Contacts of the helix formed by residues 48 - 59 (chain A) in PDB entry 4HNF
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 GLN 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 2.8 21.8 + - - +
20A PHE* 2.8 39.7 - - + +
38A LYS* 5.5 1.1 - - - +
40A GLU* 2.5 12.0 + - - +
47A PRO* 1.3 89.4 - - - +
49A LEU* 1.3 63.8 + - - +
50A HIS 3.3 3.3 - - - +
51A ILE* 2.9 16.0 + - + +
52A GLU* 2.9 33.6 + - + +
151A GLY* 5.4 4.4 - - - +
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Residues in contact with LEU 49 (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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38A LYS* 3.1 55.0 - - + +
40A GLU* 2.7 35.8 + - + +
48A GLN* 1.3 70.8 - - - +
50A HIS* 1.3 59.3 + - - +
52A GLU* 3.1 6.6 + - - +
53A SER* 2.8 28.7 + - - -
71A CYS* 6.2 1.6 - - - -
78A ASN* 3.3 37.0 - - + +
79A VAL 4.1 0.9 - - - -
80A MET* 3.9 26.7 - - + +
301A 16W 4.2 7.9 - - + -
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Residues in contact with HIS 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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40A GLU* 4.8 2.0 + - - +
48A GLN 3.3 1.0 - - - +
49A LEU* 1.3 77.4 - - - +
51A ILE* 1.3 66.8 + - + +
53A SER* 3.0 28.5 + - - -
54A LYS* 3.4 27.7 + - + +
71A CYS* 4.7 13.9 - - - -
78A ASN* 6.3 1.3 - - - +
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Residues in contact with ILE 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 PRO* 3.9 22.2 - - + +
48A GLN* 2.9 14.2 + - + +
50A HIS* 1.3 79.3 - - + +
52A GLU* 1.3 64.3 + - + +
54A LYS* 3.5 5.7 + - - +
55A ILE* 3.2 32.7 + - + +
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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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19A SER* 4.6 5.7 - - - -
38A LYS* 3.3 16.6 + - - -
48A GLN* 2.9 18.4 + - + +
49A LEU* 3.5 8.1 - - - +
51A ILE* 1.3 73.9 - - + +
53A SER* 1.3 57.6 + - - +
54A LYS 2.9 2.2 - - - -
55A ILE* 2.7 8.7 + - - +
56A TYR* 2.5 58.1 + - + +
80A MET* 4.9 0.7 - - + -
149A ASP* 4.2 4.5 - - - +
150A PHE* 3.3 39.6 + - + +
151A GLY* 3.9 9.6 + - - +
301A 16W 2.8 28.1 - - + +
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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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49A LEU 2.8 18.9 + - - -
50A HIS* 3.0 23.1 + - - -
52A GLU* 1.3 71.8 - - - +
54A LYS* 1.3 64.9 + - - +
56A TYR* 3.5 3.7 - - - +
57A LYS* 2.6 42.3 + - - +
68A ILE* 5.1 1.9 - - - +
71A CYS* 3.7 28.4 - - - -
80A MET* 3.7 16.5 - - - -
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Residues in contact with LYS 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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50A HIS* 3.4 30.0 + - + +
51A ILE* 3.7 9.0 - - - +
52A GLU 2.8 1.4 + - - -
53A SER* 1.3 84.4 + - - +
55A ILE* 1.3 66.7 + - + +
56A TYR 3.0 1.6 - - - -
57A LYS* 3.2 11.5 + - + +
58A MET* 2.9 38.7 + - + +
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Residues in contact with ILE 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 ILE* 3.2 23.9 + - + +
52A GLU* 2.7 11.6 + - - +
54A LYS* 1.3 75.4 - - + +
56A TYR* 1.3 59.3 + - - +
58A MET* 3.4 10.0 + - - +
59A MET* 3.1 45.4 + - + +
124A PHE* 3.6 32.8 - - + -
150A PHE* 4.0 31.2 - - + +
153A ALA* 3.8 24.2 - - + +
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Residues in contact with TYR 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 GLU* 2.5 45.3 + - + +
53A SER 3.5 5.2 - - - +
55A ILE* 1.3 69.7 - - - +
57A LYS* 1.3 60.9 + - - +
58A MET 3.0 4.9 - - - -
59A MET* 3.3 6.5 + - + +
60A GLN* 3.2 18.7 + - - -
65A ILE* 4.6 8.2 - - + +
66A PRO* 3.5 35.3 - - + +
68A ILE* 3.8 20.1 - - + +
80A MET* 3.4 17.7 - - + -
82A MET* 3.7 23.2 - - + +
148A ILE* 3.7 11.8 - - - +
149A ASP 3.5 21.7 + - - -
150A PHE* 3.6 28.9 - + + -
301A 16W 3.8 10.1 - - + +
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Residues in contact with LYS 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* 2.6 23.0 + - - +
54A LYS* 3.2 14.9 + - + +
56A TYR* 1.3 71.8 - - - +
58A MET* 1.3 61.7 + - - +
59A MET 3.4 0.2 - - - -
60A GLN* 3.6 35.0 + - + +
68A ILE* 3.8 47.6 - - + +
69A ARG 6.2 0.2 - - - -
70A TRP 6.2 0.2 - - - +
71A CYS* 4.5 16.6 - - - +
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Residues in contact with MET 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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54A LYS* 2.9 34.9 + - + +
55A ILE* 3.5 6.3 - - - +
56A TYR 3.0 0.2 - - - -
57A LYS* 1.3 79.4 - - - +
59A MET* 1.3 61.1 - - + +
60A GLN* 3.1 8.4 + - - +
118A TYR* 4.5 0.2 + - - -
122A LYS* 4.2 21.5 + - + +
124A PHE* 4.0 33.4 - - + -
155A LYS* 6.4 1.6 - - + -
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Residues in contact with MET 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.1 28.0 + - + +
56A TYR* 3.3 5.8 + - - +
58A MET* 1.3 74.4 - - + +
60A GLN* 1.3 70.8 + - - +
62A GLY 3.3 7.6 + - - -
65A ILE* 3.6 25.2 - - + +
118A TYR* 2.9 21.7 + - + -
119A ILE* 3.9 27.8 - - + -
122A LYS* 3.9 20.0 - - + -
124A PHE* 3.2 46.9 - - + -
150A PHE* 4.3 17.3 - - + -
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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