Contacts of the helix formed by residues 50 - 61 (chain A) in PDB entry 4BL5
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP* 3.2 19.2 + - + +
48A LEU 3.2 0.6 - - - -
49A THR* 1.3 80.2 + - - +
51A THR* 1.3 63.7 + - - +
52A ALA* 4.6 2.0 - - + +
53A GLN* 3.8 23.8 - - + +
54A THR* 2.8 28.6 + - - -
96A ASN* 4.1 0.9 - - - -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR 3.9 1.9 + - - -
50A ASP* 1.3 71.7 - - - +
52A ALA* 1.3 55.4 + - - +
54A THR* 2.8 22.3 + - - -
55A ARG* 2.8 21.6 + - + +
96A ASN* 2.7 27.2 + - - +
100A SER* 5.1 2.6 + - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 3.4 1.9 - - + +
51A THR* 1.3 79.8 - - - +
53A GLN* 1.3 62.7 + - - +
55A ARG* 3.6 5.7 + - - +
56A ALA* 3.2 23.6 + - - +
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A SER 5.0 0.2 - - - +
46A ALA* 3.3 15.2 - - + +
47A ASP* 2.6 55.3 + - - +
50A ASP* 3.7 14.1 + - + +
51A THR 3.2 0.4 - - - -
52A ALA* 1.3 80.0 - - + +
54A THR* 1.3 64.9 + - - +
56A ALA* 3.3 6.7 + - - +
57A LEU* 3.2 19.1 + - - +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.5 37.0 + - + -
50A ASP 2.8 18.7 + - - -
51A THR* 2.8 14.3 + - - -
53A GLN* 1.3 71.3 - - - +
55A ARG* 1.3 66.0 + - - -
56A ALA 3.1 0.5 + - - -
57A LEU* 3.2 3.8 + - - +
58A PHE* 3.0 42.4 + - + -
96A ASN* 3.6 18.0 - - - +
97A VAL* 4.2 2.9 - - + -
100A SER* 3.1 22.7 - - - +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 2.8 21.4 + - + +
52A ALA* 3.9 7.9 - - - +
54A THR* 1.3 71.0 - - - +
56A ALA* 1.3 53.1 + - - +
58A PHE* 2.9 7.5 + - - +
59A GLU* 2.7 35.8 + - - +
100A SER* 4.1 11.5 + - - +
103A GLU* 4.8 12.3 - - - +
104A VAL* 5.3 0.9 - - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 3.2 15.2 + - - +
53A GLN* 3.6 6.3 - - - +
54A THR 3.1 1.0 - - - -
55A ARG* 1.3 78.8 - - - +
57A LEU* 1.3 57.1 + - - +
59A GLU* 3.3 6.9 + - - +
60A LYS* 2.8 30.4 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.7 11.0 - - + -
13A THR* 6.0 0.9 - - + -
41A VAL* 4.0 39.5 - - + -
45A ASP* 4.6 11.7 - - + +
46A ALA* 3.8 25.6 - - + -
48A LEU* 4.8 9.9 - - + -
53A GLN 3.2 8.6 + - - +
54A THR* 3.2 8.9 + - - +
56A ALA* 1.3 78.2 - - - +
58A PHE* 1.3 63.0 + - + +
60A LYS* 4.4 6.1 - - + -
61A VAL* 2.9 49.2 + - + +
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Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.8 21.3 - - + -
13A THR* 4.9 5.2 - - + -
48A LEU* 5.3 1.6 - - + -
54A THR* 3.0 39.0 + - + +
55A ARG* 2.9 9.6 + - - +
57A LEU* 1.3 80.6 - - + +
59A GLU* 1.3 54.9 + - - +
61A VAL* 2.1 27.8 - - - +
62A GLN* 3.9 0.9 + - - -
63A PRO* 3.4 28.8 - - + +
66A VAL* 4.0 17.0 - - + -
97A VAL* 3.6 31.6 - - + -
100A SER* 3.7 12.6 - - - -
101A ALA* 3.7 35.4 - - + -
104A VAL* 3.6 16.4 - - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG 2.7 18.8 + - - +
56A ALA* 3.7 6.7 - - - +
58A PHE* 1.3 69.0 - - - +
60A LYS* 1.3 66.4 + - - +
61A VAL 2.9 3.6 - - - +
62A GLN* 2.8 31.1 + - - +
104A VAL* 4.2 7.3 - - + +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA 2.8 21.1 + - - +
57A LEU* 3.2 9.6 + - + +
59A GLU* 1.3 75.8 - - - +
61A VAL* 1.3 63.4 + - + +
62A GLN* 3.7 4.7 + - - +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG* 4.8 9.4 - - + +
10A ILE 5.6 0.2 - - - +
11A LEU* 4.4 17.5 - - + +
39A VAL* 4.3 33.4 - - + -
57A LEU* 2.9 34.1 + - + +
58A PHE 2.1 33.3 - - - +
59A GLU 2.9 4.5 - - - +
60A LYS* 1.3 74.5 - - + +
62A GLN* 1.3 56.7 + - - +
63A PRO* 3.4 22.9 - - + -
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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