Contacts of the helix formed by residues 49 - 57 (chain A) in PDB entry 3HPD
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 GLU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.4 25.9 - - + +
45A HIS 5.5 0.2 - - - -
46A ALA* 3.0 26.8 + - + +
48A GLU* 1.3 79.3 - - + +
50A LEU* 1.3 68.0 + - - +
51A GLU 3.3 2.7 - - - -
52A GLU* 3.3 15.1 + - + +
53A MET* 2.9 43.1 + - + +
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Residues in contact with LEU 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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19A HIS* 4.1 22.4 - - + -
21A ILE* 4.1 14.1 - - + -
44A ALA* 4.3 1.3 - - + +
45A HIS* 3.8 21.3 - - - +
46A ALA 3.1 14.3 + - - +
47A GLU* 3.7 20.0 + - + +
49A GLU* 1.3 76.7 - - + +
51A GLU* 1.3 64.7 + - - +
53A MET* 3.8 2.6 - - - -
54A ILE* 2.9 32.9 + - + +
74A SER* 3.5 33.4 - - - +
77A LYS* 4.0 18.2 - - + -
78A ALA* 4.2 5.4 - - + +
81A ILE* 4.0 11.2 - - + -
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Residues in contact with GLU 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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47A GLU 5.0 1.4 + - - -
49A GLU 3.3 0.8 - - - -
50A LEU* 1.3 78.2 - - - +
52A GLU* 1.3 65.2 + - + +
54A ILE* 3.9 1.2 - - - +
55A ARG* 3.0 67.8 + - + +
81A ILE* 3.9 33.3 - - + +
84A GLU* 5.1 5.7 - - - +
85A LEU* 5.7 2.4 - - - +
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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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48A GLU 4.4 12.8 - - - +
49A GLU* 3.3 13.5 + - + +
51A GLU* 1.3 78.9 - - + +
53A MET* 1.3 62.5 + - - +
55A ARG* 3.5 18.7 + - - +
56A LEU* 3.1 28.1 + - + +
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Residues in contact with MET 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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17A LEU* 5.3 1.5 - - - +
19A HIS* 4.2 19.3 - - + +
42A VAL* 3.7 33.4 - - + -
44A ALA* 3.9 24.5 - - + -
49A GLU* 2.9 40.6 + - + +
50A LEU* 3.9 3.1 - - - +
52A GLU* 1.3 75.6 - - - +
54A ILE* 1.3 59.9 + - - +
56A LEU* 3.1 23.3 + - - +
57A ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 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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19A HIS* 3.4 23.8 - - + +
50A LEU* 2.9 24.9 + - + +
53A MET* 1.3 72.4 - - - +
55A ARG* 1.3 61.9 + - - +
57A ALA* 3.4 10.5 + - - +
60A VAL* 3.9 21.3 - - + -
78A ALA* 3.6 44.2 - - + +
81A ILE* 3.8 21.3 - - + -
82A ALA* 3.9 20.2 - - + -
85A LEU* 4.1 5.2 - - + -
87A LYS* 2.9 24.1 + - + +
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Residues in contact with ARG 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 GLU* 3.0 59.4 + - + +
52A GLU* 3.5 17.5 - - - +
54A ILE* 1.3 76.7 - - - +
56A LEU* 1.3 60.3 + - + +
85A LEU* 3.8 27.3 - - + +
87A LYS* 2.8 20.5 + - - +
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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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17A LEU* 3.7 24.3 - - + +
52A GLU* 3.1 13.1 + - + +
53A MET* 3.1 26.8 + - - +
55A ARG* 1.3 82.8 - - + +
57A ALA* 1.3 60.6 + - - +
58A ASP* 4.6 4.5 - - - +
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Residues in contact with ALA 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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17A LEU* 3.8 17.2 - - + +
19A HIS* 3.6 28.5 - - + +
42A VAL* 5.2 0.2 - - + -
53A MET 2.9 15.8 + - - +
54A ILE* 3.5 7.5 - - - +
55A ARG 3.4 0.6 - - - -
56A LEU* 1.3 79.5 - - - +
58A ASP* 1.3 63.2 + - - +
59A ALA 3.5 10.3 - - - +
60A VAL* 5.0 1.6 - - + -
87A LYS* 2.7 32.7 + - + +
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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