Contacts of the helix formed by residues 46 - 51 (chain N) in PDB entry 2QJK
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 PRO 46 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M ARG* 4.3 14.8 - - + +
86M ASN* 4.7 7.0 - - - +
44N PHE 3.4 10.5 - - - +
45N VAL* 1.3 83.7 - - + +
47N ILE* 1.3 61.0 + - - +
48N ARG* 3.2 38.4 - - + +
49N SER* 2.2 51.5 + - - +
52N GLU* 4.8 0.9 - - - +
85N PRO 5.1 0.2 - - - +
86N THR 5.8 1.6 - - - +
87N ASP 3.8 5.2 - - - +
88N HIS* 3.1 24.4 - - + +
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Residues in contact with ILE 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N VAL 3.3 1.6 + - - -
46N PRO* 1.3 69.0 - - - +
48N ARG* 1.3 51.0 + - - +
50N LEU* 2.6 62.2 + - + +
63N VAL* 4.2 9.4 - - + +
66N TYR* 4.3 7.9 - - + -
67N ALA* 4.1 25.4 - - + +
70N PHE* 3.5 33.0 - - + -
83N GLY 5.7 0.2 - - - -
84N LYS 4.1 4.7 - - - +
85N PRO* 3.9 5.2 - - + +
87N ASP* 2.8 34.8 + - + +
88N HIS 4.2 6.7 - - - +
89N PHE* 3.8 24.5 - - + +
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Residues in contact with ARG 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M ASN* 3.1 27.9 + - - +
46N PRO* 3.9 21.0 - - + +
47N ILE* 1.3 71.6 - - - +
49N SER* 1.3 62.2 + - - +
50N LEU 3.0 1.1 - - - -
51N SER* 3.3 18.7 + - - +
52N GLU* 3.2 29.0 + - - +
63N VAL* 4.3 5.8 - - - -
85N PRO* 2.8 41.8 + - + +
86N THR* 4.1 19.4 + - - +
88N HIS* 5.8 0.8 - - - -
42O ALA* 3.4 23.8 + - - +
43O ASP* 3.5 26.1 - - - +
46O ALA* 4.8 7.2 - - - +
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Residues in contact with SER 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M ARG* 6.0 1.6 - - - -
45N VAL* 3.7 15.1 - - - +
46N PRO* 2.2 40.0 + - - +
47N ILE 2.6 4.2 + - - -
48N ARG* 1.3 72.8 - - - +
50N LEU* 1.3 67.1 + - - +
51N SER 2.9 2.9 + - - -
52N GLU* 3.1 46.5 + - - +
56N PRO* 4.6 0.2 - - - +
217N TRP* 3.5 23.6 - - - -
221N PRO* 5.7 2.9 - - - -
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Residues in contact with LEU 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N LEU* 3.6 29.2 - - + -
47N ILE* 2.6 42.5 + - + +
49N SER* 1.3 79.8 + - - +
51N SER* 1.3 54.0 + - - +
56N PRO* 3.9 10.0 - - + +
57N GLU 3.1 13.9 + - - -
58N LEU* 3.0 26.3 + - + -
63N VAL* 3.9 17.7 - - + -
66N TYR* 4.2 17.5 - - + -
89N PHE* 3.9 22.4 - - + -
214N PHE* 4.7 2.0 - - + -
217N TRP* 4.1 23.1 - - + -
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Residues in contact with SER 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N ARG* 3.5 10.2 + - - +
49N SER 2.9 1.4 - - - -
50N LEU* 1.3 76.0 - - - +
52N GLU* 1.3 68.2 + - - +
53N PRO* 3.6 1.2 - - - +
57N GLU* 3.5 14.6 - - - +
58N LEU 3.4 16.8 + - - +
60N GLU* 4.2 19.6 - - - +
63N VAL* 2.9 31.2 - - - +
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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