Contacts of the helix formed by residues 49 - 57 (chain A) in PDB entry 4HRG
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 LEU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP* 2.7 17.4 + - - +
48A PRO* 1.3 84.8 - - + +
50A ALA* 1.3 58.5 + - - +
51A VAL 3.3 2.2 - - - -
52A ASP* 3.0 26.9 + - + +
53A LYS* 2.8 47.6 + - + +
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Residues in contact with ALA 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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42A LEU* 4.6 12.6 - - + +
45A GLN* 4.2 24.2 - - + -
47A ASP* 3.3 25.1 + - + +
48A PRO 3.2 2.8 - - - -
49A LEU* 1.3 78.8 - - - +
51A VAL* 1.3 59.0 + - + +
53A LYS* 3.2 7.2 + - - +
54A ILE* 2.8 38.1 + - + +
112A LEU* 4.5 6.0 - - + +
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Residues in contact with VAL 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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27A LYS* 4.2 24.2 - - + +
30A LEU* 3.9 27.1 - - + -
31A ARG* 4.0 32.1 - - + +
34A MET* 4.9 3.1 - - - -
42A LEU* 3.6 37.5 - - + -
48A PRO 5.1 0.6 + - - -
49A LEU 3.3 0.4 - - - -
50A ALA* 1.3 76.7 - - + +
52A ASP* 1.3 62.1 + - - +
54A ILE* 3.6 7.5 - - - +
55A MET* 2.8 28.9 + - - +
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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
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27A LYS* 2.6 41.2 + - - +
31A ARG* 4.1 12.1 + - - -
48A PRO 4.0 4.0 - - - +
49A LEU* 3.0 39.6 + - + +
51A VAL* 1.3 77.1 + - - +
53A LYS* 1.3 58.1 + - + +
55A MET* 3.6 7.1 - - - +
56A LYS* 3.0 27.0 + - - +
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Residues in contact with LYS 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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47A ASP* 2.8 32.1 + - - +
49A LEU* 2.8 35.3 + - + +
50A ALA* 3.7 5.4 - - - +
52A ASP* 1.3 74.8 - - + +
54A ILE* 1.3 68.1 + - - +
56A LYS* 3.2 13.5 + - + +
57A ASP* 3.1 22.0 + - - +
112A LEU* 3.9 18.7 - - + +
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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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30A LEU* 4.6 9.0 - - + -
34A MET* 3.9 28.9 - - + -
41A PHE* 4.7 3.8 - - + -
42A LEU* 4.6 5.2 - - + -
45A GLN* 6.4 0.7 - - + -
50A ALA* 2.8 27.7 + - + +
51A VAL* 3.6 6.3 - - - +
53A LYS* 1.3 76.3 - - - +
55A MET* 1.3 57.1 + - - +
57A ASP* 2.7 28.0 + - - +
58A LEU* 3.2 24.8 + - + +
74A LEU* 4.0 22.4 - - + -
112A LEU* 3.9 22.7 - - + -
5664C PRO* 5.5 3.5 - - + +
5666C PHE* 4.3 18.6 - - + -
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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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27A LYS* 3.7 41.7 - - + +
30A LEU* 4.6 8.9 - - + +
51A VAL* 2.8 21.4 + - + +
52A ASP* 3.6 8.5 - - - +
54A ILE* 1.3 75.0 - - - +
56A LYS* 1.3 61.4 + - - +
57A ASP 3.4 0.2 + - - -
58A LEU* 3.6 14.5 + - - -
61A CYS* 3.5 28.2 - - - +
64A GLY* 3.2 41.3 - - - +
65A LYS 3.9 0.9 - - - +
66A VAL* 3.3 32.5 - - + -
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Residues in contact with LYS 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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52A ASP 3.0 16.2 + - - +
53A LYS* 3.4 15.0 - - + +
54A ILE 3.0 0.4 + - - -
55A MET* 1.3 76.8 - - - +
57A ASP* 1.3 72.2 + - - +
58A LEU 3.4 2.2 + - - +
61A CYS 4.7 8.1 - - - +
5662C LYS* 5.5 0.5 - - - -
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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 LYS 3.1 13.0 + - - +
54A ILE* 2.7 15.1 + - - +
56A LYS* 1.3 91.0 - - - +
58A LEU* 1.3 59.9 + - - +
59A ASP 3.7 1.4 + - - -
112A LEU* 5.1 11.8 - - + +
5662C LYS* 3.4 39.8 + - - +
5664C PRO* 4.0 24.0 - - + +
5665C LYS 5.8 0.5 + - - -
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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