Contacts of the helix formed by residues 40 - 50 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35P PRO* 3.8 26.5 - - + -
37P ASP* 3.3 37.1 + - + +
39P LEU* 1.3 79.5 - - + +
41P TYR* 1.3 53.3 + - - +
43P ILE* 2.8 32.2 + - - +
44P ALA* 3.2 10.2 + - + -
72P LEU* 5.0 8.1 - - + -
75P ASP* 3.6 36.3 - - + +
76P ALA* 3.8 18.4 - - + +
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Residues in contact with TYR 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P GLU* 2.7 40.2 + - - -
34P TYR* 3.6 28.1 - + + -
35P PRO 3.5 24.2 + - - +
36P LYS* 4.5 9.9 - - + -
37P ASP 4.6 0.4 - - - +
38P GLU* 4.1 17.6 - - - +
40P ILE* 1.3 77.7 - - - +
42P PRO* 1.4 74.1 - - + +
44P ALA* 3.6 4.8 + - - +
45P LYS* 3.2 42.0 + - + +
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Residues in contact with PRO 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLU 3.3 18.2 - - - +
39P LEU* 3.2 20.0 - - - +
40P ILE 3.4 0.4 - - - -
41P TYR* 1.4 98.8 - - + +
43P ILE* 1.3 55.7 + - + +
45P LYS* 4.0 5.1 - - + +
46P ALA* 3.1 28.1 + - - +
54P ASP* 4.6 3.4 - - - +
58P GLY* 5.0 13.2 - - - +
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Residues in contact with ILE 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P LEU 3.5 20.9 - - - +
40P ILE* 2.8 8.9 + - - +
42P PRO* 1.3 74.5 - - + +
44P ALA* 1.3 58.3 + - - +
46P ALA* 3.2 7.5 + - - +
47P ILE* 2.9 34.3 + - + +
54P ASP 5.2 0.7 - - - -
55P VAL* 4.2 8.0 - - + +
58P GLY* 3.8 28.5 - - - +
59P LEU* 3.8 22.0 - - + +
62P ALA* 4.1 10.3 - - + -
72P LEU* 4.5 2.9 - - + -
76P ALA* 3.8 26.7 - - + -
77P LEU* 3.5 31.6 - - + -
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Residues in contact with ALA 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P TYR* 3.8 11.3 - - + -
35P PRO* 3.8 31.2 - - + -
40P ILE* 3.2 5.3 + - + +
41P TYR* 4.0 6.7 - - - +
43P ILE* 1.3 79.2 - - - +
45P LYS* 1.3 56.1 + - - +
47P ILE* 3.2 7.3 + - - +
48P PHE* 3.0 27.7 + - - +
76P ALA 4.7 4.6 + - - +
80P GLY* 3.7 29.9 - - - +
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Residues in contact with LYS 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P GLU* 5.0 4.2 + - - +
34P TYR* 3.4 32.8 - - + +
41P TYR* 3.2 41.4 + - + +
42P PRO* 4.2 4.9 - - + +
44P ALA* 1.3 76.2 - - - +
46P ALA* 1.3 64.1 + - - +
48P PHE* 3.9 1.4 - - - +
49P GLU* 3.2 49.7 + - - +
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Residues in contact with ALA 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P PRO 3.1 19.3 + - - +
43P ILE 3.2 2.2 + - - +
45P LYS* 1.3 76.3 - - - +
47P ILE* 1.3 65.4 + - - +
49P GLU* 3.4 5.4 + - - -
50P GLY* 3.1 17.8 + - - -
51P GLU* 3.2 13.3 + - - +
54P ASP* 3.6 29.6 - - + +
55P VAL* 3.5 26.5 - - + +
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Residues in contact with ILE 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P ILE* 2.9 29.5 + - + +
44P ALA* 3.5 7.2 - - - +
46P ALA* 1.3 75.0 - - - +
48P PHE* 1.3 60.2 + - - +
50P GLY* 3.1 9.2 + - - -
55P VAL* 3.7 12.5 - - + +
76P ALA 4.3 3.1 - - - +
77P LEU* 3.5 45.5 - - + +
80P GLY* 3.6 26.5 - - - +
81P MET* 3.8 22.7 - - - +
84P VAL* 4.1 3.4 - - + -
101P SER* 2.9 25.5 + - - +
104P ALA* 4.9 2.9 - - - -
105P MET* 4.2 19.3 - - + +
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Residues in contact with PHE 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PRO* 3.7 29.6 - - + -
27P GLU* 4.3 21.8 - - + -
30P ALA* 3.8 12.8 - - + -
34P TYR* 3.3 31.2 - - + +
44P ALA 3.0 13.5 + - - +
45P LYS 3.9 0.7 - - - +
46P ALA 3.4 0.2 - - - -
47P ILE* 1.3 76.6 - - - +
49P GLU* 1.3 72.7 + - + +
50P GLY 3.2 0.9 + - - -
80P GLY 5.4 0.2 - - - +
83P VAL* 4.9 2.7 - - + -
84P VAL* 3.7 24.5 - - + -
87P LEU* 3.6 24.7 - - + -
93P ILE* 3.9 20.1 - - + +
97P ASN* 5.0 6.5 - - + +
101P SER* 3.5 7.6 + - - -
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Residues in contact with GLU 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P GLU* 5.9 4.0 - - + +
34P TYR* 5.2 0.2 + - - -
45P LYS* 3.2 51.7 + - + +
46P ALA* 4.1 5.1 - - - +
47P ILE 3.2 0.4 - - - -
48P PHE* 1.3 90.5 - - + +
50P GLY* 1.3 63.2 + - - +
51P GLU* 3.2 18.1 + - + +
54P ASP* 5.3 3.5 - - - +
100P MET* 4.4 13.5 - - - +
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Residues in contact with GLY 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ALA 3.1 1.7 + - - -
47P ILE 3.1 15.0 + - - -
48P PHE 3.2 2.0 + - - -
49P GLU* 1.3 78.0 - - - +
51P GLU* 1.3 60.0 + - - +
52P GLU* 3.4 14.9 + - - +
100P MET* 3.6 40.8 - - - +
104P ALA* 3.8 8.9 - - - +
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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