Contacts of the helix formed by residues 40 - 49 (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 ILE 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35F PRO* 3.6 27.4 - - + -
37F ASP* 3.4 28.5 + - + +
39F LEU* 1.3 80.6 - - + +
41F TYR* 1.3 66.2 + - - +
42F PRO 3.3 0.2 - - - -
43F ILE* 2.8 20.5 + - - +
44F ALA* 3.0 13.0 + - + -
72F LEU* 5.1 8.3 - - + -
75F ASP* 3.4 37.7 - - + +
76F ALA* 3.8 20.4 - - + +
79F VAL* 5.4 0.4 - - + -
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Residues in contact with TYR 41 (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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31F GLU* 2.8 39.2 + - - -
34F TYR* 3.6 26.0 - + + -
35F PRO 3.6 25.9 + - - +
36F LYS* 5.1 4.0 - - - -
37F ASP 4.9 0.4 - - - +
38F GLU* 4.0 19.0 - - - +
40F ILE* 1.3 78.4 - - - +
42F PRO* 1.4 76.6 - - + +
44F ALA* 3.1 5.5 + - - +
45F LYS* 3.0 47.8 + - + +
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Residues in contact with PRO 42 (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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38F GLU 3.4 23.3 - - - +
39F LEU* 3.6 7.6 - - - +
40F ILE 3.4 5.2 - - - -
41F TYR* 1.4 101.7 - - + +
43F ILE* 1.3 58.4 + - + +
45F LYS* 4.0 7.8 - - + +
46F ALA* 3.1 26.3 + - - +
54F ASP* 4.5 3.6 - - - +
58F GLY* 5.4 7.4 - - - -
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Residues in contact with ILE 43 (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 3.5 18.6 - - - +
40F ILE* 2.8 7.2 + - - +
42F PRO* 1.3 77.1 - - + +
44F ALA* 1.3 65.7 + - - +
46F ALA* 3.0 8.0 + - - +
47F ILE* 2.9 28.5 + - + +
54F ASP 5.1 1.3 - - - -
55F VAL* 4.6 5.8 - - + +
58F GLY* 3.3 39.7 - - - +
59F LEU* 4.1 13.2 - - + +
62F ALA* 4.2 8.7 - - + -
72F LEU* 4.6 1.8 - - + -
76F ALA* 3.9 28.5 - - + -
77F LEU* 3.8 29.4 - - + -
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Residues in contact with ALA 44 (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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34F TYR* 3.6 18.2 - - + -
35F PRO* 3.7 36.3 - - + -
40F ILE* 3.0 9.7 + - + +
41F TYR* 3.5 8.5 - - - +
43F ILE* 1.3 77.5 - - - +
45F LYS* 1.3 59.4 + - - +
47F ILE* 3.6 3.6 + - - +
48F PHE* 3.3 17.0 + - - +
76F ALA 4.6 2.2 + - - -
80F GLY* 3.9 26.6 - - - +
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Residues in contact with LYS 45 (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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31F GLU* 5.4 2.6 + - - -
34F TYR* 3.5 31.3 - - + +
41F TYR* 3.0 43.1 + - + +
42F PRO* 4.0 6.7 - - + +
44F ALA* 1.3 74.3 - - - +
46F ALA* 1.3 66.5 + - - +
48F PHE* 3.3 3.8 + - - +
49F GLU* 3.0 47.8 + - - +
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Residues in contact with ALA 46 (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 3.1 20.9 + - - +
43F ILE 3.0 6.5 + - - +
45F LYS* 1.3 76.6 - - - +
47F ILE* 1.3 60.0 + - - +
49F GLU* 3.4 8.8 + - - -
50F GLY 3.1 3.3 + - - -
51F GLU* 3.0 28.6 + - - +
54F ASP* 3.6 41.5 - - + +
55F VAL* 3.8 10.3 - - + +
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Residues in contact with ILE 47 (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* 2.9 19.8 + - + +
44F ALA 3.8 6.1 - - - +
45F LYS 3.3 0.2 - - - -
46F ALA* 1.3 74.0 - - - +
48F PHE* 1.3 56.2 + - - +
50F GLY* 2.9 12.3 + - - -
55F VAL* 3.7 21.8 - - + -
76F ALA 5.2 0.2 - - - +
77F LEU* 3.6 39.7 - - + +
80F GLY* 3.4 32.8 - - - +
81F MET* 3.6 14.1 - - - +
84F VAL* 3.9 8.3 - - + -
101F SER* 2.6 33.7 + - - +
104F ALA* 4.4 2.0 - - - +
105F MET* 4.2 19.7 - - + -
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Residues in contact with PHE 48 (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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26F PRO* 3.8 18.2 - - + -
27F GLU* 4.3 22.9 - - + -
30F ALA* 3.6 19.1 - - + -
34F TYR* 3.4 28.5 - - + +
44F ALA 3.3 7.6 + - - +
45F LYS 3.3 4.1 + - - +
47F ILE* 1.3 78.3 - - - +
49F GLU* 1.3 69.7 + - + +
50F GLY 3.2 0.2 - - - -
80F GLY 5.3 1.1 - - - +
83F VAL* 4.6 2.7 - - + -
84F VAL* 3.7 20.9 - - + -
87F LEU* 3.5 27.1 - - + -
93F ILE* 3.9 26.2 - - + -
97F ASN* 4.6 6.1 - - - +
101F SER* 3.3 14.2 + - - -
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Residues in contact with GLU 49 (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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27F GLU* 6.5 1.3 - - + -
45F LYS* 3.0 52.4 + - - +
46F ALA* 3.8 7.6 - - - +
47F ILE 3.2 0.4 - - - -
48F PHE* 1.3 86.6 - - + +
50F GLY* 1.3 62.5 + - - +
51F GLU* 3.4 24.7 + - + +
54F ASP* 5.0 5.9 - - - +
100F MET* 4.4 13.1 - - - +
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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