Contacts of the helix formed by residues 27 - 47 (chain C) in PDB entry 2ODG
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 5.7 1.3 - - + -
39B PHE* 4.5 11.2 - - + -
48B GLN* 3.9 33.4 - - - +
62B TRP* 4.6 15.7 - - + +
25C PRO* 3.7 11.3 + - + +
26C VAL* 1.3 84.1 - - - +
28C GLY* 1.3 55.4 + - - +
29C SER* 3.9 15.5 - - - +
30C THR* 2.6 16.5 + - - +
31C ARG* 2.3 39.6 + - - +
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Residues in contact with GLY 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 1.3 77.6 - - - +
29C SER* 1.3 61.6 + - - +
30C THR 3.3 0.2 + - - -
31C ARG* 3.6 22.8 + - - +
32C ARG* 4.2 6.8 + - - +
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 4.8 6.2 + - - -
62A TRP* 5.6 3.3 + - - -
48B GLN* 5.7 3.1 + - - -
51B VAL* 5.2 12.6 - - - +
27C VAL* 2.7 17.6 + - - +
28C GLY* 1.3 74.9 - - - +
30C THR* 1.3 67.7 + - - -
32C ARG* 5.1 2.8 + - - +
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Residues in contact with THR 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 4.0 16.2 + - - +
51A VAL* 5.5 5.8 - - - +
52A LEU* 5.3 7.4 - - + -
62A TRP* 4.7 13.4 + - + +
25C PRO 4.7 7.0 - - - -
27C VAL* 2.6 14.5 + - - +
29C SER* 1.3 84.3 + - - +
31C ARG* 1.3 63.5 + - - -
32C ARG 3.2 2.7 - - - -
33C LEU* 3.2 33.6 + - + +
34C TYR* 3.0 38.6 + - + +
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TYR 5.5 0.6 + - - -
5C ALA* 3.7 21.6 + - - +
7C LEU 3.4 20.1 + - - -
8C SER* 4.5 1.6 - - - +
9C ASP* 3.3 26.4 + - - +
12C LEU* 4.6 7.8 - - + +
26C VAL* 4.4 14.5 - - + +
27C VAL 2.3 37.5 + - - +
28C GLY* 3.6 12.8 + - - +
30C THR* 1.3 70.5 - - - +
32C ARG* 1.3 64.0 + - - +
34C TYR* 3.0 12.3 + - - +
35C GLU* 2.9 41.6 + - + +
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 6.0 2.2 - - - +
2C ASP* 5.9 2.0 + - - -
28C GLY 4.2 6.4 + - - +
29C SER 5.6 2.5 - - - +
30C THR 5.1 0.2 - - - -
31C ARG* 1.3 80.9 - - - +
33C LEU* 1.3 65.2 + - - +
35C GLU* 3.0 25.7 + - + +
36C LYS* 3.0 15.0 + - + +
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 6.6 0.2 - - + -
58A LEU* 5.6 4.9 - - + +
61A GLU* 5.6 3.6 - - + +
62A TRP* 4.3 28.3 - - + +
65A ASP* 3.6 28.3 - - + +
30C THR* 3.2 29.9 + - + +
31C ARG 3.2 0.6 - - - -
32C ARG* 1.3 81.2 - - - +
34C TYR* 1.3 64.8 + - + +
36C LYS* 3.4 11.2 + - + +
37C LYS* 3.2 52.0 + - + +
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.9 6.1 - - - +
58A LEU* 4.6 13.1 - - + +
12C LEU* 3.9 17.7 - - + -
16C LEU* 3.9 21.3 - - + -
21C ILE* 6.3 0.2 - - + -
22C PRO 4.8 1.3 - - - -
23C HIS* 3.3 23.5 - - + -
24C GLY* 2.7 33.9 + - - -
25C PRO* 3.5 21.2 + - - +
26C VAL* 4.3 11.2 - - + -
30C THR* 3.0 40.1 + - + +
31C ARG* 3.0 9.6 + - - +
33C LEU* 1.3 81.2 - - + +
35C GLU* 1.3 67.3 + - - +
37C LYS* 3.2 23.7 + - + +
38C ILE* 3.2 20.3 + - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ASP* 3.8 14.6 - - - +
4C TYR* 3.9 27.0 - - + +
5C ALA* 3.1 42.2 + - - +
12C LEU* 4.8 6.5 - - + -
31C ARG* 2.9 43.2 + - + +
32C ARG* 3.0 14.8 + - + +
34C TYR* 1.3 76.0 - - - +
36C LYS* 1.3 64.1 + - - +
38C ILE* 3.5 7.4 + - - +
39C PHE* 3.2 21.3 + - - +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 4.4 21.1 + - - +
32C ARG* 3.0 14.3 + - + +
33C LEU* 3.7 15.3 - - + +
35C GLU* 1.3 79.0 - - - +
37C LYS* 1.3 62.6 + - + +
39C PHE* 3.1 9.4 + - + +
40C GLU* 3.0 31.0 + - + +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.4 17.7 - - + +
61A GLU* 2.3 39.0 + - - +
16C LEU* 5.0 7.6 - - + -
21C ILE* 4.6 19.4 - - + +
22C PRO 5.6 0.7 - - - +
33C LEU* 3.2 43.4 + - + +
34C TYR* 3.2 19.0 + - + +
36C LYS* 1.3 78.9 - - + +
38C ILE* 1.3 62.6 + - + +
40C GLU* 3.3 7.7 + - - +
41C TYR* 3.2 21.5 + - - +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TYR* 3.7 19.1 - - + -
12C LEU* 3.4 38.6 - - + -
15C LEU* 4.8 12.1 - - + -
16C LEU* 3.6 26.0 - - + -
19C TYR* 4.1 19.1 - - + +
21C ILE* 5.0 2.9 - - - -
34C TYR 3.2 16.0 + - - +
35C GLU* 3.9 6.3 - - - +
37C LYS* 1.3 76.9 - - - +
39C PHE* 1.3 58.4 + - - +
41C TYR* 3.3 4.6 + - - +
42C GLU* 2.9 51.3 + - + +
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Residues in contact with PHE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TYR* 3.8 35.6 - + + -
35C GLU 3.2 12.0 + - - +
36C LYS* 3.1 15.6 + - + +
38C ILE* 1.3 80.2 - - - +
40C GLU* 1.3 57.0 + - - +
42C GLU* 3.9 0.3 - - - +
43C THR* 2.4 60.3 + - + -
46C ARG* 5.3 12.8 - - - -
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS* 3.0 22.1 + - + +
37C LYS* 3.8 10.6 - - - +
38C ILE 3.3 0.2 - - - -
39C PHE* 1.3 82.7 - - - +
41C TYR* 1.3 63.4 + - - +
43C THR* 3.4 7.2 - - - -
44C GLN* 3.3 25.3 + - + +
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Residues in contact with TYR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.3 52.9 + + + +
21C ILE* 4.1 21.5 - - + -
37C LYS 3.2 11.0 + - - +
38C ILE* 3.8 6.1 - - - +
40C GLU* 1.3 77.3 - - - +
42C GLU* 1.3 72.9 + - + +
44C GLN* 2.8 37.8 + - + +
45C ARG* 3.3 38.9 + - + +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C TYR* 3.9 21.4 + - + +
19C TYR* 2.8 44.2 + - + -
38C ILE* 2.9 38.9 + - + +
39C PHE 3.9 1.8 - - - +
41C TYR* 1.3 73.7 - - + +
43C THR* 1.3 62.8 + - - +
45C ARG* 3.2 15.0 + - - +
46C ARG* 3.0 35.9 + - - +
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 2.4 54.1 + - + -
40C GLU* 3.4 9.0 - - - +
41C TYR 3.0 0.2 - - - -
42C GLU* 1.3 77.0 - - - +
44C GLN* 1.3 65.6 + - + +
46C ARG* 2.9 22.3 + - + +
47C ARG* 3.0 44.9 + - - +
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Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU* 3.3 14.5 + - + +
41C TYR* 2.8 27.7 + - + +
43C THR* 1.3 81.6 - - + +
45C ARG* 1.3 57.3 + - + +
47C ARG* 2.6 38.2 + - - +
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 4.7 13.9 - - - +
19C TYR* 4.0 18.4 - - - -
41C TYR* 3.5 51.0 + - + +
42C GLU* 3.2 17.9 + - - +
44C GLN* 1.3 76.9 - - + +
46C ARG* 1.3 62.3 + - + +
47C ARG 3.3 4.0 + - - +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASN* 6.2 0.2 - - - +
4C TYR* 3.6 23.8 + - - -
39C PHE* 5.3 12.9 - - - -
42C GLU* 3.0 23.1 + - - +
43C THR* 2.9 16.6 + - + +
45C ARG* 1.3 78.2 - - + +
47C ARG* 1.3 61.2 + - + +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C THR* 3.0 34.7 + - - +
44C GLN* 2.6 28.6 + - - +
45C ARG 4.1 3.7 - - - +
46C ARG* 1.3 83.2 - - + +
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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
------------------------------------------------------------
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