Contacts of the helix formed by residues 47 - 55 (chain B) in PDB entry 1HTI
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 TYR 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASP* 5.5 0.7 - - - -
82A MET* 3.4 29.9 - - + +
85A ASP* 2.8 39.6 + - - +
86A CYS* 3.8 13.7 - - - -
16B GLY 3.3 20.4 - - - -
17B ARG* 3.5 10.0 - - - -
18B LYS* 3.4 34.5 - - + -
21B LEU* 3.5 24.2 - - + -
43B PRO* 3.7 4.6 - - + +
44B PRO* 2.9 25.2 + - + +
46B ALA* 1.4 81.4 - - + +
48B ILE* 1.3 63.1 + - - -
49B ASP* 3.3 2.0 - - - +
50B PHE* 3.9 17.0 - - + +
51B ALA* 3.1 20.5 + - + +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 4.6 15.8 + - + +
43B PRO* 3.8 15.7 - - + -
44B PRO 5.0 0.2 - - - -
45B THR* 3.6 43.6 + - + +
46B ALA 3.8 1.2 + - - -
47B TYR* 1.3 75.1 - - - +
49B ASP* 1.3 58.0 + - - +
51B ALA* 3.5 2.4 - - - +
52B ARG* 2.9 25.7 + - + +
61B VAL* 3.6 19.6 - - + +
62B ALA 4.8 0.2 - - - +
63B ALA* 4.2 25.8 - - + -
78B ILE* 5.3 4.7 - - + -
83B ILE* 4.8 5.2 - - + +
86B CYS* 3.8 21.5 - - + -
88B ALA* 3.6 18.6 - - + +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.0 34.8 + - - -
46A ALA 4.8 7.0 + - - +
49A ASP* 5.7 7.2 - - + +
50A PHE* 4.6 12.5 + - + +
46B ALA 5.2 0.4 + - - -
47B TYR* 3.3 0.4 - - - +
48B ILE* 1.3 75.9 - - - +
50B PHE* 1.3 55.7 + - - +
51B ALA 3.1 1.3 - - - -
52B ARG* 2.9 6.0 + - - +
53B GLN* 2.8 61.3 + - - +
86B CYS* 3.6 29.6 - - - +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 4.5 12.8 + - - +
18B LYS* 3.3 53.4 - - + -
21B LEU* 3.7 26.0 - - + -
22B GLY* 3.8 9.6 - - - -
25B ILE* 3.8 14.8 - - + -
47B TYR* 3.9 30.4 + - + +
49B ASP* 1.3 76.0 - - - +
51B ALA* 1.3 71.6 + - + +
53B GLN* 3.3 16.7 + - - +
54B LYS* 3.0 58.5 + - + +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 4.9 3.4 - - + -
21B LEU* 6.2 0.4 - - + -
25B ILE* 3.9 16.9 - - + +
43B PRO* 4.0 20.4 - - + -
47B TYR 3.1 18.1 + - - +
48B ILE 3.5 4.0 - - - +
50B PHE* 1.3 85.7 - - + +
52B ARG* 1.3 61.8 + - - +
54B LYS* 3.4 0.7 + - - +
55B LEU* 2.8 38.5 + - + +
61B VAL* 4.4 6.7 - - + -
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE 2.9 16.1 + - - +
49B ASP* 2.9 6.4 + - - +
51B ALA* 1.3 79.0 - - - +
53B GLN* 1.3 62.8 + - - +
55B LEU* 3.3 29.3 + - - +
56B ASP 3.0 28.3 + - - -
57B PRO* 3.9 9.2 + - - +
59B ILE 2.8 20.4 + - - -
60B ALA* 3.8 3.0 - - - +
61B VAL* 3.4 34.1 - - + +
86B CYS 3.8 21.8 - - - +
87B GLY* 3.4 27.8 + - - +
89B THR* 5.4 1.2 + - - -
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 5.2 1.0 - - - +
49A ASP* 5.1 4.8 + - - +
53A GLN* 5.2 10.3 + - - +
49B ASP* 2.8 49.6 + - - +
50B PHE* 3.3 19.7 - - - +
52B ARG* 1.3 72.8 - - - +
54B LYS* 1.3 74.1 + - + +
55B LEU 4.1 2.8 - - - +
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLY* 5.7 2.9 - - - -
25B ILE* 3.6 22.6 - - + +
29B ASN* 2.9 16.8 + - - -
50B PHE* 3.0 46.1 + - + +
51B ALA 3.9 1.8 - - - +
53B GLN* 1.3 89.8 - - - +
55B LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 5.2 3.6 - - + -
25B ILE* 4.0 26.5 - - + -
28B LEU* 4.4 13.0 - - + -
29B ASN* 3.2 16.8 - - - +
41B CYS* 4.6 11.7 - - + -
51B ALA* 2.8 24.6 + - + +
52B ARG* 3.3 20.5 + - - +
53B GLN 3.6 3.0 - - - +
54B LYS* 1.3 78.6 - - - +
56B ASP* 1.3 65.3 + - - +
57B PRO* 3.5 6.4 - - - +
59B ILE* 3.9 35.0 - - + +
61B VAL* 3.9 24.2 - - + -
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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