Contacts of the helix formed by residues 42 - 53 (chain B) in PDB entry 4OL0
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 HIS 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ALA* 3.2 39.1 + - - +
5B LYS* 3.7 38.4 + - + +
6B PRO* 5.2 0.7 - - + -
40B SER* 3.0 13.3 + - - +
41B VAL* 1.3 91.4 + - + +
43B ALA* 1.3 62.1 + - - +
44B TRP 3.1 6.6 + - - -
45B GLU* 3.2 13.0 + - - +
46B ILE* 3.1 26.6 + - + +
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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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37B LEU* 3.4 34.1 - - + +
38B GLN* 4.2 0.9 - - - -
40B SER* 3.8 1.6 + - - -
42B HIS* 1.3 74.9 - - - +
44B TRP* 1.3 53.5 + - - +
46B ILE* 3.7 11.8 - - + +
47B SER* 2.4 39.4 + - - +
66B THR* 4.0 17.8 - - + +
70B LYS* 3.4 21.4 - - + +
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Residues in contact with TRP 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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41B VAL* 3.3 26.9 - - + +
42B HIS 3.1 0.4 - - - -
43B ALA* 1.3 76.6 - - - +
45B GLU* 1.3 58.7 + - - +
47B SER* 2.8 19.8 + - - -
48B ASP* 2.9 19.4 + - - +
67B MET* 3.7 26.3 - - + +
70B LYS* 3.6 26.3 - - + +
71B ILE* 3.4 45.5 - - + -
74B SER 3.4 22.0 - - - -
75B PHE* 5.5 0.2 - - - -
77B GLU* 2.7 24.6 + - - +
78B LEU* 3.9 28.9 - - + +
86B LEU* 4.1 11.2 - - + -
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Residues in contact with GLU 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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5B LYS* 3.2 31.4 + - - +
42B HIS* 3.2 11.5 + - - +
44B TRP* 1.3 79.0 - - - +
46B ILE* 1.3 58.7 + - + +
48B ASP* 3.3 8.0 + - - +
49B GLN* 2.8 54.2 + - + +
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Residues in contact with ILE 46 (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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5B LYS* 4.6 11.4 - - + -
6B PRO* 3.7 30.1 - - + +
8B LEU* 4.5 11.2 - - + -
11B VAL* 4.2 21.3 - - + -
37B LEU* 3.9 22.9 - - + -
42B HIS* 3.1 23.2 + - + +
43B ALA* 3.8 11.9 - - + +
45B GLU* 1.3 74.8 - - - +
47B SER* 1.3 53.5 + - - +
49B GLN* 3.0 13.4 + - - +
50B LEU* 2.7 55.9 + - + +
62B PHE* 6.0 0.4 - - + -
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Residues in contact with SER 47 (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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43B ALA* 2.4 30.3 + - - -
44B TRP 2.8 11.3 + - - -
46B ILE* 1.3 72.7 - - - +
48B ASP* 1.3 55.4 + - - +
50B LEU* 3.2 4.4 + - - -
51B LEU* 2.8 37.1 + - - +
62B PHE* 6.5 0.2 - - - -
63B ALA* 3.6 35.1 - - - +
66B THR* 4.2 10.8 - - - +
67B MET* 3.0 22.5 - - - -
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Residues in contact with ASP 48 (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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44B TRP 2.9 19.4 + - - +
45B GLU* 3.4 9.1 - - - +
47B SER* 1.3 76.8 + - - +
49B GLN* 1.3 59.5 + - - +
51B LEU* 3.1 5.1 + - - +
52B GLN* 2.8 42.9 + - - +
67B MET* 4.7 3.8 - - - -
89B SER* 5.1 5.1 - - - -
93B HIS* 3.1 34.7 + - + -
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Residues in contact with GLN 49 (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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5B LYS* 4.6 7.8 + - - +
8B LEU* 3.6 42.3 - - + +
45B GLU* 2.8 47.5 + - + +
46B ILE* 3.3 8.2 - - - +
48B ASP* 1.3 74.9 - - + +
50B LEU* 1.3 60.1 + - - +
52B GLN* 3.2 15.7 + - - +
53B ILE* 3.0 36.6 + - + +
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Residues in contact with LEU 50 (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 LEU* 4.4 17.3 - - + +
11B VAL* 3.9 25.8 - - + -
12B TYR* 3.4 42.7 + - + +
15B VAL* 5.3 1.1 - - + -
46B ILE* 2.7 37.6 + - + +
47B SER* 3.6 6.5 - - - +
49B GLN* 1.3 74.5 - - - +
51B LEU* 1.3 53.7 + - - +
53B ILE* 2.6 24.9 - - - +
59B SER* 4.3 13.2 + - - +
60B CYS* 4.2 10.0 - - - -
62B PHE* 4.3 19.7 - - + -
63B ALA* 3.6 12.8 - - + -
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Residues in contact with LEU 51 (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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47B SER 2.8 19.8 + - - +
48B ASP 3.1 4.7 + - - +
50B LEU* 1.3 75.7 - - - +
52B GLN* 1.3 64.7 + - - +
53B ILE 3.2 6.3 - - - +
54B ARG* 3.9 11.8 + - - +
60B CYS* 3.7 25.6 - - - +
63B ALA* 3.7 8.1 - - + -
64B ALA* 4.0 10.8 - - + +
67B MET* 4.0 24.2 - - + -
90B LEU* 5.6 0.2 - - + -
93B HIS* 3.3 40.4 - - + +
97B LEU* 4.1 30.8 - - + +
108B LEU* 4.2 15.3 - - + -
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Residues in contact with GLN 52 (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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48B ASP* 2.8 41.1 + - - +
49B GLN* 3.2 16.8 + - - +
51B LEU* 1.3 72.5 - - - +
53B ILE* 1.3 62.5 + - + +
54B ARG* 3.2 27.3 + - - +
93B HIS* 4.3 8.5 - - + +
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Residues in contact with ILE 53 (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 LEU* 4.1 20.9 - - + -
12B TYR* 3.6 30.3 - - + +
49B GLN* 3.0 16.9 + - + +
50B LEU 2.6 22.8 - - - +
51B LEU 3.2 7.8 - - - +
52B GLN* 1.3 76.5 - - + +
54B ARG* 1.3 64.8 + - - +
55B GLN* 4.0 15.5 - - + +
59B SER* 5.4 0.3 + - - -
60B CYS* 4.0 2.4 - - - -
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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