Contacts of the helix formed by residues 51 - 61 (chain A) in PDB entry 1SR0
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 ASN 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLN* 2.9 25.5 + - - +
13A TYR* 3.7 2.1 + - - -
21A PHE* 5.1 2.0 - - - -
49A GLU* 3.5 10.6 - - - +
50A TRP* 1.3 123.1 + - + +
52A ASP* 1.3 64.8 + - - +
53A VAL* 3.3 5.6 - - - +
54A THR* 2.9 24.4 + - + +
55A LEU* 3.0 32.5 + - - +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.3 9.3 + - - -
35A TYR* 2.8 32.1 + - - -
37A PHE 5.9 0.2 - - - -
47A THR* 3.8 4.7 - - + -
48A TRP* 3.0 14.6 + - - -
49A GLU* 2.5 52.1 + - - +
50A TRP 3.8 0.2 - - - -
51A ASN* 1.3 74.0 - - - +
53A VAL* 1.3 60.7 + - - +
55A LEU 4.1 0.7 - - - +
56A TYR* 2.5 62.7 + - + +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 4.4 17.3 - - + -
50A TRP 5.6 1.3 - - - +
51A ASN* 4.8 4.9 - - - -
52A ASP* 1.3 79.7 - - - +
54A THR* 1.3 73.4 + - - +
56A TYR* 3.4 11.3 - - + +
57A ASP* 3.2 20.6 + - - +
109A HIS* 3.8 28.3 + - + +
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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
----------------------------------------------------------
51A ASN* 2.9 20.6 + - + +
52A ASP 2.9 1.2 + - - -
53A VAL* 1.3 84.6 - - - +
55A LEU* 1.3 67.1 + - + +
57A ASP* 3.1 10.8 - - + +
58A THR* 2.6 35.0 + - - +
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Residues in contact with LEU 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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7A TYR* 4.7 11.7 - - + +
9A SER 4.9 0.9 - - - +
12A GLN* 3.2 36.1 - - - +
21A PHE* 3.7 28.9 - - + -
22A PRO* 3.7 11.6 - - + +
35A TYR* 3.2 31.1 - - + +
51A ASN* 3.0 26.2 + - - +
52A ASP* 4.0 0.7 - - - +
54A THR* 1.3 87.0 - - + +
56A TYR* 1.3 60.9 + - - +
58A THR* 3.2 12.0 - - + +
59A LEU* 3.1 24.4 + - - +
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Residues in contact with TYR 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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35A TYR* 3.6 29.8 - + - -
38A ALA* 4.5 3.1 - - - +
47A THR* 4.1 18.6 - - + +
52A ASP* 2.5 45.8 + - + +
53A VAL* 3.4 9.2 - - - +
55A LEU* 1.3 70.5 - - - +
57A ASP* 1.3 55.1 + - - +
59A LEU* 3.3 6.1 + - - +
60A ASN* 2.9 40.6 + - - +
73A LEU* 3.5 29.1 - - + +
105A PHE* 3.7 27.3 - + - -
109A HIS* 3.6 36.8 - + + +
111A PHE* 4.1 20.2 - + + -
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Residues in contact with ASP 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 VAL 3.3 10.1 - - - +
54A THR* 3.1 14.4 + - - +
56A TYR* 1.3 79.7 - - - +
58A THR* 1.3 52.0 + - - +
60A ASN* 3.5 4.9 + - - +
61A THR* 2.6 50.5 + - - +
109A HIS 5.7 1.3 - - - -
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Residues in contact with THR 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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21A PHE* 5.6 0.4 - - + -
22A PRO* 4.0 7.0 - - + +
23A ASP* 3.8 38.0 - - + +
54A THR* 2.6 26.6 + - - +
55A LEU* 3.2 18.8 - - + +
57A ASP* 1.3 73.1 + - - +
59A LEU* 1.4 55.7 + - - +
61A THR* 2.3 28.6 + - - +
62A LEU* 4.2 9.9 + - - +
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Residues in contact with LEU 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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7A TYR* 5.5 2.7 - - + -
22A PRO* 3.8 14.6 - - + -
25A ILE* 4.5 8.1 - - + -
33A VAL* 3.7 33.0 - - + -
35A TYR* 3.8 37.2 - - + +
55A LEU 3.1 16.0 + - - +
56A TYR 3.7 2.7 - - - +
58A THR* 1.4 72.6 - - - +
60A ASN* 1.3 74.1 + - - +
61A THR 3.1 1.1 - - - -
62A LEU* 3.2 39.7 + - + +
63A LYS* 4.5 0.7 + - - +
69A LEU* 5.6 0.4 - - + -
71A THR* 3.9 18.0 - - + +
111A PHE* 4.4 11.7 - - + -
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR 2.9 18.1 + - - +
57A ASP* 4.2 4.3 - - - +
59A LEU* 1.3 82.4 - - - +
61A THR* 1.3 63.7 + - - +
62A LEU 3.2 0.9 + - - -
63A LYS* 3.3 24.5 + - + +
64A ASN* 4.5 1.4 + - - +
71A THR* 2.5 41.6 + - - +
109A HIS 2.8 27.5 - - - +
110A GLY* 3.1 19.8 - - - +
111A PHE* 3.4 12.9 + - - -
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Residues in contact with THR 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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57A ASP* 2.6 37.1 + - - +
58A THR* 2.3 35.0 + - - +
60A ASN* 1.3 74.0 - - - +
62A LEU* 1.3 50.9 + - - +
63A LYS 2.9 6.5 - - - -
64A ASN* 2.7 47.3 + - - +
65A ARG* 4.2 2.3 + - - +
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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