Contacts of the helix formed by residues 43 - 55 (chain G) in PDB entry 5BMU
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 GLY 43 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G ILE* 4.1 8.3 - - - -
31G PRO* 3.2 23.6 + - - -
42G THR* 1.3 74.1 - - - +
44G LEU* 1.3 68.0 + - - +
45G THR 3.3 2.9 - - - -
46G THR* 3.4 3.0 + - - -
47G ILE* 3.0 26.4 + - - +
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Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ALA* 3.7 39.7 - - + +
6G GLU* 3.6 17.0 - - + +
7G LEU* 4.2 13.1 - - + +
10G LEU* 6.1 0.2 - - + -
31G PRO* 3.4 14.2 - - + +
43G GLY* 1.3 70.3 - - - +
45G THR* 1.3 58.3 + - - +
47G ILE* 3.9 2.1 - - - +
48G ALA* 3.0 28.5 + - + +
78G ARG* 3.5 48.2 - - + +
79G VAL* 4.4 11.5 - - + +
83G ASP* 4.3 6.3 - - - +
119G LEU* 4.3 13.2 - - + -
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Residues in contact with THR 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G GLY 3.3 0.8 - - - -
44G LEU* 1.3 77.1 - - - +
46G THR* 1.3 72.4 + - - +
48G ALA* 3.5 6.8 - - - +
49G ALA* 2.9 27.9 + - - +
75G LEU* 3.9 44.8 - - + +
76G GLU* 5.7 0.2 - - - -
79G VAL* 3.4 33.4 - - + -
119G LEU* 4.6 10.3 - - + -
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Residues in contact with THR 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU* 3.8 14.9 - - - +
42G THR 2.9 33.3 + - - +
43G GLY* 3.5 1.3 + - - -
45G THR* 1.3 84.1 + - - +
47G ILE* 1.3 66.5 + - - +
49G ALA* 3.7 7.1 - - + +
50G HIS* 3.3 20.8 + - - +
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Residues in contact with ILE 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU* 3.6 22.4 - - + -
22G TYR* 3.7 19.1 - - + -
31G PRO* 3.6 42.6 - - + +
32G VAL 4.1 0.7 - - - -
33G LEU* 3.9 31.4 - - + +
41G LEU* 4.0 15.9 - - + +
43G GLY 3.0 22.2 + - - +
44G LEU 4.0 2.2 - - - +
46G THR* 1.3 75.9 - - - +
48G ALA* 1.3 56.2 + - - +
50G HIS* 3.1 8.3 - - - +
51G LEU* 2.9 31.2 + - + +
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 4.4 2.9 - - + -
10G LEU* 3.5 30.8 - - + +
44G LEU* 3.0 20.8 + - + +
45G THR* 3.5 8.5 - - - +
46G THR 3.3 0.4 - - - -
47G ILE* 1.3 72.8 - - - +
49G ALA* 1.3 66.9 + - - +
51G LEU* 3.2 3.4 + - - +
52G VAL* 2.9 27.9 + - - +
115G LEU* 3.9 17.0 - - + -
119G LEU* 4.5 7.4 - - + -
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G THR 2.9 18.2 + - - +
46G THR* 3.7 10.8 - - + +
48G ALA* 1.3 75.0 - - - +
50G HIS* 1.3 61.9 + - - +
52G VAL* 3.3 4.3 + - - +
53G LYS* 3.0 32.0 + - + +
61G LEU* 4.1 28.2 - - + +
75G LEU* 5.7 3.6 - - + -
115G LEU* 4.0 2.6 - - + +
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Residues in contact with HIS 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G LEU* 3.7 18.8 - - + +
35G THR* 3.5 24.1 + - + -
36G ASN* 3.9 8.4 + - - -
37G ASN* 5.9 2.7 - - + -
41G LEU* 3.7 19.7 - - + +
46G THR 3.3 11.8 + - - +
47G ILE* 3.1 11.3 + - - +
49G ALA* 1.3 77.8 - - - +
51G LEU* 1.3 60.0 + - + +
53G LYS* 3.1 16.8 + - + +
54G GLN* 2.9 63.8 + - + +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU* 3.7 28.9 - - + +
10G LEU* 4.5 4.5 - - + -
11G GLU* 3.8 24.0 - - + +
14G LEU* 3.6 17.8 - - + +
16G LEU* 3.9 6.8 - - + +
20G ASN* 3.4 28.7 - - - +
22G TYR* 3.5 17.9 - - - +
33G LEU* 5.1 1.1 - - + -
47G ILE* 2.9 23.2 + - + +
48G ALA* 3.8 4.7 - - - +
50G HIS* 1.3 73.2 - - + +
52G VAL* 1.3 67.3 + - - +
54G GLN* 3.4 22.4 + - - +
55G ALA* 3.2 20.3 + - - +
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Residues in contact with VAL 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.5 27.3 - - + +
48G ALA 2.9 16.1 + - - +
49G ALA* 3.4 9.6 - - - +
51G LEU* 1.3 76.1 - - - +
53G LYS* 1.3 61.7 + - - +
55G ALA* 3.6 2.8 + - - +
56G ASN 3.5 3.3 + - - -
57G LYS* 2.9 49.9 + - + +
58G GLU* 4.1 0.4 - - - -
60G LEU* 4.2 6.3 - - + -
61G LEU* 3.8 24.5 - - + -
115G LEU* 4.1 31.0 - - + -
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Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ALA* 3.0 21.7 + - - +
50G HIS* 3.1 20.6 + - - +
52G VAL* 1.3 73.4 - - - +
54G GLN* 1.3 67.1 + - - +
56G ASN* 3.1 16.8 + - - +
57G LYS 5.2 0.7 - - - +
58G GLU* 3.7 36.8 - - + +
61G LEU* 4.5 12.8 - - + -
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Residues in contact with GLN 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU* 4.0 18.9 - - + +
18G LYS* 5.5 4.5 - - - +
20G ASN* 4.1 16.3 + - - +
33G LEU* 4.7 2.6 - - - +
36G ASN* 3.8 21.3 + - - +
50G HIS* 2.9 53.5 + - + +
51G LEU* 3.7 25.9 - - - +
53G LYS* 1.3 72.5 - - - +
55G ALA* 1.3 58.3 + - - +
56G ASN* 3.1 13.5 + - - -
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 3.7 27.1 - - + +
15G GLY 5.5 0.4 - - - -
16G LEU* 3.7 24.0 - - + -
51G LEU 3.2 13.1 + - - +
52G VAL 4.0 4.5 - - - +
53G LYS 3.2 1.4 + - - -
54G GLN* 1.3 76.4 - - - +
56G ASN* 1.3 69.6 + - - +
57G LYS* 3.6 13.8 - - + +
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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