Contacts of the helix formed by residues 51 - 61 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ALA* 3.1 13.3 + - - +
49D GLU* 4.2 26.4 - - + +
50D GLY* 1.3 76.1 - - - +
52D GLU* 1.3 67.5 + - - +
53D ASP* 3.4 3.5 - - + +
54D ASP* 3.3 38.6 + - + +
55D VAL* 3.4 13.8 + - - +
104D ALA* 4.1 0.4 - - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLY 3.5 12.3 + - - +
51D GLU* 1.3 73.8 - - - +
53D ASP* 1.3 81.8 + - - +
55D VAL* 3.0 16.3 + - - +
56D VAL* 3.2 17.1 + - - +
103D ASP* 5.2 2.9 - - - +
104D ALA* 4.0 25.5 - - - +
107D GLU* 3.6 34.0 - - + +
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Residues in contact with ASP 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU* 3.4 3.3 - - + +
52D GLU* 1.3 91.8 - - - +
54D ASP* 1.3 65.1 + - - +
56D VAL* 3.3 8.5 + - - +
57D GLU* 2.8 34.3 + - - +
107D GLU* 5.1 2.6 - - - +
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Residues in contact with ASP 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PRO 4.4 4.4 - - - +
43D ILE* 5.2 0.2 - - - -
46D ALA* 3.8 19.2 - - + +
49D GLU* 5.2 3.3 - - - +
51D GLU* 3.3 29.5 + - + +
52D GLU 3.3 0.4 - - - -
53D ASP* 1.3 82.1 - - - +
55D VAL* 1.3 59.4 + - - +
57D GLU* 4.0 15.7 - - - +
58D GLY* 2.9 24.7 + - - -
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 4.6 5.6 - - + +
46D ALA* 3.8 17.0 - - + -
47D ILE* 3.7 31.6 - - + -
51D GLU 3.4 15.5 - - - +
52D GLU* 3.0 10.7 + - - +
54D ASP* 1.3 74.5 - - - +
56D VAL* 1.3 59.1 + - + +
58D GLY 3.5 1.9 + - - -
59D LEU* 2.9 40.4 + - + +
77D LEU* 3.8 16.8 - - + -
104D ALA* 3.7 28.0 - - + +
108D GLY* 4.0 5.6 - - - -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU 3.2 11.9 + - - +
53D ASP* 3.6 8.5 - - - +
55D VAL* 1.3 75.1 - - + +
57D GLU* 1.3 58.9 + - - +
59D LEU* 2.8 27.0 + - - +
60D GLN* 2.8 37.8 + - - +
107D GLU* 4.6 26.5 - - + +
108D GLY* 5.4 1.1 - - - -
111D TYR* 4.0 31.2 - - + -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ASP* 2.8 23.9 + - - +
54D ASP* 4.0 17.7 - - - +
56D VAL* 1.3 74.3 - - - +
58D GLY* 1.3 60.1 + - - +
59D LEU 3.5 0.2 + - - -
60D GLN* 3.6 13.3 + - - +
61D ALA* 3.5 20.3 + - - +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU 4.7 1.4 - - - +
42D PRO* 5.4 7.0 - - - -
43D ILE* 3.3 30.3 - - - +
54D ASP 2.9 19.8 + - - -
55D VAL 3.7 2.2 - - - -
57D GLU* 1.3 76.7 - - - +
59D LEU* 1.3 58.6 + - - +
61D ALA* 4.2 5.7 - - - +
62D ALA* 3.7 13.5 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 4.3 12.8 - - + -
55D VAL* 2.9 29.6 + - + +
56D VAL* 2.8 14.4 + - - +
58D GLY* 1.3 72.7 - - - +
60D GLN* 1.3 59.0 + - - +
61D ALA 3.3 0.7 - - - -
62D ALA* 3.5 3.1 + - - +
63D ILE* 3.1 31.2 + - + +
72D LEU* 3.6 40.4 - - + +
77D LEU* 4.1 14.4 - - + -
108D GLY* 3.6 36.3 - - - +
111D TYR* 4.4 17.5 - - + -
112D CYS* 4.2 10.3 - - - -
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Residues in contact with GLN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 2.8 36.6 + - - +
57D GLU* 3.8 11.6 - - - +
58D GLY 3.5 0.2 - - - -
59D LEU* 1.3 77.0 - - - +
61D ALA* 1.3 58.3 + - - +
63D ILE* 3.4 14.7 - - - +
64D GLU* 3.1 34.5 - - - +
111D TYR* 3.0 30.1 + - + +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.1 4.8 - - + +
57D GLU 3.5 12.4 + - - +
58D GLY* 4.5 4.9 - - - +
59D LEU 3.3 0.4 - - - -
60D GLN* 1.3 78.8 - - - +
62D ALA* 1.3 57.7 + - - +
64D GLU* 3.9 6.9 - - - +
65D ALA* 3.1 30.3 + - - +
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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