Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 2H1R
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ASP* 2.8 14.0 + - - +
51A ILE* 1.3 85.2 - - + +
53A SER* 1.3 66.4 + - - +
54A ARG* 2.9 21.1 + - - +
55A MET* 2.7 48.1 + - + +
56A ILE* 3.3 25.9 + - - +
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Residues in contact with SER 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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51A ILE 4.1 2.2 + - - -
52A ASP* 1.3 75.2 + - - +
54A ARG* 1.3 63.4 + - - +
55A MET 3.5 0.2 - - - -
56A ILE* 3.7 13.0 - - - +
57A SER* 3.6 19.6 + - - -
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Residues in contact with ARG 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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52A ASP* 2.9 18.4 + - - +
53A SER* 1.3 80.9 - - - +
55A MET* 1.3 66.3 + - + +
56A ILE 3.3 0.2 - - - -
57A SER* 3.7 16.0 + - - -
58A GLU* 3.9 10.2 + - - +
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Residues in contact with MET 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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3A LEU* 3.9 29.8 - - + -
30A CYS* 5.7 0.7 - - - -
31A GLY* 3.9 28.0 - - - +
32A THR* 5.1 3.4 - - + -
50A ASP* 4.6 13.9 - - - +
52A ASP* 2.7 34.7 + - - +
54A ARG* 1.3 72.0 - - + +
56A ILE* 1.3 65.2 + - - +
58A GLU* 3.2 16.5 + - - +
59A VAL* 3.3 18.6 + - - +
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Residues in contact with ILE 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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30A CYS* 3.7 16.6 - - - -
48A THR* 4.5 3.4 - - + -
50A ASP* 3.5 33.0 - - + +
52A ASP 3.3 17.9 + - - +
53A SER* 3.7 14.4 - - - +
54A ARG 3.3 0.2 - - - -
55A MET* 1.3 77.6 - - - +
57A SER* 1.3 59.2 - - - +
59A VAL* 3.2 6.7 + - + +
60A LYS* 3.0 30.7 + - + +
73A VAL* 4.0 46.1 - - + +
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Residues in contact with SER 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 SER 3.6 11.7 + - - -
54A ARG* 3.7 9.4 + - - -
55A MET 3.3 0.8 - - - -
56A ILE* 1.3 81.1 - - - +
58A GLU* 1.3 61.6 + - - +
60A LYS* 3.7 7.3 - - - +
61A LYS* 3.1 51.4 + - - +
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Residues in contact with GLU 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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32A THR* 5.6 1.1 - - - -
54A ARG 3.9 9.4 + - - +
55A MET* 3.2 12.0 + - - +
57A SER* 1.3 81.2 + - - +
59A VAL* 1.3 60.6 + - + +
61A LYS* 3.4 29.9 + - - +
62A ARG* 2.9 29.2 + - - +
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Residues in contact with VAL 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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30A CYS* 4.0 18.6 - - - -
31A GLY 3.4 25.6 - - - +
32A THR* 3.6 17.7 - - - -
33A GLY* 3.7 17.0 - - - +
36A THR* 4.1 12.6 - - + +
48A THR* 5.6 2.0 - - + -
55A MET 3.3 10.1 + - - +
56A ILE* 3.2 6.8 + - + +
58A GLU* 1.3 72.5 - - + +
60A LYS* 1.3 60.7 + - - +
62A ARG* 3.1 6.5 + - - +
63A CYS* 2.8 44.2 + - - -
71A LEU* 4.3 6.5 - - + -
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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 ILE* 3.0 19.9 + - + +
57A SER* 3.7 8.5 - - - +
59A VAL* 1.3 76.9 - - - +
61A LYS* 1.3 63.3 + - + +
63A CYS* 4.5 0.8 - - - +
64A LEU* 3.1 55.0 + - + +
68A TYR 4.7 2.4 + - - -
69A ASN* 6.0 1.0 - - - +
71A LEU* 3.9 45.9 - - + +
73A VAL* 4.6 15.3 - - + -
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Residues in contact with LYS 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 SER* 3.1 35.5 + - - +
58A GLU* 3.6 27.6 + - - +
60A LYS* 1.3 75.7 - - + +
62A ARG* 1.3 59.1 + - - +
64A LEU* 3.5 10.7 + - + +
65A TYR* 2.9 30.9 + - - +
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Residues in contact with ARG 62 (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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32A THR* 3.0 28.7 + - - +
33A GLY* 3.4 13.5 - - - -
34A ASN* 2.8 29.7 + - - +
37A VAL* 3.5 27.6 - - + +
58A GLU 2.9 15.0 + - - +
59A VAL* 3.3 9.4 - - - +
61A LYS* 1.3 78.0 - - - +
63A CYS* 1.3 64.3 + - - +
65A TYR* 3.3 7.4 + - + +
66A GLU* 3.0 44.9 + - - +
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Residues in contact with CYS 63 (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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36A THR* 3.8 10.5 - - - -
37A VAL* 3.8 21.3 - - - -
40A LEU* 3.4 33.2 - - + -
59A VAL* 2.8 26.0 + - - +
60A LYS* 3.9 2.7 - - - +
62A ARG* 1.3 71.8 - - - +
64A LEU* 1.3 65.5 + - - +
66A GLU 3.2 7.4 + - - -
67A GLY 3.2 0.2 + - - -
68A TYR* 2.9 36.6 + - - +
71A LEU* 3.7 20.9 - - + -
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Residues in contact with LEU 64 (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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60A LYS* 3.1 48.7 + - + +
61A LYS* 3.7 9.2 - - + +
63A CYS* 1.3 73.8 - - - +
65A TYR* 1.3 57.5 + - - +
67A GLY* 2.9 22.2 + - - -
68A TYR 3.7 9.3 + - - +
69A ASN* 3.3 27.8 - - - +
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Residues in contact with TYR 65 (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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61A LYS 2.9 19.5 + - - +
62A ARG* 3.4 8.5 - - + +
64A LEU* 1.3 77.8 - - - +
66A GLU* 1.3 70.7 + - + +
67A GLY* 3.1 1.3 + - - -
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Residues in contact with GLU 66 (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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37A VAL* 3.7 26.3 - - - +
62A ARG* 3.0 48.1 + - - +
63A CYS 3.2 1.9 + - - +
65A TYR* 1.3 86.9 - - + +
67A GLY* 1.3 59.1 + - - +
68A TYR* 3.6 29.7 + - + +
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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