Contacts of the helix formed by residues 52 - 61 (chain P) in PDB entry 1HNX
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ILE* 3.6 8.9 - - - +
50P LYS* 3.5 29.3 + - - +
51P VAL* 1.3 79.1 - - - +
53P VAL* 1.3 64.2 - - - +
54P GLU* 2.8 15.8 - - - +
55P ARG* 2.5 47.3 + - - +
56P ALA 3.4 5.5 + - - -
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Residues in contact with VAL 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P VAL* 3.1 10.7 + - + -
52P ASP* 1.3 75.4 - - - +
54P GLU* 1.3 71.7 + - - +
56P ALA* 3.4 8.8 + - - +
57P ARG* 3.1 49.4 + - - +
77P ALA* 3.5 23.6 - - + +
78P GLY 4.7 1.8 - - - +
79P VAL* 4.3 14.6 - - + -
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Residues in contact with GLU 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P ASP* 2.8 11.8 + - - +
53P VAL* 1.3 88.9 - - + +
55P ARG* 1.3 78.4 + - + +
57P ARG* 3.3 14.4 + - - +
58P TYR* 3.4 12.6 + - - +
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Residues in contact with ARG 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P GLU* 2.8 43.3 + - - +
35P LYS 5.6 0.4 - - - +
36P ILE* 3.8 17.7 - - + -
52P ASP* 2.5 36.7 + - - +
54P GLU* 1.3 81.2 + - + +
56P ALA* 1.3 69.4 + - - +
58P TYR* 2.7 67.7 + - - +
59P TRP* 3.1 11.3 + - + +
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Residues in contact with ALA 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P ILE* 4.8 1.3 - - - -
36P ILE* 4.0 25.8 - - + +
51P VAL* 4.7 3.1 - - + +
52P ASP 3.4 5.7 + - - +
53P VAL* 3.5 13.9 - - - +
54P GLU 3.3 0.2 - - - -
55P ARG* 1.3 76.8 - - - +
57P ARG* 1.3 66.0 + - - +
59P TRP* 2.8 19.1 + - - +
60P LEU* 2.9 16.5 + - + +
74P LEU* 4.3 11.0 - - + -
79P VAL* 3.8 22.4 - - + -
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Residues in contact with ARG 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P VAL* 3.1 33.0 + - - +
54P GLU* 3.6 10.5 - - - +
56P ALA* 1.3 78.7 - - - +
58P TYR* 1.3 56.6 + - - +
60P LEU* 3.8 11.6 - - + +
61P SER* 2.8 28.9 + - - -
78P GLY 3.5 15.4 + - - -
79P VAL* 3.4 31.0 + - + +
80P PHE 5.3 2.2 + - - -
81P ARG 4.0 15.6 + - - -
82P GLN* 6.2 0.8 - - - +
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Residues in contact with TYR 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A A 3.7 28.1 + - - -
229A U 5.7 0.2 + - - -
54P GLU* 3.4 10.2 + - - +
55P ARG* 2.7 53.2 + - - +
57P ARG* 1.3 73.1 - - - +
59P TRP* 1.3 100.2 + + - +
61P SER* 2.3 44.0 + - - -
62P VAL* 3.2 20.2 - - + +
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Residues in contact with TRP 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A A 3.6 31.0 - - - -
229A U 3.6 23.3 - - - -
2P VAL* 4.6 4.3 - - + -
4P ILE* 4.2 7.0 - - + -
21P VAL* 3.0 40.6 - - + +
33P ILE* 3.6 25.6 - - + -
34P GLU* 3.3 27.4 + - - -
36P ILE* 4.1 9.2 - - + -
55P ARG* 3.1 16.2 + - - +
56P ALA* 2.8 11.6 + - - +
58P TYR* 1.3 101.4 - + - +
60P LEU* 1.3 53.7 + - - +
62P VAL* 2.6 33.3 + - + +
64P ALA* 3.3 24.9 + - + +
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Residues in contact with LEU 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A C 4.7 6.9 + - - +
4P ILE* 4.0 13.2 - - + -
56P ALA 2.9 17.7 + - - +
57P ARG* 3.8 10.1 - - + +
59P TRP* 1.3 77.1 - - - +
61P SER* 1.3 58.1 + - - +
62P VAL 2.8 6.2 + - - -
63P GLY* 3.5 8.7 + - - -
64P ALA* 3.7 12.9 + - - +
65P GLN* 6.1 0.2 - - - +
66P PRO* 3.7 33.9 - - + -
71P ARG* 6.0 0.7 - - - +
74P LEU* 4.7 3.8 - - + -
79P VAL* 4.1 20.0 - - + +
80P PHE* 3.9 28.3 - - + -
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Residues in contact with SER 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A C 3.7 12.6 + - - -
57P ARG 2.8 15.6 + - - -
58P TYR* 2.3 34.1 + - - -
60P LEU* 1.3 75.2 - - - +
62P VAL* 1.3 68.1 + - - +
63P GLY 4.0 0.2 - - - -
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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