Contacts of the helix formed by residues 49 - 60 (chain A) in PDB entry 5BZR
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 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A SER 4.0 0.6 + - - -
48A ILE* 1.3 78.1 - - - +
50A ARG* 1.3 59.8 + - - +
51A THR* 3.2 6.3 + - - -
52A GLU* 3.1 17.2 + - - +
53A ALA* 2.8 25.6 + - - +
85A PHE* 3.6 3.4 - - - -
117A SER* 4.1 7.4 - - - -
118A HIS* 3.8 25.2 + - - -
172A ASP* 2.7 28.1 + - - -
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Residues in contact with ARG 50 (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 SER* 1.3 73.6 - - - +
51A THR* 1.3 68.7 + - + +
53A ALA* 3.2 3.9 + - - +
54A ALA* 3.2 32.8 + - - +
64A LEU* 4.7 8.8 - - - +
85A PHE* 3.4 43.8 - - + -
86A ILE 4.4 10.1 + - - -
87A GLU* 3.2 35.4 + - - +
88A GLY 4.9 4.4 - - - +
117A SER 4.5 1.6 + - - -
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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 SER* 3.2 7.3 + - - -
50A ARG* 1.3 84.6 - - + +
52A GLU* 1.3 61.0 + - - +
54A ALA* 3.4 5.6 + - - +
55A ASP* 3.2 25.6 + - - -
169A HIS* 3.6 32.0 + - + +
171A GLU* 4.3 11.4 + - - +
172A ASP* 2.7 26.2 + - - -
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Residues in contact with GLU 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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42A LYS* 2.8 31.5 + - - +
47A SER 4.5 5.0 - - - +
48A ILE* 3.9 14.3 - - + +
49A SER* 3.1 21.8 + - - +
51A THR* 1.3 77.5 + - - +
53A ALA* 1.3 57.4 + - - +
55A ASP* 3.2 6.7 + - - +
56A LEU* 2.8 29.5 + - + +
166A TYR* 2.7 37.1 + - + -
167A ARG* 3.6 15.9 - - + -
172A ASP* 3.2 27.5 + - - +
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Residues in contact with ALA 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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48A ILE* 3.4 8.4 - - + +
49A SER 2.8 14.3 + - - +
50A ARG* 3.2 10.3 + - - +
52A GLU* 1.3 75.9 - - - +
54A ALA* 1.3 62.7 + - - +
56A LEU* 3.2 3.5 + - - +
57A CYS* 2.9 28.9 + - - -
64A LEU* 4.0 5.2 - - + -
85A PHE* 3.5 21.8 - - + -
121A THR* 3.3 26.9 + - - +
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Residues in contact with ALA 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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50A ARG* 3.2 26.0 + - - +
51A THR* 3.7 8.7 - - - +
53A ALA* 1.3 79.3 - - - +
55A ASP* 1.3 61.0 + - - +
57A CYS* 3.5 2.3 + - - +
58A GLN* 3.0 30.8 + - - +
62A SER 5.1 0.2 - - - +
63A THR* 5.9 0.2 - - - -
64A LEU* 3.4 17.4 - - + +
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Residues in contact with ASP 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 3.2 12.1 + - - +
52A GLU* 3.6 9.2 - - - +
54A ALA* 1.3 77.3 - - - +
56A LEU* 1.3 65.6 + - - +
58A GLN* 3.3 16.4 + - - +
59A ALA* 3.1 20.4 + - - +
166A TYR* 3.3 25.2 - - + +
167A ARG* 3.9 3.5 - - - -
168A THR* 2.7 48.5 + - - +
169A HIS* 3.4 15.1 + - - -
172A ASP* 5.0 0.7 - - - +
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Residues in contact with LEU 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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28A LEU* 3.6 35.0 - - + -
40A VAL* 3.8 23.6 - - + -
42A LYS* 5.3 0.2 - - + -
48A ILE* 3.9 25.6 - - + -
52A GLU* 2.8 21.0 + - + +
53A ALA 3.6 4.7 - - - +
55A ASP* 1.3 70.9 - - - +
57A CYS* 1.3 66.6 + - - +
59A ALA* 3.0 15.6 + - + +
60A PHE* 3.4 28.1 + - + -
121A THR* 4.1 8.5 - - + -
123A CYS* 5.3 0.2 - - - -
140A LEU* 5.4 0.4 - - + -
166A TYR* 3.7 33.6 - - + +
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Residues in contact with CYS 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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53A ALA 2.9 19.1 + - - +
54A ALA 3.9 3.6 - - - +
56A LEU* 1.3 76.1 - - - +
58A GLN* 1.3 61.3 + - - +
60A PHE* 2.9 10.1 + - - +
62A SER* 2.9 43.0 + - - +
63A THR* 3.9 6.1 - - - -
64A LEU* 3.7 12.6 - - + -
121A THR* 4.1 3.1 - - - -
122A TYR 3.2 14.1 - - - -
123A CYS* 2.1 51.6 - - - -
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Residues in contact with GLN 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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54A ALA* 3.0 15.0 + - - +
55A ASP* 3.5 20.2 + - - +
56A LEU 3.2 0.4 - - - -
57A CYS* 1.3 75.5 - - - +
59A ALA* 1.3 57.4 + - - +
61A ASN* 3.0 17.4 + - - +
62A SER 3.4 10.6 + - - +
142A ASN* 3.0 33.5 + - - +
168A THR* 6.2 1.7 - - - +
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Residues in contact with ALA 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 ASP 3.1 4.6 + - - +
56A LEU* 3.0 12.1 + - + +
58A GLN* 1.3 75.7 - - - +
60A PHE* 1.3 56.3 + - - +
61A ASN 3.3 0.6 + - - -
140A LEU* 3.6 22.0 - - + +
141A PRO* 3.5 6.6 - - - +
142A ASN* 2.9 36.6 + - - +
143A SER* 4.2 9.9 - - - +
166A TYR* 3.6 31.0 - - + -
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Residues in contact with PHE 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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28A LEU* 4.2 4.5 - - + -
30A VAL* 4.0 17.7 - - + -
38A PHE* 3.9 23.6 - + + -
40A VAL* 4.2 14.8 - - + -
56A LEU* 3.4 38.1 + - + -
57A CYS* 2.9 10.3 + - - +
59A ALA* 1.3 76.3 - - - +
61A ASN* 1.3 70.2 + - - +
62A SER* 2.9 15.3 + - - +
123A CYS* 4.7 1.6 - - - -
125A ASN* 4.9 5.2 + - - -
137A VAL* 4.1 21.8 - - + -
139A ASP 4.2 8.7 - - - -
140A LEU* 3.6 24.9 - - + -
141A PRO* 4.2 10.6 - - + +
152A ILE* 3.8 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