4 - - - -
17A LYS 3.9 4.3 - - - -
18A ALA* 4.6 2.7 - - + -
38A PHE* 2.5 40.7 + + + +
39A CYS* 3.9 2.5 - - - +
41A ARG* 1.3 71.8 - - - +
43A ASN* 1.3 73.4 + - - +
44A ALA 2.8 10.7 + - - -
45A GLU* 3.4 8.7 + - - +
46A THR* 2.9 41.6 + - + +
54A LEU* 3.9 8.5 - - + -
56A VAL* 3.7 21.3 - - + -
68A PHE* 3.6 4.2 - - - -
70A ILE* 3.6 22.0 - - + -
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Residues in contact with ASN 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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15A ALA 3.3 0.7 - - - +
16A GLY* 4.0 6.8 - - - -
17A LYS* 2.7 37.3 + - - +
18A ALA* 3.4 25.2 + - - +
39A CYS* 2.9 22.4 + - - +
40A LYS* 3.7 5.5 - - - +
42A PHE* 1.3 85.8 - - - +
44A ALA* 1.3 62.7 + - - +
46A THR* 2.9 12.3 + - - -
47A ALA* 4.0 9.2 + - - +
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Residues in contact with ALA 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 LYS 3.0 13.3 + - - +
41A ARG* 2.9 19.7 + - - +
42A PHE 2.8 2.4 + - - -
43A ASN* 1.3 76.2 - - - +
45A GLU* 1.3 59.4 + - - +
47A ALA* 3.1 27.0 - - - +
48A ASP* 4.8 0.7 - - - +
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Residues in contact with GLU 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* 2.5 23.5 - - - +
42A PHE 3.7 3.3 - - - +
44A ALA* 1.3 74.8 - - - +
46A THR* 1.3 60.3 + - + +
47A ALA 2.8 10.8 + - - -
48A ASP* 2.8 35.0 + - - +
49A LYS* 4.4 2.9 + - - +
68A PHE* 3.2 26.1 - - - -
70A ILE* 4.2 19.1 - - + -
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Residues in contact with THR 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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15A ALA* 2.8 34.7 + - - +
16A GLY* 4.0 2.0 + - - -
42A PHE* 2.9 58.8 + - + +
43A ASN* 2.9 13.8 + - - -
45A GLU* 1.3 75.4 - - - +
47A ALA* 1.3 56.6 + - - +
48A ASP 3.5 0.4 - - - -
49A LYS* 2.9 25.1 - - - +
50A ALA* 3.9 1.7 + - - +
54A LEU* 3.5 20.0 - - + -
70A ILE* 4.0 8.1 - - + -
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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