Contacts of the helix formed by residues 27 - 40 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B THR* 3.5 22.9 + - - +
23B LEU* 4.4 8.6 - - - +
24B PRO* 2.7 36.6 + - - +
25B LYS 2.7 5.1 + - - -
26B GLU* 1.3 74.4 - - - +
28B LEU* 1.3 63.2 + - - -
29B PRO 3.3 0.9 - - - -
30B LYS* 3.0 25.6 + - - +
31B LEU* 3.2 9.5 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 3.7 32.3 - - + +
23B LEU* 4.7 8.5 - - + -
24B PRO 4.2 1.3 - - - +
25B LYS* 2.6 28.8 + - - +
27B SER* 1.3 72.5 - - - +
29B PRO* 1.3 63.8 - - + +
31B LEU* 2.9 21.0 + - + +
32B CYS* 3.1 16.5 + - - -
61B VAL* 3.8 9.8 - - + +
65B TYR* 3.6 32.1 - - + -
259B VAL* 4.0 11.7 - - + -
260B LEU* 4.7 1.1 - - + -
263B ILE* 3.2 33.9 - - + -
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Residues in contact with PRO 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS 3.3 11.0 - - - +
26B GLU* 3.4 14.4 - - - +
27B SER 3.4 0.2 - - - -
28B LEU* 1.3 92.3 - - + +
30B LYS* 1.3 61.0 + - - +
32B CYS* 3.1 13.2 + - - +
33B ASP* 3.3 18.8 + - - +
259B VAL* 4.1 20.0 - - + -
260B LEU* 4.1 26.0 - - + -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 3.9 14.9 - - + +
10B THR* 2.4 27.1 + - - +
26B GLU 5.0 1.7 + - - +
27B SER* 3.0 19.6 + - - +
29B PRO* 1.3 78.5 - - - +
31B LEU* 1.3 64.5 + - - +
33B ASP* 3.2 12.4 + - + +
34B GLU* 3.0 44.9 + - + +
37B ARG* 5.9 0.9 - - - +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 3.8 19.4 - - + +
11B LEU* 3.6 44.9 - - + +
14B VAL* 4.6 6.5 - - + -
20B LEU* 3.4 32.5 - - + -
23B LEU* 4.3 8.3 - - + -
27B SER 3.2 2.4 + - - +
28B LEU* 2.9 23.0 + - + +
30B LYS* 1.3 79.3 - - - +
32B CYS* 1.3 51.5 + - - +
34B GLU* 3.3 2.3 + - - +
35B LEU* 2.7 42.5 + - + +
61B VAL* 4.3 14.4 - - + -
88B LEU* 4.8 7.2 - - + -
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Residues in contact with CYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 3.1 14.3 + - - -
29B PRO 3.1 8.5 + - - +
31B LEU* 1.3 77.2 - - - +
33B ASP* 1.3 59.0 + - - +
35B LEU* 4.3 0.7 - - - -
36B ARG* 2.8 33.5 + - - +
57B VAL* 3.6 12.5 - - + +
58B GLU* 3.8 27.6 - - - +
61B VAL* 3.8 20.2 - - - -
259B VAL* 3.2 40.2 - - + -
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Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PRO* 3.3 13.2 + - - +
30B LYS* 3.2 13.7 + - + +
32B CYS* 1.3 79.1 - - - +
34B GLU* 1.3 63.5 + - + +
36B ARG* 3.3 11.0 + - - +
37B ARG* 3.0 42.3 + - - +
58B GLU* 5.6 0.9 - - - +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.2 21.7 - - + -
9B PRO* 3.3 23.3 - - - +
10B THR* 3.0 43.7 + - - -
11B LEU* 3.1 16.4 + - + -
30B LYS* 3.0 23.8 + - + +
31B LEU* 3.6 5.6 - - - +
33B ASP* 1.3 73.3 - - - +
35B LEU* 1.3 55.4 + - - +
37B ARG* 2.9 27.7 + - - +
38B TYR* 2.7 36.7 + - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 20.1 - - + +
31B LEU* 2.7 24.9 + - + +
32B CYS 3.8 3.6 - - - +
34B GLU* 1.3 72.4 - - - +
36B ARG* 1.3 58.8 + - - +
38B TYR* 3.7 2.4 - - + +
39B LEU* 3.1 35.6 + - + +
57B VAL* 3.9 21.8 - - + +
60B THR* 5.8 0.2 - - + -
61B VAL* 4.3 17.5 - - + -
84B PRO* 4.3 18.4 - - + -
87B ILE* 3.6 39.5 - - + -
88B LEU* 4.3 19.5 - - + -
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B CYS 2.8 18.2 + - - +
33B ASP* 3.6 11.7 + - - +
34B GLU 3.1 0.2 - - - -
35B LEU* 1.3 79.1 - - - +
37B ARG* 1.3 59.0 + - + +
39B LEU* 4.0 5.6 + - - +
40B LEU* 3.1 36.8 + - + +
54B LEU* 3.3 47.2 + - + +
57B VAL* 4.1 12.4 - - + +
58B GLU* 2.8 42.7 + - - -
257B HIS* 4.0 11.5 + - - -
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.8 19.9 + - + +
9B PRO* 6.0 0.8 - - - +
30B LYS* 5.9 1.0 - - - +
33B ASP* 3.0 27.5 + - + +
34B GLU* 2.9 34.2 + - - +
36B ARG* 1.3 77.9 - - + +
38B TYR* 1.3 66.6 + - - +
39B LEU 3.3 0.2 - - - -
40B LEU* 3.3 27.6 + - + +
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.4 39.8 + + + -
11B LEU* 4.1 21.3 - - + -
34B GLU 2.7 15.7 + - - +
35B LEU* 3.7 5.4 - - + +
37B ARG* 1.3 76.1 - - - +
39B LEU* 1.3 72.8 + - + +
40B LEU 3.8 3.6 - - - -
87B ILE* 4.0 33.0 - - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.1 20.0 - - + +
36B ARG* 4.0 4.7 - - - +
37B ARG 3.3 0.2 - - - -
38B TYR* 1.3 85.3 - - + +
40B LEU* 1.3 68.9 + - + +
53B GLY 5.0 0.7 - - - -
54B LEU* 4.4 27.1 - - + +
57B VAL* 4.4 11.7 - - + -
83B TYR* 4.3 17.9 - - + -
84B PRO* 4.5 16.8 - - + -
87B ILE* 3.6 34.8 - - + -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG* 3.1 26.0 + - + +
37B ARG* 3.3 24.6 + - + +
38B TYR 3.2 4.4 - - - -
39B LEU* 1.3 84.5 - - + +
54B LEU* 3.8 29.4 - - + -
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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