Contacts of the helix formed by residues 27 - 43 (chain C) in PDB entry 2O1S
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 SER 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C THR* 3.6 20.1 + - - +
23C LEU* 4.7 10.1 - - - +
24C PRO* 2.8 32.0 + - - -
25C LYS 2.7 0.4 + - - -
26C GLU* 1.3 78.6 - - - +
28C LEU* 1.3 64.4 + - - +
29C PRO* 3.4 1.6 - - - -
30C LYS* 3.2 11.5 + - - +
31C LEU* 3.2 17.9 + - - +
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.9 28.5 - - + -
23C LEU* 4.6 11.7 - - + -
24C PRO 4.0 1.6 - - - +
25C LYS* 2.8 32.0 + - + +
27C SER* 1.3 75.5 - - - +
29C PRO* 1.3 65.7 - - + +
31C LEU* 3.0 9.0 + - + +
32C CYS* 2.9 28.5 + - - -
61C VAL* 4.0 9.2 - - + -
65C TYR* 3.7 23.6 - - + -
259C VAL* 4.3 14.8 - - + -
260C LEU* 4.7 0.4 - - + -
263C ILE* 3.3 32.3 - - + -
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Residues in contact with PRO 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS 3.3 11.7 - - - +
26C GLU* 3.7 11.0 - - - +
27C SER 3.5 3.6 - - - -
28C LEU* 1.3 92.6 - - + +
30C LYS* 1.3 59.4 + - - +
32C CYS* 3.4 6.4 - - + +
33C ASP* 3.1 29.5 + - - +
259C VAL* 4.0 21.1 - - + -
260C LEU* 4.1 17.3 - - + -
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Residues in contact with LYS 30 (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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7C LYS 5.9 0.2 + - - -
9C PRO* 4.4 11.2 - - - +
10C THR* 3.2 19.1 - - + +
26C GLU 5.3 1.1 + - - +
27C SER* 3.2 13.6 + - - +
28C LEU 3.1 0.4 - - - -
29C PRO* 1.3 76.0 - - - +
31C LEU* 1.3 66.7 + - - +
33C ASP* 3.1 11.0 + - + +
34C GLU* 2.8 45.1 + - + +
37C ARG* 3.8 19.3 - - - +
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 4.1 20.2 - - + +
11C LEU* 4.0 33.2 - - + -
14C VAL* 4.0 14.4 - - + -
20C LEU* 3.4 32.8 - - + -
23C LEU* 4.5 0.9 - - + -
27C SER 3.2 8.8 + - - +
28C LEU* 3.0 15.4 + - + +
30C LYS* 1.3 76.5 - - - +
32C CYS* 1.3 53.7 + - - +
34C GLU* 2.9 5.6 + - - +
35C LEU* 2.6 41.4 + - + +
61C VAL* 4.1 17.3 - - + -
88C LEU* 4.7 10.3 - - + -
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Residues in contact with CYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU 2.9 16.6 + - - -
29C PRO* 3.4 9.9 - - + +
30C LYS 3.2 0.2 - - - -
31C LEU* 1.3 77.7 - - - +
33C ASP* 1.3 64.3 + - - +
35C LEU* 3.1 2.8 + - - -
36C ARG* 2.9 24.0 + - - +
57C VAL* 3.5 14.9 - - + +
58C GLU* 3.8 27.8 - - + +
61C VAL* 3.7 24.9 - - - -
259C VAL* 3.8 29.8 - - - -
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 3.1 18.6 + - - +
30C LYS* 3.1 11.5 + - + +
32C CYS* 1.3 78.1 - - - +
34C GLU* 1.3 61.7 + - - +
36C ARG* 3.5 14.7 + - - +
37C ARG* 3.1 50.0 + - - +
58C GLU* 5.6 0.2 - - - +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS 4.8 2.0 - - - +
8C TYR* 3.0 25.8 - - + +
9C PRO* 3.3 12.2 - - + +
10C THR* 2.6 37.7 + - - -
11C LEU* 2.7 35.5 + - + -
30C LYS* 2.8 31.2 + - - +
31C LEU* 3.3 9.0 - - - +
33C ASP* 1.3 75.7 - - - +
35C LEU* 1.3 59.2 + - - +
37C ARG* 3.3 18.9 + - - +
38C TYR* 2.9 29.7 + - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.4 13.6 - - + +
31C LEU* 2.6 23.4 + - + +
32C CYS* 3.1 5.6 + - - +
34C GLU* 1.3 70.6 - - - +
36C ARG* 1.3 61.0 + - - +
38C TYR* 3.4 2.8 + - + +
39C LEU* 2.9 29.3 + - + +
57C VAL* 4.1 18.4 - - + +
61C VAL* 4.3 8.1 - - + -
84C PRO* 4.0 25.8 - - + -
87C ILE* 3.7 40.8 - - + -
88C LEU* 4.0 30.1 - - + -
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C CYS 2.9 17.9 + - - +
33C ASP* 3.7 13.8 + - - +
35C LEU* 1.3 77.6 - - - +
37C ARG* 1.3 63.4 + - + +
39C LEU* 3.3 8.0 + - - +
40C LEU* 3.2 29.7 + - + +
54C LEU* 3.1 43.9 + - + +
57C VAL* 3.9 13.9 - - + +
58C GLU* 2.9 41.0 + - - -
257C HIS* 4.1 8.7 + - - -
283C LYS* 5.8 2.8 - - - +
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 5.3 7.9 + - - +
8C TYR* 4.1 10.9 - - + -
30C LYS* 3.8 24.7 - - - +
33C ASP* 3.1 43.9 + - - +
34C GLU* 3.7 15.1 - - - +
35C LEU 3.3 0.2 - - - -
36C ARG* 1.3 80.3 - - + +
38C TYR* 1.3 62.7 + - - +
40C LEU* 2.9 20.3 + - + +
41C ASP* 3.1 23.7 + - - +
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Residues in contact with TYR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.6 21.5 - + + +
8C TYR* 3.5 31.3 - + + -
11C LEU* 3.5 24.9 - - + -
34C GLU 2.9 17.9 + - - +
35C LEU* 3.6 4.0 - - + +
37C ARG* 1.3 76.3 - - - +
39C LEU* 1.3 53.8 + - - +
41C ASP* 5.5 0.2 - - + -
42C SER* 2.5 65.8 + - - -
87C ILE* 3.9 21.5 - - + -
92C ARG* 2.6 45.3 + - + +
93C ASP* 4.0 8.3 + - - -
95C ILE* 4.0 6.8 - - + +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 2.9 16.2 + - + +
36C ARG 3.4 7.4 - - - +
37C ARG 3.2 0.2 - - - -
38C TYR* 1.3 77.4 - - - +
40C LEU* 1.3 61.2 + - - +
41C ASP 3.6 0.3 + - - -
42C SER* 4.3 2.5 - - - -
43C VAL* 3.8 31.3 + - + +
45C ARG* 5.3 0.2 + - - -
50C PHE* 3.6 46.2 - - + +
53C GLY* 4.1 8.5 - - - +
54C LEU* 4.2 11.4 - - + +
57C VAL* 4.6 4.7 - - + -
83C TYR* 4.1 10.3 - - + -
84C PRO* 3.8 28.5 - - + -
87C ILE* 4.2 17.5 - - + -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 3.2 26.6 + - + +
37C ARG* 2.9 13.8 + - + +
39C LEU* 1.3 77.0 - - - +
41C ASP* 1.3 65.3 + - - +
43C VAL 4.8 1.8 - - - +
45C ARG* 2.9 48.7 + - - +
50C PHE* 3.7 30.5 - - + -
54C LEU* 4.4 15.5 - - + -
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Residues in contact with ASP 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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7C LYS* 4.2 11.2 + - - +
8C TYR* 2.5 30.9 + - - +
37C ARG* 3.1 17.7 + - - +
38C TYR 3.2 1.5 + - - +
40C LEU* 1.3 89.2 - - - +
42C SER* 1.3 62.5 + - - +
43C VAL 3.7 3.3 - - - +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C TYR* 2.5 55.7 + - - -
39C LEU* 4.3 1.9 - - - -
41C ASP* 1.3 77.7 - - - +
43C VAL* 1.3 62.0 + - - +
44C SER 3.9 0.9 + - - -
95C ILE* 3.4 18.0 - - - +
96C GLY* 3.5 18.0 - - - -
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.8 31.5 + - + +
40C LEU 4.8 0.5 - - - +
41C ASP 3.7 5.3 - - - +
42C SER* 1.3 79.4 + - - +
44C SER* 1.3 78.0 + - - +
45C ARG* 3.5 14.9 + - - +
47C SER* 4.1 8.7 - - - +
50C PHE* 4.4 7.0 - - + -
83C TYR* 4.0 22.9 - - + -
95C ILE* 3.4 40.2 - - + +
96C GLY* 4.6 2.9 - - - +
98C ILE* 4.2 8.3 - - + -
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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