Contacts of the helix formed by residues 51 - 66 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ALA* 3.0 13.5 + - - +
49B GLU* 4.1 22.8 - - + +
50B GLY* 1.3 75.1 - - - +
52B GLU* 1.3 71.6 + - - +
53B ASP* 3.4 12.2 + - - +
54B ASP* 3.1 41.5 + - + +
55B VAL* 3.1 15.2 + - - +
104B ALA* 3.9 0.8 - - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 3.8 11.2 - - - +
51B GLU* 1.3 75.7 + - - +
53B ASP* 1.3 71.5 + - - +
55B VAL* 2.9 26.4 + - + +
56B VAL* 3.2 18.2 + - - +
100B MET 5.0 0.2 - - - +
103B ASP* 5.0 6.4 - - - +
104B ALA* 4.2 21.9 + - - +
107B GLU* 3.2 37.2 - - + +
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Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.4 11.5 + - - +
52B GLU* 1.3 87.0 - - - +
54B ASP* 1.3 69.4 + - - +
56B VAL* 4.1 4.1 + - - +
57B GLU* 3.6 23.0 + - - +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 4.6 3.7 - - - +
46B ALA* 3.9 16.7 - - + +
49B GLU* 5.1 4.2 - - - +
51B GLU* 3.1 28.9 + - + +
52B GLU 3.1 0.6 - - - -
53B ASP* 1.3 88.5 - - - +
55B VAL* 1.3 59.5 + - - +
57B GLU* 4.3 13.8 - - - +
58B GLY* 3.1 24.4 + - - -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 4.3 6.1 - - + +
46B ALA* 3.6 15.0 - - + -
47B ILE* 3.5 35.0 - - + -
51B GLU 3.1 18.8 - - - +
52B GLU* 2.9 15.8 + - - +
54B ASP* 1.3 77.3 - - - +
56B VAL* 1.3 60.5 + - + +
58B GLY* 3.5 1.0 + - - -
59B LEU* 3.0 46.0 + - + +
77B LEU* 4.1 7.4 - - + -
104B ALA* 4.0 15.7 - - + +
107B GLU 6.2 0.2 - - - -
108B GLY* 4.4 5.4 - - - -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU 3.2 13.3 + - - +
53B ASP* 4.4 4.9 - - - +
55B VAL* 1.3 73.9 - - + +
57B GLU* 1.3 54.9 + - - +
59B LEU* 2.9 11.2 + - + +
60B GLN* 2.8 58.9 + - - +
107B GLU* 4.6 21.8 - - - +
111B TYR* 3.8 33.0 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ASP 3.6 18.3 + - - +
54B ASP* 4.2 13.0 - - - +
56B VAL* 1.3 79.1 - - - +
58B GLY* 1.3 61.7 + - - +
60B GLN* 3.8 7.8 + - - +
61B ALA* 3.3 23.8 + - + +
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 4.5 2.8 - - - +
42B PRO* 5.1 11.0 - - - -
43B ILE* 3.4 26.4 - - - +
54B ASP 3.1 19.2 + - - -
55B VAL 3.9 0.9 - - - -
56B VAL 3.2 0.2 - - - -
57B GLU* 1.3 76.4 - - - +
59B LEU* 1.3 61.7 + - - +
61B ALA* 4.0 5.8 - - - +
62B ALA* 3.3 15.9 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 3.9 21.8 - - + -
55B VAL* 3.0 38.5 + - + +
56B VAL* 2.9 9.4 + - - +
58B GLY* 1.3 76.4 - - - +
60B GLN* 1.3 64.9 + - - +
62B ALA* 3.1 4.2 + - - +
63B ILE* 3.0 28.1 + - + +
72B LEU* 3.5 39.6 - - + +
76B ALA* 4.7 0.7 - - + -
77B LEU* 4.3 8.5 - - + -
108B GLY* 4.1 24.2 - - - +
111B TYR* 4.8 15.0 - - + -
112B CYS* 4.3 11.7 - - - -
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 2.8 34.8 + - - +
57B GLU* 4.0 7.6 - - - +
59B LEU* 1.3 71.8 - - - +
61B ALA* 1.3 63.2 + - - +
62B ALA 3.2 0.3 + - - -
63B ILE* 3.2 13.0 - - + +
64B GLU* 3.1 39.7 + - - +
111B TYR* 2.6 40.3 + - + +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 6.1 0.2 - - - -
57B GLU* 3.3 16.5 + - + +
58B GLY* 4.0 6.5 - - - +
59B LEU 3.3 0.4 - - - -
60B GLN* 1.3 76.9 - - - +
62B ALA* 1.3 56.7 + - - +
64B GLU* 3.8 7.8 - - - +
65B ALA* 3.1 31.4 + - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.6 26.6 - - + +
40B ILE* 6.3 0.4 - - + -
43B ILE* 4.1 14.6 - - + -
58B GLY 3.3 13.2 + - - +
59B LEU 3.1 9.7 + - - +
61B ALA* 1.3 76.0 - - - +
63B ILE* 1.3 55.8 + - - +
64B GLU 3.1 4.5 - - - -
65B ALA* 3.9 0.6 - - - -
66B GLY* 3.0 28.1 + - - -
67B LYS 4.0 4.0 - - - +
72B LEU* 4.2 18.2 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.0 20.4 + - + +
60B GLN* 3.2 20.6 - - + +
62B ALA* 1.3 76.3 - - - +
64B GLU* 1.3 56.9 + - + +
66B GLY 2.7 18.0 - - - +
67B LYS* 3.1 25.6 - - - +
69B PRO* 3.9 21.3 - - + -
72B LEU* 3.9 17.5 - - + -
111B TYR* 4.4 8.1 - - + -
115B ASN* 3.6 29.2 - - + +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN* 3.1 31.8 + - - +
61B ALA* 3.8 7.9 - - - +
62B ALA 3.1 0.4 - - - -
63B ILE* 1.3 80.6 - - + +
65B ALA* 1.3 59.6 + - - +
66B GLY 3.3 5.8 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.3 19.0 - - + +
61B ALA 3.1 17.3 + - - +
62B ALA* 4.7 1.1 - - - +
64B GLU* 1.3 75.5 - - - +
66B GLY* 1.3 55.9 + - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.4 5.8 - - - -
62B ALA 3.0 14.9 + - - -
63B ILE 2.7 20.4 - - - +
64B GLU 3.9 2.8 - - - +
65B ALA* 1.3 78.4 - - - +
67B LYS* 1.3 70.2 + - - +
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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