Contacts of the helix formed by residues 40 - 49 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H PRO* 3.5 22.7 - - + -
37H ASP* 2.8 39.2 + - + +
39H LEU* 1.3 73.7 - - + +
41H TYR* 1.3 65.2 + - - +
43H ILE* 3.2 10.6 + - + +
44H ALA* 3.0 21.2 + - + +
72H LEU* 5.6 4.9 - - + -
75H ASP* 3.5 39.9 - - + +
76H ALA* 3.9 17.7 - - + -
79H VAL* 4.8 2.7 - - + -
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Residues in contact with TYR 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H GLU* 2.6 38.8 + - - -
34H TYR* 3.5 28.6 - + + -
35H PRO* 3.5 30.9 - - - +
36H LYS* 5.4 2.5 - - - -
37H ASP* 4.3 0.4 - - - +
38H GLU* 3.7 21.3 - - - +
40H ILE* 1.3 78.6 - - - +
42H PRO* 1.4 74.3 - - + +
43H ILE 3.2 0.2 + - - -
44H ALA* 3.3 2.0 + - - +
45H LYS* 3.1 49.9 + - + +
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Residues in contact with PRO 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H GLU 3.3 19.5 - - - +
39H LEU* 3.2 19.1 - - - +
41H TYR* 1.4 99.3 - - + +
43H ILE* 1.3 59.7 + - + +
45H LYS* 4.2 6.0 - - + +
46H ALA* 3.6 20.8 + - - +
54H ASP 4.1 4.9 - - - +
58H GLY* 5.2 8.1 - - - -
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Residues in contact with ILE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU 3.4 20.6 - - - +
40H ILE* 3.6 6.5 - - + +
41H TYR 3.1 0.4 - - - -
42H PRO* 1.3 76.9 - - + +
44H ALA* 1.3 58.9 + - - +
46H ALA* 3.1 6.1 + - - +
47H ILE* 3.0 46.4 + - + +
54H ASP 5.1 2.0 - - - -
55H VAL* 4.8 4.5 - - + +
58H GLY* 3.3 37.0 - - - +
59H LEU* 4.4 12.1 - - + -
62H ALA* 4.4 9.4 - - + -
72H LEU* 5.2 2.9 - - + -
76H ALA* 3.4 41.3 - - + +
77H LEU* 3.9 9.9 - - + -
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Residues in contact with ALA 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H TYR* 3.8 11.3 - - + -
35H PRO* 3.7 28.3 - - + -
40H ILE* 3.0 18.2 + - + +
41H TYR 3.8 3.4 - - - +
43H ILE* 1.3 75.4 - - - +
45H LYS* 1.3 59.7 - - - +
47H ILE* 4.0 3.1 - - - +
48H PHE* 3.3 21.7 + - - +
76H ALA 4.3 2.0 + - - +
80H GLY* 3.7 32.7 - - - +
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Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H GLU* 4.9 4.9 + - - -
34H TYR* 3.3 30.7 - - + +
41H TYR* 3.1 44.8 + - + +
42H PRO* 4.4 6.1 - - + +
44H ALA* 1.3 75.6 - - - +
46H ALA* 1.3 59.7 + - - +
48H PHE* 3.3 2.8 + - - +
49H GLU* 2.9 57.2 + - + +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H PRO 3.6 11.7 + - - +
43H ILE 3.1 4.6 + - - +
45H LYS* 1.3 77.0 - - - +
47H ILE* 1.3 61.7 + - - +
49H GLU* 3.5 7.7 + - - -
50H GLY 3.1 2.1 + - - -
51H GLU* 2.7 35.2 + - - +
54H ASP* 3.3 47.3 - - + +
55H VAL* 3.8 5.6 - - + +
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Residues in contact with ILE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H ILE* 3.0 48.1 + - + +
44H ALA* 4.0 4.0 - - - +
46H ALA* 1.3 75.7 - - - +
48H PHE* 1.3 53.3 + - - +
50H GLY* 2.8 14.4 + - - -
55H VAL* 3.5 29.8 - - + -
76H ALA 4.4 3.1 - - - +
77H LEU* 3.9 15.9 - - + +
80H GLY 3.5 28.5 - - - +
81H MET* 3.8 23.6 - - + +
84H VAL* 4.4 1.6 - - + -
101H SER* 2.8 28.9 + - - +
104H ALA* 4.6 9.9 - - - +
105H MET* 4.7 9.4 - - + +
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Residues in contact with PHE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PRO* 4.0 20.0 - - + -
27H GLU* 4.6 14.4 - - + -
30H ALA* 3.8 18.2 - - + -
34H TYR* 3.6 22.7 - - + +
44H ALA 3.3 14.3 + - - +
45H LYS 3.3 3.2 + - - +
47H ILE* 1.3 80.0 - - - +
49H GLU* 1.3 70.4 + - + +
50H GLY 3.0 0.2 - - - -
80H GLY 4.9 0.9 - - - +
83H VAL* 4.8 2.7 - - + -
84H VAL* 3.6 24.0 - - + -
87H LEU* 3.3 28.0 - - + -
93H ILE* 4.0 27.6 - - + -
97H ASN* 4.9 5.0 - - + +
100H MET* 5.7 1.6 - - - +
101H SER* 3.2 14.9 + - - -
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LYS* 2.9 50.9 + - + +
46H ALA* 3.9 8.9 - - - +
48H PHE* 1.3 84.8 - - + +
50H GLY* 1.3 62.9 + - - +
51H GLU* 3.2 18.1 + - + +
100H MET* 4.1 15.0 - - - +
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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