Contacts of the helix formed by residues 27 - 47 (chain I) in PDB entry 2ODC
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 VAL 27 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ASP* 5.0 1.6 - - - -
25I PRO* 4.4 7.6 - - + +
26I VAL* 1.3 78.0 - - - +
28I GLY* 1.3 56.2 + - - +
29I SER* 3.7 17.3 - - - +
30I THR* 2.6 40.8 + - + +
31I ARG* 2.3 37.6 + - - -
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Residues in contact with GLY 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I VAL* 1.3 76.4 - - - +
29I SER* 1.3 60.7 + - - +
30I THR 3.3 0.3 + - - -
31I ARG* 3.6 22.8 + - - +
32I ARG* 4.2 6.6 + - - +
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Residues in contact with SER 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I VAL* 2.7 22.9 + - - +
28I GLY* 1.3 75.5 - - - +
30I THR* 1.3 64.6 + - - +
32I ARG* 5.1 2.3 + - - +
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Residues in contact with THR 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I PRO 3.4 15.6 + - - -
27I VAL* 2.6 32.0 + - + +
29I SER* 1.3 82.3 - - - +
31I ARG* 1.3 63.9 + - - -
32I ARG 3.2 2.2 - - - -
33I LEU* 3.2 25.3 + - + +
34I TYR* 3.0 23.8 + - - -
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Residues in contact with ARG 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR 5.5 0.6 + - - -
5I ALA* 3.7 22.2 + - - +
7I LEU 3.4 22.1 + - - -
8I SER* 4.5 2.0 - - - +
9I ASP* 3.7 24.4 + - - +
12I LEU* 4.6 7.5 - - + +
26I VAL* 4.4 13.9 - - + +
27I VAL 2.3 35.2 + - - +
28I GLY* 3.6 12.2 + - - +
30I THR* 1.3 69.9 - - - +
32I ARG* 1.3 64.6 + - - +
34I TYR* 3.0 12.4 + - - +
35I GLU* 2.9 41.7 + - + +
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Residues in contact with ARG 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ASP* 5.9 1.8 + - - -
28I GLY 4.2 6.8 + - - +
29I SER 5.6 2.2 - - - +
30I THR 3.2 0.4 - - - -
31I ARG* 1.3 80.7 - - - +
33I LEU* 1.3 64.5 + - - +
35I GLU* 3.0 26.1 + - + +
36I LYS* 3.0 14.3 + - + +
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I THR* 3.2 21.5 + - + +
31I ARG 3.2 0.6 - - - -
32I ARG* 1.3 82.8 - - - +
34I TYR* 1.3 68.2 + - + +
36I LYS* 3.4 13.6 + - + +
37I LYS* 3.2 51.6 + - + +
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Residues in contact with TYR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 3.9 17.9 - - + -
16I LEU* 3.9 21.1 - - + -
22I PRO 4.8 2.2 - - - -
23I HIS* 3.3 23.4 - - + -
24I GLY* 2.7 32.3 + - - -
25I PRO* 3.5 21.6 + - - +
26I VAL* 4.3 12.8 - - + -
30I THR* 3.0 33.1 + - - -
31I ARG* 3.0 10.0 + - - +
33I LEU* 1.3 83.1 - - + +
35I GLU* 1.3 66.1 + - - +
37I LYS* 3.2 28.3 + - + +
38I ILE* 3.2 20.3 + - - +
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Residues in contact with GLU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ASP* 3.8 14.9 - - - +
4I TYR* 3.9 25.8 - - + +
5I ALA* 3.1 42.3 + - - +
12I LEU* 4.8 7.0 - - + -
31I ARG* 2.9 42.2 + - + +
32I ARG* 3.0 15.6 + - + +
34I TYR* 1.3 75.8 - - - +
36I LYS* 1.3 62.5 + - - +
38I ILE* 3.5 7.9 + - - +
39I PHE* 3.2 20.4 + - - +
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Residues in contact with LYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I ARG* 3.0 13.7 + - + +
33I LEU* 3.7 18.6 - - + +
35I GLU* 1.3 78.1 - - - +
37I LYS* 1.3 64.0 + - + +
39I PHE* 3.1 9.4 + - + +
40I GLU* 3.0 26.6 + - + +
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Residues in contact with LYS 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I LEU* 5.0 6.7 - - + -
21I ILE* 4.6 21.9 - - + +
22I PRO 5.5 3.6 + - - +
33I LEU* 3.2 45.9 + - + +
34I TYR* 3.2 25.1 + - + +
36I LYS* 1.3 80.6 - - + +
38I ILE* 1.3 63.9 + - + +
40I GLU* 3.3 7.8 + - - +
41I TYR* 3.2 20.6 + - - +
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Residues in contact with ILE 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I TYR* 3.7 20.6 - - + -
12I LEU* 3.4 38.1 - - + -
15I LEU* 4.8 11.4 - - + -
16I LEU* 3.6 26.7 - - + -
19I TYR* 4.1 18.8 - - + +
21I ILE* 5.0 2.9 - - - -
34I TYR 3.2 15.4 + - - +
35I GLU* 3.9 6.5 - - - +
37I LYS* 1.3 76.1 - - - +
39I PHE* 1.3 57.3 + - - +
41I TYR* 3.3 4.7 + - - +
42I GLU* 2.9 51.1 + - + +
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Residues in contact with PHE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR* 3.8 35.4 - + + -
35I GLU 3.2 11.3 + - - +
36I LYS* 3.1 15.4 + - + +
38I ILE* 1.3 80.0 - - - +
40I GLU* 1.3 55.3 + - - +
42I GLU* 3.9 0.6 - - + +
43I THR* 2.4 59.6 + - + -
46I ARG* 5.3 12.8 - - - -
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Residues in contact with GLU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I LYS* 3.0 17.8 + - + +
37I LYS* 3.8 9.7 - - - +
38I ILE 3.3 0.2 - - - -
39I PHE* 1.3 81.5 - - - +
41I TYR* 1.3 64.1 + - - +
43I THR* 3.4 7.4 - - - -
44I GLN* 3.3 25.3 + - + +
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Residues in contact with TYR 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I TYR* 3.3 52.1 + + + +
21I ILE* 4.1 20.6 - - + -
37I LYS 3.2 10.7 + - - +
38I ILE* 3.8 5.8 - - - +
40I GLU* 1.3 77.5 - - - +
42I GLU* 1.3 73.0 + - - +
44I GLN* 2.8 38.2 + - - +
45I ARG* 3.3 40.7 + - + +
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Residues in contact with GLU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR* 3.9 21.6 + - + +
19I TYR* 2.8 45.2 + - + -
38I ILE* 2.9 39.0 + - + +
39I PHE* 3.9 1.8 - - + +
41I TYR* 1.3 74.3 - - + +
43I THR* 1.3 64.2 + - - +
45I ARG* 3.2 14.7 + - - +
46I ARG* 3.0 35.3 + - - +
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Residues in contact with THR 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I PHE* 2.4 54.3 + - + -
40I GLU* 3.4 8.7 - - - -
42I GLU* 1.3 77.7 - - - +
44I GLN* 1.3 66.0 + - + +
46I ARG* 2.9 23.9 + - + +
47I ARG* 3.0 44.7 + - - +
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Residues in contact with GLN 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I GLU* 3.3 15.2 + - + +
41I TYR* 2.8 26.2 + - + +
43I THR* 1.3 80.8 - - + +
45I ARG* 1.3 57.8 + - + +
47I ARG* 2.6 39.0 + - - +
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Residues in contact with ARG 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ARG* 4.7 13.7 - - - +
19I TYR* 4.0 17.9 - - - -
41I TYR* 3.5 51.1 + - + +
42I GLU* 3.2 17.0 + - - +
44I GLN* 1.3 77.4 - - + +
46I ARG* 1.3 61.6 + - + +
47I ARG 3.3 3.6 + - - +
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Residues in contact with ARG 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ASN* 6.2 0.2 - - - +
4I TYR* 3.6 23.4 + - - -
39I PHE* 5.3 13.1 - - - -
42I GLU* 3.0 23.6 + - - +
43I THR* 2.9 17.5 + - + +
45I ARG* 1.3 79.1 - - + +
47I ARG* 1.3 61.1 + - + +
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Residues in contact with ARG 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I THR* 3.0 35.8 + - + +
44I GLN* 2.6 26.9 + - - +
45I ARG 4.1 3.9 - - - +
46I ARG* 1.3 83.9 - - + +
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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
------------------------------------------------------------
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