Contacts of the helix formed by residues 44 - 52 (chain D) in PDB entry 3BBB
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 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D ARG 3.6 3.2 + - - -
43D ALA* 1.3 76.4 - - - +
45D GLU* 1.3 64.4 + - - +
46D GLU* 3.7 13.3 + - - +
47D HIS* 3.1 27.5 + - - +
48D LEU* 2.9 21.9 + - - +
69D ASN* 3.9 5.2 - - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER* 1.3 69.0 - - - +
46D GLU* 1.3 80.9 + - - +
48D LEU* 3.2 5.0 + - - +
49D LYS* 2.9 47.9 + - - +
65D VAL* 4.3 21.0 - - + +
66D LYS* 5.8 2.2 - - - +
69D ASN* 3.9 23.5 - - + +
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER* 3.9 11.9 - - - +
45D GLU* 1.3 91.8 - - - +
47D HIS* 1.3 62.9 + - - +
49D LYS* 3.3 26.1 + - - +
50D GLN* 3.5 20.4 + - - +
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Residues in contact with HIS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 5.3 2.2 - - + +
43D ALA* 3.9 10.8 - - + -
44D SER* 3.1 27.4 + - - +
46D GLU* 1.3 76.5 - - - +
48D LEU* 1.3 56.2 + - - +
50D GLN* 3.2 19.3 + - - +
51D HIS* 3.1 21.3 + - - +
132D LEU* 3.4 44.6 - - + +
133D TRP* 3.3 51.4 + + - -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA* 3.7 28.0 - - + +
44D SER 2.9 20.6 + - - +
45D GLU* 3.2 5.1 + - - +
47D HIS* 1.3 72.6 - - - +
49D LYS* 1.3 65.8 + - - +
51D HIS* 3.5 4.4 - - + +
52D TYR* 3.0 36.2 + - + +
65D VAL* 3.8 18.3 - - + +
68D MET* 3.5 56.5 - - + +
69D ASN* 3.5 11.4 - - + +
73D VAL* 6.2 0.2 - - + -
133D TRP* 4.1 19.5 - - + -
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 2.9 40.2 + - - +
46D GLU* 3.5 21.9 + - - +
48D LEU* 1.3 76.5 - - - +
50D GLN* 1.3 61.8 + - + +
52D TYR 3.7 1.7 - - - -
53D ILE* 3.3 30.3 + - + +
61D PHE* 4.0 34.0 - - + -
65D VAL* 4.2 18.6 - - + -
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 3.5 19.3 + - - +
47D HIS* 3.3 19.6 + - - +
49D LYS* 1.3 76.2 - - + +
51D HIS* 1.3 58.1 + - - +
53D ILE* 3.4 19.3 - - + +
128D LYS* 2.5 29.9 + - - +
132D LEU* 3.7 26.4 - - + +
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Residues in contact with HIS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PHE* 3.9 8.0 - + - -
10D ALA* 6.1 0.4 - - - +
47D HIS 3.1 10.8 + - - +
48D LEU* 3.3 13.4 + - + +
50D GLN* 1.3 79.7 - - - +
52D TYR* 1.3 93.1 + + - +
53D ILE* 3.2 3.9 + - - +
54D ASP* 5.0 1.0 + - - -
68D MET* 5.4 2.7 - - + +
118D HIS* 3.8 25.5 + - - +
128D LYS* 3.7 8.9 + - - +
129D GLU* 3.7 39.6 - - + +
132D LEU* 3.5 15.4 - - + +
133D TRP* 3.0 36.8 + + + +
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Residues in contact with TYR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 3.8 19.8 + - - -
48D LEU* 3.0 23.8 + - + +
49D LYS 3.7 3.1 - - - -
51D HIS* 1.3 106.0 + + - +
53D ILE* 1.3 53.9 + - - +
54D ASP* 3.1 3.4 - - - -
55D LEU* 2.8 44.7 + - + +
61D PHE* 3.5 23.5 - - + -
64D LEU* 3.8 32.9 - - + +
65D VAL* 4.6 7.9 - - + -
68D MET* 3.5 43.6 - - + +
118D HIS* 4.7 12.5 + + - +
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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