Contacts of the helix formed by residues 51 - 61 (chain N) in PDB entry 2I2X
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 51 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46N ALA* 3.2 10.4 + - - +
49N GLU* 4.3 20.0 - - + +
50N GLY* 1.3 77.7 - - - +
52N GLU* 1.3 72.1 + - - +
53N ASP* 3.3 6.7 - - + +
54N ASP* 3.3 30.6 + - + +
55N VAL* 3.3 24.0 + - - +
104N ALA* 4.0 0.2 - - - +
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Residues in contact with GLU 52 (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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50N GLY 3.7 11.6 + - - +
51N GLU* 1.3 80.4 - - - +
53N ASP* 1.3 70.4 + - - +
54N ASP 3.2 0.2 - - - -
55N VAL* 3.3 9.3 + - - +
56N VAL* 3.1 32.8 + - + +
103N ASP* 4.4 12.5 - - - +
104N ALA* 4.0 20.1 + - - +
107N GLU* 3.3 36.8 - - + +
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Residues in contact with ASP 53 (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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51N GLU* 3.3 5.2 - - + +
52N GLU* 1.3 91.0 + - - +
54N ASP* 1.3 65.3 + - - +
56N VAL* 4.1 5.7 + - - +
57N GLU* 3.2 26.4 + - - +
107N GLU* 5.2 2.1 - - - +
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Residues in contact with ASP 54 (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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42N PRO 4.9 2.1 - - - +
43N ILE* 5.4 0.2 - - - -
46N ALA* 3.8 22.0 - - + +
51N GLU* 3.3 26.2 + - + +
52N GLU 3.2 0.6 - - - -
53N ASP* 1.3 82.7 - - - +
55N VAL* 1.3 60.0 + - - +
56N VAL 3.4 0.2 - - - -
57N GLU* 4.0 14.1 - - - +
58N GLY* 2.9 26.6 + - - -
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Residues in contact with VAL 55 (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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43N ILE* 5.0 6.3 - - + +
46N ALA* 3.6 19.5 - - + -
47N ILE* 3.8 19.7 - - + +
51N GLU 3.3 15.1 + - - +
52N GLU 3.3 8.2 + - - +
54N ASP* 1.3 75.8 - - - +
56N VAL* 1.3 59.5 + - + +
58N GLY* 3.7 1.1 + - - -
59N LEU* 3.1 34.0 + - + +
77N LEU* 3.8 26.9 - - + -
104N ALA* 3.5 32.1 - - + +
108N GLY* 4.3 7.2 - - - -
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Residues in contact with VAL 56 (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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52N GLU* 3.1 19.1 + - + +
53N ASP* 4.5 5.6 - - - +
55N VAL* 1.3 79.5 - - + +
57N GLU* 1.3 62.2 + - - +
59N LEU* 3.3 17.5 + - - +
60N GLN* 3.3 34.9 + - - +
107N GLU* 4.2 20.6 - - - +
108N GLY* 5.2 2.0 - - - -
111N TYR* 3.6 38.0 - - + -
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Residues in contact with GLU 57 (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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53N ASP 3.2 18.7 + - - +
54N ASP* 4.0 15.1 - - - +
55N VAL 3.4 0.2 - - - -
56N VAL* 1.3 79.9 - - - +
58N GLY* 1.3 60.5 + - - +
60N GLN* 3.5 21.8 + - - +
61N ALA* 3.6 12.0 + - - +
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Residues in contact with GLY 58 (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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39N LEU 5.1 1.6 - - - +
42N PRO* 5.4 7.9 - - - -
43N ILE* 3.4 32.7 - - - +
54N ASP 2.9 19.9 + - - -
55N VAL* 3.9 1.1 - - - -
57N GLU* 1.3 74.3 - - - +
59N LEU* 1.3 61.9 + - - +
60N GLN 3.3 0.8 + - - -
61N ALA* 3.9 8.6 + - - +
62N ALA* 3.8 10.2 + - - +
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Residues in contact with LEU 59 (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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43N ILE* 4.7 8.1 - - + -
55N VAL* 3.1 29.9 + - + +
56N VAL* 3.3 7.6 + - - +
58N GLY* 1.3 77.1 - - - +
60N GLN* 1.3 57.6 + - - +
61N ALA 3.5 0.2 - - - -
62N ALA* 3.4 5.6 + - - +
63N ILE* 3.0 37.6 + - + +
72N LEU* 3.6 39.0 - - + +
77N LEU* 4.0 29.8 - - + -
108N GLY* 4.1 20.0 - - - +
111N TYR* 4.1 22.2 - - + -
112N CYS* 4.5 8.7 - - - -
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Residues in contact with GLN 60 (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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56N VAL* 3.3 29.4 + - - +
57N GLU* 3.8 15.3 - - - +
58N GLY 3.3 0.4 - - - -
59N LEU* 1.3 75.3 - - - +
61N ALA* 1.3 59.4 + - - +
62N ALA 3.1 2.0 + - - -
63N ILE* 4.2 8.3 - - + +
64N GLU* 3.0 46.1 + - - +
111N TYR* 2.7 32.2 + - + +
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Residues in contact with ALA 61 (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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57N GLU 3.6 10.5 + - - +
58N GLY* 4.3 9.4 - - - +
59N LEU 3.5 0.2 - - - -
60N GLN* 1.3 77.4 - - - +
62N ALA* 1.3 57.0 + - - +
63N ILE 3.8 0.2 - - - -
64N GLU* 3.9 4.7 - - - -
65N ALA* 3.0 32.4 + - - +
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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