Contacts of the helix formed by residues 31 - 45 (chain B) in PDB entry 1OSL
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B VAL* 1.3 78.8 - - - +
32B ALA* 1.3 66.9 + - - +
33B LYS* 4.2 14.3 - - - +
34B THR* 2.7 17.9 + - - -
35B ARG* 3.7 27.0 + - - +
2D G 4.0 7.1 + - - -
3D A 2.7 25.1 + - - -
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Residues in contact with ALA 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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31B SER* 1.3 70.9 - - - +
33B LYS* 1.3 68.7 + - + +
34B THR 3.1 1.3 - - - -
35B ARG* 3.0 33.4 + - - +
36B GLU* 3.2 28.0 + - - +
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Residues in contact with LYS 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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31B SER* 4.2 16.2 - - - +
32B ALA* 1.3 77.2 - - + +
34B THR* 1.3 63.0 + - - +
36B GLU* 3.4 11.2 + - - +
37B LYS* 2.9 45.7 + - + +
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Residues in contact with THR 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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15B VAL* 4.7 5.2 - - + +
19B THR* 3.3 33.4 - - + +
23B VAL* 4.3 10.8 - - + -
30B VAL* 4.9 4.0 - - + -
31B SER* 2.7 29.5 + - - -
32B ALA 3.0 1.0 + - - -
33B LYS* 1.3 82.1 - - - +
35B ARG* 1.3 63.4 + - - +
37B LYS* 3.1 11.5 + - - +
38B VAL* 2.9 35.3 + - + +
3D A 3.0 13.7 + - - +
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Residues in contact with ARG 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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23B VAL* 4.1 17.7 - - + -
27B ALA* 3.8 16.5 + - - -
28B SER 5.9 0.4 - - - -
30B VAL* 3.2 35.4 + - + +
31B SER 3.7 13.3 + - - +
32B ALA* 3.0 25.1 + - - +
34B THR* 1.3 78.4 - - - +
36B GLU* 1.3 56.5 + - + +
38B VAL* 3.1 11.0 - - - +
39B GLU* 2.8 47.1 + - + +
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Residues in contact with GLU 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 ALA* 3.2 32.2 - - - +
33B LYS* 3.7 10.0 + - - +
34B THR 3.2 0.4 - - - -
35B ARG* 1.3 78.3 - - + +
37B LYS* 1.3 57.2 + - - +
39B GLU* 3.8 9.7 - - - +
40B ALA* 2.9 28.6 + - - +
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Residues in contact with LYS 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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13B ALA* 2.7 40.9 + - + +
14B GLY* 4.2 11.3 + - - -
15B VAL* 4.2 13.2 - - + +
33B LYS* 2.9 31.2 + - + +
34B THR* 3.5 7.0 - - - +
36B GLU* 1.3 76.0 - - - +
38B VAL* 1.3 60.2 + - + +
40B ALA* 3.3 6.0 + - + +
41B ALA* 2.9 29.1 + - - +
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Residues in contact with VAL 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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9B VAL* 3.3 2.5 - - - +
13B ALA* 3.8 8.1 - - - -
15B VAL* 3.9 11.7 - - + -
20B VAL* 3.1 44.0 - - + -
23B VAL* 3.3 31.0 - - + -
34B THR* 2.9 21.4 + - + +
35B ARG 3.1 12.3 - - - +
37B LYS* 1.3 71.8 - - - +
39B GLU* 1.3 64.6 + - + +
41B ALA* 3.2 0.8 + - - -
42B MET* 2.8 47.9 + - + +
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Residues in contact with GLU 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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23B VAL* 5.8 2.0 - - + -
35B ARG* 2.8 28.9 + - + +
36B GLU* 3.8 9.8 + - - +
38B VAL* 1.3 79.9 - - + +
40B ALA* 1.3 61.6 + - - +
42B MET* 3.2 17.8 - - - +
43B ALA* 3.0 25.6 + - - +
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Residues in contact with ALA 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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12B TYR* 5.7 0.7 - - + -
36B GLU 2.9 20.6 + - - +
37B LYS* 3.5 7.0 - - + +
38B VAL 3.2 0.2 - - - -
39B GLU* 1.3 76.7 - - - +
41B ALA* 1.3 64.2 + - - +
43B ALA* 3.0 6.5 + - - +
44B GLU* 2.9 37.2 + - + +
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Residues in contact with ALA 41 (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 VAL* 3.1 35.4 - - + +
12B TYR* 3.0 25.1 - - + -
13B ALA* 3.6 7.4 - - + +
37B LYS 2.9 18.6 + - - +
40B ALA* 1.3 77.1 - - - +
42B MET* 1.3 62.3 + - - +
44B GLU 3.3 0.2 + - - -
45B LEU* 3.0 31.7 + - - +
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Residues in contact with MET 42 (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 VAL* 3.2 24.0 - - + +
20B VAL* 4.3 3.8 - - + -
23B VAL* 5.4 0.9 - - + -
24B VAL* 3.8 28.9 - - + -
38B VAL* 2.8 44.1 + - + +
39B GLU* 3.2 24.7 - - - +
41B ALA* 1.3 72.4 - - - +
43B ALA* 1.3 57.5 + - + +
45B LEU* 4.8 0.2 - - - -
46B ASN 2.9 36.4 + - - +
47B TYR* 3.4 26.2 + - + -
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Residues in contact with ALA 43 (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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39B GLU 3.0 19.2 + - - +
40B ALA* 3.0 8.2 + - - +
42B MET* 1.3 79.3 - - + +
44B GLU* 1.3 66.6 + - + +
46B ASN* 3.3 12.4 + - - +
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Residues in contact with GLU 44 (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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12B TYR* 3.3 39.6 + - + +
40B ALA* 2.9 27.6 + - + +
43B ALA* 1.3 78.1 - - - +
45B LEU* 1.3 62.7 + - + +
46B ASN* 3.0 8.8 + - - +
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Residues in contact with LEU 45 (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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3B PRO* 5.7 0.3 - - - +
4B VAL* 3.1 27.1 - - + +
8B ASP* 3.4 43.7 - - + +
9B VAL* 3.9 4.9 - - + +
12B TYR* 3.6 36.8 - - + -
41B ALA 3.0 16.2 + - - +
42B MET* 4.4 2.2 - - - +
44B GLU* 1.3 78.1 - - + +
46B ASN* 1.3 58.3 + - - +
47B TYR 2.7 15.9 + - - +
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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
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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