Contacts of the helix formed by residues 47 - 64 (chain v) in PDB entry 5OOM
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 ASP 47 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46v GLU* 1.3 77.5 + - - +
48v ALA* 1.3 78.8 + - - +
49v GLU* 3.1 26.0 + - + +
50v ALA* 3.2 20.3 + - + +
51v ARG* 3.2 12.7 + - - +
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Residues in contact with ALA 48 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2v ALA* 3.0 46.5 - - + +
46v GLU 3.9 1.2 + - - -
47v ASP* 1.3 82.1 + - - +
49v GLU* 1.3 60.0 + - + +
51v ARG* 3.8 7.2 - - - +
52v GLU* 3.9 7.8 + - - +
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Residues in contact with GLU 49 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47v ASP* 3.1 16.1 + - - +
48v ALA* 1.3 79.1 - - + +
50v ALA* 1.3 60.7 + - - +
51v ARG 3.2 0.4 - - - -
52v GLU* 3.1 31.7 + - - +
53v ARG* 3.4 16.5 + - - +
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Residues in contact with ALA 50 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46v GLU* 4.8 9.9 - - - +
47v ASP* 3.2 13.8 + - + +
49v GLU* 1.3 75.1 - - - +
51v ARG* 1.3 58.9 - - - +
53v ARG* 3.8 10.0 - - - +
54v GLN* 3.0 31.3 + - + +
101v PNS 3.3 19.6 - - - -
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Residues in contact with ARG 51 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2v ALA* 3.3 48.5 - - - +
3v PRO* 3.6 13.4 - - + +
43v GLN 5.3 0.4 + - - -
44v LYS 3.8 13.3 + - - -
45v LEU* 3.9 1.6 - - - +
46v GLU* 2.6 49.0 + - - +
47v ASP 3.2 12.5 + - - +
48v ALA* 3.8 2.2 - - - +
49v GLU 3.2 0.2 - - - -
50v ALA* 1.3 76.4 - - - +
52v GLU* 1.3 56.2 + - - +
55v LEU* 3.0 36.0 + - - +
101v PNS 1.4 80.9 + - - +
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Residues in contact with GLU 52 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2v ALA 4.8 0.4 + - - -
3v PRO 6.0 0.2 - - - -
4v TRP* 3.3 45.3 - - + +
48v ALA 3.9 6.4 + - - +
49v GLU* 3.1 18.7 + - - +
51v ARG* 1.3 79.9 - - - +
53v ARG* 1.3 60.4 + - + +
55v LEU* 3.3 5.5 + - - +
56v GLU* 2.9 52.8 + - - +
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Residues in contact with ARG 53 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49v GLU* 3.4 15.1 + - - +
50v ALA* 3.4 11.9 + - - +
52v GLU* 1.3 78.1 - - + +
54v GLN* 1.3 60.6 + - + +
56v GLU* 3.2 16.9 + - - +
57v LYS* 2.9 27.6 + - - +
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Residues in contact with GLN 54 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38v GLU 5.3 0.3 - - - +
39v PHE* 5.5 4.9 - - - -
42v ASN* 3.6 28.0 + - - +
43v GLN* 5.1 1.4 + - - +
46v GLU* 5.8 2.6 + - - +
50v ALA* 3.0 22.6 + - + +
53v ARG* 1.3 76.3 - - + +
55v LEU* 1.3 63.5 + - - +
57v LYS* 3.3 36.6 - - + +
58v GLY* 3.0 22.2 + - - -
101v PNS 3.3 38.5 - - - +
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Residues in contact with LEU 55 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3v PRO* 4.6 3.6 - - + -
4v TRP* 5.2 11.0 - - + +
8v ALA* 5.2 0.4 - - + -
9v VAL* 3.8 41.7 - - + +
12v LEU* 3.8 26.0 - - + -
39v PHE* 5.8 4.7 - - + -
43v GLN* 4.0 12.8 - - - +
51v ARG 3.0 26.7 + - - +
52v GLU* 3.9 4.5 - - - +
54v GLN* 1.3 77.0 - - - +
56v GLU* 1.3 59.0 + - + +
58v GLY* 3.6 5.3 - - - +
59v LEU* 2.9 31.4 + - + +
101v PNS 3.4 29.2 - - - +
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Residues in contact with GLU 56 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199u TYR* 5.9 1.3 - - - -
4v TRP* 4.7 6.3 - - + -
52v GLU* 2.9 45.6 + - + +
53v ARG* 3.2 17.8 + - - +
55v LEU* 1.3 76.7 - - - +
57v LYS* 1.3 58.9 + - - +
58v GLY 3.2 0.2 - - - -
59v LEU* 3.2 22.7 + - + +
60v VAL* 3.0 32.0 + - + +
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Residues in contact with LYS 57 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196u LEU* 3.3 26.0 - - + +
199u TYR* 3.2 37.9 + - + +
200u ASP* 4.9 8.3 - - - +
201u ASP 5.7 0.8 - - - +
42v ASN* 6.1 2.5 - - - +
53v ARG 2.9 10.7 + - - +
54v GLN* 3.3 55.2 - - + +
56v GLU* 1.3 75.9 - - - +
58v GLY* 1.3 58.0 + - - +
60v VAL* 4.4 2.5 - - - +
61v PHE* 2.9 30.1 + - - +
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Residues in contact with GLY 58 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12v LEU* 4.5 8.5 - - - +
16v LEU* 4.7 6.2 - - - +
39v PHE* 5.2 15.7 - - - -
54v GLN 3.0 16.4 + - - -
55v LEU* 3.4 8.5 + - - -
56v GLU 3.2 0.4 - - - -
57v LYS* 1.3 77.2 - - - +
59v LEU* 1.3 57.8 + - - +
61v PHE* 3.7 7.7 - - - +
62v LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 59 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12v LEU* 3.8 28.7 - - + +
55v LEU 2.9 22.7 + - - +
56v GLU* 3.2 27.8 + - + +
58v GLY* 1.3 76.0 - - - +
60v VAL* 1.3 60.6 + - + +
62v LEU* 3.1 9.5 + - + +
63v ASN* 2.9 28.7 + - - +
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Residues in contact with VAL 60 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195u THR 4.3 3.8 - - - +
196u LEU* 4.2 5.2 - - + -
199u TYR* 3.6 29.8 - - + +
56v GLU* 3.0 17.0 + - + +
57v LYS 4.1 3.1 - - - +
59v LEU* 1.3 76.7 - - + +
61v PHE* 1.3 58.3 + - - +
63v ASN* 4.0 5.3 - - + +
64v GLY* 2.9 29.3 + - - -
65v LYS* 5.7 1.6 - - + +
66v LEU* 3.7 37.0 + - + +
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Residues in contact with PHE 61 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191u GLU 5.0 1.8 - - - -
195u THR* 3.4 37.9 - - + -
196u LEU* 4.0 11.6 - - + +
16v LEU* 3.7 29.5 - - + +
19v GLN* 4.7 1.9 - - - +
31v TYR* 4.5 2.7 - + - -
35v ILE* 3.8 23.1 - - + -
38v GLU* 3.8 32.8 - - - -
39v PHE* 5.9 0.7 - + - -
57v LYS 2.9 20.5 + - - +
58v GLY* 3.8 5.6 - - - +
60v VAL* 1.3 78.0 - - - +
62v LEU* 1.3 60.9 + - - +
64v GLY* 4.3 5.0 + - - -
69v ILE* 3.6 32.3 - - + -
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Residues in contact with LEU 62 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12v LEU* 3.7 27.1 - - + +
15v ALA* 3.8 28.0 - - + -
16v LEU* 3.7 26.0 - - + +
19v GLN* 3.2 50.7 + - - +
58v GLY 2.9 14.7 + - - +
59v LEU* 3.1 12.3 + - + +
61v PHE* 1.3 77.2 - - - +
63v ASN* 1.3 68.3 + - - +
64v GLY* 4.4 0.5 - - - -
68v ARG* 5.6 1.0 + - - +
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Residues in contact with ASN 63 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19v GLN* 5.3 0.5 + - - -
59v LEU 2.9 14.5 + - - +
60v VAL* 4.0 6.1 - - + +
62v LEU* 1.3 82.0 - - + +
64v GLY* 1.3 62.7 + - - +
65v LYS* 4.1 34.6 - - + +
68v ARG* 3.5 20.0 + - - +
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Residues in contact with GLY 64 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115u PRO* 6.1 0.2 - - - +
195u THR 6.1 0.4 - - - -
60v VAL 2.9 15.2 + - - -
61v PHE* 4.7 3.8 - - - -
62v LEU 3.4 2.4 - - - -
63v ASN* 1.3 78.6 - - - +
65v LYS* 1.3 64.1 + - - +
66v LEU 3.2 2.2 - - - -
67v GLY* 3.3 31.5 + - - +
68v ARG* 4.1 20.0 + - - +
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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