Contacts of the helix formed by residues 40 - 50 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L PRO* 3.9 24.2 - - + -
37L ASP* 3.3 35.4 + - + +
39L LEU* 1.3 78.8 - - + +
41L TYR* 1.3 67.8 + - - +
42L PRO 3.6 0.2 - - - -
43L ILE* 3.2 11.1 + - - +
44L ALA* 3.2 13.6 + - + +
62L ALA* 6.6 0.2 - - + -
72L LEU* 5.0 9.2 - - + -
75L ASP* 3.3 39.7 - - + +
76L ALA* 3.8 18.8 - - + +
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Residues in contact with TYR 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L GLU* 3.0 37.9 + - - -
34L TYR* 4.0 22.0 - + + -
35L PRO 3.7 24.9 + - - +
36L LYS* 4.8 6.3 - - - +
38L GLU* 3.8 20.0 - - - +
40L ILE* 1.3 76.0 - - - +
42L PRO* 1.4 80.6 - - + +
43L ILE 2.8 1.9 + - - -
44L ALA* 3.0 15.3 + - - +
45L LYS* 3.1 34.8 + - + +
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Residues in contact with PRO 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L GLU 3.2 23.1 - - - +
39L LEU 3.5 11.4 - - - +
41L TYR* 1.4 96.0 - - + +
43L ILE* 1.3 55.4 + - + +
45L LYS* 4.1 5.1 - - + +
46L ALA* 3.1 28.2 + - - +
54L ASP* 4.6 4.4 - - - +
58L GLY* 5.1 11.7 - - - -
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Residues in contact with ILE 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L LEU 4.0 13.9 - - - +
40L ILE* 3.5 7.4 - - - +
41L TYR 2.8 2.0 + - - -
42L PRO* 1.3 77.3 - - + +
44L ALA* 1.3 58.9 + - - +
45L LYS 3.3 0.2 - - - -
46L ALA* 3.3 4.3 + - - +
47L ILE* 2.9 54.8 + - + +
54L ASP 5.2 1.8 - - - -
55L VAL* 4.6 7.0 - - + +
58L GLY* 3.5 37.9 - - - +
59L LEU* 3.8 17.0 - - + +
62L ALA* 4.4 8.3 - - + -
72L LEU* 4.9 1.1 - - + -
76L ALA* 3.7 35.2 - - + +
77L LEU* 4.1 9.9 - - + -
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Residues in contact with ALA 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L TYR* 3.7 17.9 - - + -
35L PRO* 3.8 30.1 - - + -
40L ILE* 3.2 4.9 + - + +
41L TYR* 3.0 8.8 + - - +
43L ILE* 1.3 77.9 - - - +
45L LYS* 1.3 58.3 + - - +
47L ILE* 3.4 2.9 + - - +
48L PHE* 3.0 26.9 + - - +
76L ALA 4.3 2.8 + - - +
80L GLY* 3.7 27.5 - - - +
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Residues in contact with LYS 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L GLU* 4.9 4.0 + - - -
34L TYR* 3.6 30.6 - - + +
41L TYR* 3.1 42.2 + - + +
42L PRO* 4.1 7.0 - - + +
44L ALA* 1.3 73.9 - - - +
46L ALA* 1.3 65.5 + - - +
48L PHE* 3.2 3.8 + - - +
49L GLU* 3.0 49.3 + - - +
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Residues in contact with ALA 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L PRO 3.1 21.3 + - - +
43L ILE 3.3 5.1 + - - +
45L LYS* 1.3 76.9 - - - +
47L ILE* 1.3 62.3 + - - +
49L GLU* 3.1 11.6 + - - -
50L GLY 3.0 18.2 + - - -
51L GLU* 3.0 12.4 + - - +
54L ASP* 3.8 29.4 - - + +
55L VAL* 3.7 19.7 - - + +
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Residues in contact with ILE 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ILE* 2.9 48.5 + - + +
44L ALA 3.7 3.1 - - - +
46L ALA* 1.3 74.1 - - - +
48L PHE* 1.3 55.6 + - - +
50L GLY* 3.1 7.1 + - - -
55L VAL* 3.7 20.4 - - + -
76L ALA 4.4 0.9 - - - +
77L LEU* 3.7 23.6 - - + +
80L GLY* 3.6 7.6 - - - +
81L MET* 3.6 40.2 - - + +
84L VAL* 4.3 5.6 - - + -
101L SER* 2.6 31.6 + - - +
104L ALA* 4.5 2.7 - - - -
105L MET* 4.5 21.1 - - + +
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Residues in contact with PHE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PRO* 3.5 32.8 - - + -
27L GLU* 4.4 19.3 - - + -
30L ALA* 3.7 11.4 - - + -
34L TYR* 3.1 31.9 - - + +
44L ALA 3.0 12.0 + - - +
45L LYS 3.2 3.1 + - - +
47L ILE* 1.3 76.5 - - - +
49L GLU* 1.3 73.1 + - + +
50L GLY 3.3 1.2 + - - -
80L GLY 5.5 0.4 - - - +
83L VAL* 4.8 4.0 - - + -
84L VAL* 3.9 23.7 - - + +
87L LEU* 3.7 25.6 - - + -
93L ILE* 4.1 16.5 - - + +
97L ASN* 5.0 5.2 - - - +
101L SER* 3.4 8.3 + - - -
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Residues in contact with GLU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LYS* 3.0 49.4 + - - +
46L ALA* 3.1 9.3 + - - +
48L PHE* 1.3 86.2 - - + +
50L GLY* 1.3 62.3 + - - +
51L GLU* 3.4 20.7 + - + +
54L ASP* 5.1 4.7 - - - +
100L MET* 4.0 15.5 - - - +
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Residues in contact with GLY 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L ALA 3.0 3.0 + - - -
47L ILE 3.1 14.1 + - - -
48L PHE 3.1 1.8 + - - -
49L GLU* 1.3 78.1 - - - +
51L GLU* 1.3 60.2 + - - +
52L GLU* 3.3 20.9 - - - +
100L MET* 3.7 38.9 - - - +
101L SER* 4.1 0.9 - - - -
104L ALA* 3.9 6.3 - - - -
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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