Contacts of the helix formed by residues 51 - 65 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46F ALA 3.0 12.2 + - - +
49F GLU* 4.4 24.7 - - + +
50F GLY* 1.3 77.9 - - - +
52F GLU* 1.3 68.2 + - - +
53F ASP* 5.0 3.4 - - + +
54F ASP* 3.0 44.9 + - + +
55F VAL* 3.1 15.9 + - - +
104F ALA* 4.0 0.2 - - - +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLY 3.7 11.4 + - - +
51F GLU* 1.3 77.5 - - - +
53F ASP* 1.3 84.9 + - - +
55F VAL* 3.3 10.6 + - - +
56F VAL* 3.1 28.7 + - - +
103F ASP 5.2 0.4 - - - +
104F ALA* 4.0 17.9 - - - +
107F GLU* 3.8 34.8 - - + +
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Residues in contact with ASP 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLU* 3.4 3.5 - - + +
52F GLU* 1.3 99.3 + - - +
54F ASP* 1.3 65.1 + - - +
56F VAL* 4.1 4.5 - - - +
57F GLU* 3.1 31.7 + - - +
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Residues in contact with ASP 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PRO* 4.5 3.4 - - - +
43F ILE* 5.1 0.3 - - - -
46F ALA* 3.6 21.1 - - + +
49F GLU* 5.0 5.0 - - - +
51F GLU* 3.0 31.5 + - + +
53F ASP* 1.3 82.1 - - - +
55F VAL* 1.3 59.8 + - - +
57F GLU* 4.4 12.7 - - - +
58F GLY* 3.1 22.6 + - - -
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Residues in contact with VAL 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ILE* 4.6 5.1 - - + +
46F ALA* 3.8 18.2 - - + +
47F ILE* 3.7 17.5 - - + -
51F GLU 3.3 18.4 - - - +
52F GLU 3.3 6.3 + - - +
54F ASP* 1.3 75.8 - - - +
56F VAL* 1.3 56.8 + - + +
58F GLY 3.2 1.9 + - - -
59F LEU* 2.8 38.7 + - + +
77F LEU* 3.6 28.5 - - + -
104F ALA* 3.5 30.1 - - + +
108F GLY* 4.0 11.7 - - - -
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Residues in contact with VAL 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLU 3.1 15.3 + - - +
53F ASP* 4.1 4.7 - - - +
55F VAL* 1.3 77.9 - - + +
57F GLU* 1.3 58.6 + - - +
59F LEU* 3.0 11.1 + - - +
60F GLN* 2.8 45.9 + - - +
107F GLU* 4.4 27.8 - - + +
108F GLY* 4.9 4.5 - - - -
111F TYR* 4.0 34.5 - - + -
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ASP 3.1 21.2 + - - +
54F ASP* 4.4 11.6 - - - +
56F VAL* 1.3 75.7 - - - +
58F GLY* 1.3 60.2 + - - +
60F GLN* 3.4 24.4 + - - +
61F ALA* 3.3 22.9 + - - +
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Residues in contact with GLY 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU 4.5 2.8 - - - +
42F PRO* 5.4 7.2 - - - -
43F ILE* 3.3 29.8 - - - +
54F ASP 3.1 21.0 + - - -
55F VAL 3.2 2.6 + - - -
57F GLU* 1.3 77.4 - - - +
59F LEU* 1.3 59.1 + - - +
61F ALA* 4.1 5.9 + - - +
62F ALA* 3.5 12.8 + - - +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ILE* 4.1 14.4 - - + -
55F VAL* 2.8 18.2 + - + +
56F VAL* 3.0 8.0 + - - +
58F GLY* 1.3 76.5 - - - +
60F GLN* 1.3 63.2 + - - +
62F ALA* 3.1 5.1 + - - +
63F ILE* 3.1 31.1 + - + +
72F LEU* 3.7 36.3 - - + +
76F ALA* 5.0 0.7 - - + -
77F LEU* 4.1 24.2 - - + -
108F GLY* 3.3 34.8 - - - +
111F TYR* 4.3 15.9 - - + -
112F CYS* 3.9 12.1 - - - -
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Residues in contact with GLN 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 2.8 34.7 + - - +
57F GLU* 3.4 28.8 - - - +
59F LEU* 1.3 73.0 - - - +
61F ALA* 1.3 63.3 + - - +
63F ILE* 3.2 7.2 + - - +
64F GLU* 3.1 40.1 + - - +
111F TYR* 3.4 25.3 + - - +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.4 5.8 - - + +
57F GLU 3.3 12.6 + - - +
58F GLY* 4.2 6.3 - - - +
60F GLN* 1.3 79.1 - - - +
62F ALA* 1.3 61.1 + - - +
64F GLU* 3.8 10.0 + - - +
65F ALA* 3.4 25.5 + - - +
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Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.6 23.1 - - + +
43F ILE* 4.2 7.2 - - + -
58F GLY 3.5 13.0 + - - +
59F LEU 3.1 10.2 + - - +
61F ALA* 1.3 76.1 - - - +
63F ILE* 1.3 65.2 + - - +
65F ALA* 3.6 1.6 + - - +
66F GLY* 3.4 20.6 + - - -
67F LYS 4.0 5.9 + - - +
72F LEU* 3.8 29.4 - - + -
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F LEU* 3.1 20.8 + - + +
60F GLN* 3.8 7.4 - - - +
62F ALA* 1.3 74.9 - - - +
64F GLU* 1.3 60.1 + - + +
66F GLY 2.9 24.1 - - - +
67F LYS* 4.3 14.6 - - - +
68F ASP 4.4 0.4 - - - +
69F PRO* 3.9 35.9 - - + +
72F LEU* 4.0 12.5 - - + +
111F TYR* 5.6 4.3 - - + -
112F CYS* 5.9 3.8 - - - -
115F ASN* 4.3 21.8 - - + +
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F GLN* 3.1 36.9 + - - +
61F ALA* 3.6 10.3 + - - +
62F ALA 3.3 0.4 - - - -
63F ILE* 1.3 78.0 - - + +
65F ALA* 1.3 58.0 + - - +
66F GLY 3.6 0.2 - - - -
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.0 26.7 - - + +
61F ALA 3.4 16.3 + - - +
62F ALA 3.6 1.3 + - - +
63F ILE 3.3 0.4 - - - -
64F GLU* 1.3 78.3 - - + +
66F GLY* 1.3 57.0 + - - +
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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