Contacts of the helix formed by residues 27 - 40 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D THR* 4.1 20.0 - - - +
23D LEU* 4.7 8.0 - - - +
24D PRO* 2.8 39.1 + - - +
26D GLU* 1.3 73.4 - - - +
28D LEU* 1.3 61.6 + - - +
29D PRO 3.4 0.4 - - - -
30D LYS* 3.2 12.5 + - - +
31D LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.3 2.0 - - + -
23D LEU* 4.3 13.5 - - + -
24D PRO 4.2 1.6 - - - +
25D LYS* 2.8 23.2 + - + +
27D SER* 1.3 76.4 - - - +
29D PRO* 1.3 66.8 - - + +
31D LEU* 2.8 37.4 + - + +
32D CYS* 2.8 17.5 + - - -
61D VAL* 4.0 9.6 - - + -
65D TYR* 3.6 41.7 - - + -
259D VAL* 4.2 13.2 - - + -
260D LEU* 4.9 1.3 - - + -
263D ILE* 3.3 32.1 - - + -
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Residues in contact with PRO 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS 3.1 13.0 - - - +
26D GLU* 3.4 13.5 - - - +
28D LEU* 1.3 91.7 - - + +
30D LYS* 1.3 60.6 + - - +
32D CYS* 3.3 5.4 + - + +
33D ASP* 3.3 19.6 + - - +
259D VAL* 3.8 24.2 - - + -
260D LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PRO* 4.9 6.3 - - - +
10D THR* 3.6 15.3 - - - +
26D GLU 4.7 2.4 + - - +
27D SER* 3.2 14.9 + - - +
28D LEU 3.1 0.2 - - - -
29D PRO* 1.3 79.6 - - - +
31D LEU* 1.3 63.7 + - - +
33D ASP* 3.2 8.8 + - + +
34D GLU* 2.9 49.9 + - + +
37D ARG* 5.3 4.9 - - - +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 4.0 13.4 - - + +
11D LEU* 3.7 37.5 - - + +
14D VAL* 4.9 4.5 - - + -
20D LEU* 3.9 21.5 - - + -
23D LEU* 3.9 23.6 - - + -
27D SER 2.9 12.2 + - - +
28D LEU* 2.8 25.9 + - + +
30D LYS* 1.3 77.6 - - - +
32D CYS* 1.3 54.7 + - - +
34D GLU* 3.6 4.3 + - - +
35D LEU* 2.7 31.3 + - + +
61D VAL* 4.3 14.6 - - + -
88D LEU* 5.1 8.1 - - + -
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Residues in contact with CYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU 2.8 20.9 + - - -
29D PRO* 3.5 7.9 - - + +
30D LYS 3.2 0.2 - - - -
31D LEU* 1.3 71.6 - - - +
33D ASP* 1.3 55.9 + - - +
35D LEU* 3.1 1.6 + - - -
36D ARG* 2.7 37.6 + - - +
57D VAL* 3.3 11.4 - - + +
58D GLU* 3.4 28.3 - - + +
61D VAL* 3.8 24.5 - - - -
259D VAL* 3.8 31.6 - - + -
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PRO 3.3 8.5 + - - +
30D LYS* 3.2 11.5 + - + +
32D CYS* 1.3 78.5 - - - +
34D GLU* 1.3 52.9 + - - +
36D ARG* 3.2 11.1 + - - +
37D ARG* 2.8 71.6 + - - +
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PRO* 2.8 39.3 - - + +
10D THR* 2.8 37.4 + - - -
11D LEU* 3.0 17.6 + - + +
30D LYS* 2.9 39.1 + - + +
31D LEU* 3.6 5.2 - - - +
33D ASP* 1.3 77.8 - - - +
35D LEU* 1.3 57.5 + - - +
37D ARG* 3.3 29.3 + - - +
38D TYR* 2.8 30.1 + - - +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.0 14.1 - - + +
31D LEU* 2.7 25.3 + - + +
32D CYS* 3.6 4.0 - - - +
34D GLU* 1.3 72.9 - - - +
36D ARG* 1.3 62.4 + - - +
38D TYR* 3.3 2.3 + - - +
39D LEU* 3.0 28.1 + - + +
57D VAL* 4.0 15.9 - - + +
60D THR* 5.5 0.2 - - - -
61D VAL* 4.0 19.1 - - + -
84D PRO* 4.0 24.7 - - + -
87D ILE* 3.2 45.5 - - + -
88D LEU* 4.2 19.3 - - + -
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Residues in contact with ARG 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D CYS 2.7 20.8 + - - +
33D ASP* 3.4 11.7 - - - +
35D LEU* 1.3 74.2 - - - +
37D ARG* 1.3 63.2 + - + +
39D LEU* 3.4 4.2 + - - +
40D LEU* 3.2 31.8 + - + +
54D LEU* 2.9 55.5 + - + +
57D VAL* 3.4 16.5 - - + +
58D GLU* 2.4 40.1 + - - -
257D HIS* 3.7 16.5 + - - -
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Residues in contact with ARG 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PRO* 5.8 5.3 - - - +
30D LYS* 5.3 5.5 - - - +
33D ASP* 2.8 49.1 + - - +
34D GLU* 3.7 27.0 - - - +
36D ARG* 1.3 72.0 - - + +
38D TYR* 1.3 61.4 + - - +
40D LEU* 3.3 20.0 + - + +
41D ASP* 2.7 31.6 - - - +
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Residues in contact with TYR 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.9 20.2 - - + -
34D GLU 2.8 17.5 + - - +
35D LEU 3.6 4.3 - - - +
37D ARG* 1.3 75.1 - - - +
39D LEU* 1.3 71.2 + - + +
41D ASP* 3.0 29.1 + - + +
87D ILE* 3.3 34.8 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.0 21.5 + - + +
36D ARG 3.6 7.6 - - - +
37D ARG 3.3 0.2 - - - -
38D TYR* 1.3 80.3 - - + +
40D LEU* 1.3 59.3 + - - +
41D ASP 3.0 18.5 + - - +
53D GLY* 4.5 5.6 - - - +
54D LEU* 4.1 20.4 - - + -
57D VAL* 4.2 9.0 - - + -
83D TYR* 4.2 26.2 - - + +
84D PRO* 3.9 36.6 - - + -
87D ILE* 5.2 5.6 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 3.2 21.2 + - + +
37D ARG* 3.5 19.1 - - + +
38D TYR 3.2 0.4 - - - -
39D LEU* 1.3 75.9 - - - +
41D ASP* 1.3 63.7 + - - +
54D LEU* 3.6 31.2 - - + -
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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
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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