Contacts of the helix formed by residues 40 - 50 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35J PRO* 3.7 23.8 - - + -
37J ASP* 3.6 33.7 + - + +
39J LEU* 1.3 80.5 - - + +
41J TYR* 1.3 55.4 + - - +
42J PRO* 3.3 2.5 - - - -
43J ILE* 2.8 29.9 + - - +
44J ALA* 3.2 8.6 + - + +
72J LEU* 4.9 8.7 - - + -
75J ASP* 3.5 39.3 - - + +
76J ALA* 3.8 20.9 - - + +
79J VAL* 5.3 0.4 - - + -
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Residues in contact with TYR 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLU* 2.8 36.8 + - - -
34J TYR* 3.8 25.8 - + + -
35J PRO* 3.3 27.0 + - - +
36J LYS* 4.4 9.2 - - + -
38J GLU* 3.7 19.1 - - - +
40J ILE* 1.3 77.1 - - - +
42J PRO* 1.4 75.5 - - + +
43J ILE 3.2 0.2 + - - -
44J ALA* 3.5 5.8 + - - +
45J LYS* 3.0 47.0 + - + +
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Residues in contact with PRO 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J GLU 3.4 22.2 - - - +
39J LEU 3.8 7.6 - - - +
40J ILE 3.4 5.4 - - - -
41J TYR* 1.4 104.0 - - + +
43J ILE* 1.3 57.5 + - + +
45J LYS* 3.9 5.9 - - + +
46J ALA* 3.0 27.7 + - - +
54J ASP* 4.7 3.4 - - - +
58J GLY* 5.4 7.9 - - - -
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Residues in contact with ILE 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J LEU 3.6 17.7 - - - +
40J ILE* 2.8 10.9 + - - +
42J PRO* 1.3 77.3 - - + +
44J ALA* 1.3 59.2 + - - +
46J ALA* 3.1 6.6 + - - +
47J ILE* 2.9 38.8 + - + +
54J ASP 5.4 0.7 - - - -
55J VAL* 4.7 7.0 - - + +
58J GLY* 3.6 35.2 - - - +
59J LEU* 4.2 15.3 - - + +
62J ALA* 4.2 8.5 - - + -
72J LEU* 4.6 2.0 - - + -
76J ALA* 3.7 29.6 - - + +
77J LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J TYR* 3.8 23.1 - - + -
35J PRO* 4.0 19.7 - - + -
40J ILE* 3.2 6.2 + - + +
41J TYR 3.8 5.8 - - - +
43J ILE* 1.3 78.0 - - - +
45J LYS* 1.3 56.3 + - - +
47J ILE* 3.1 6.0 + - - +
48J PHE* 2.9 27.5 + - - +
76J ALA 4.5 2.8 + - - +
80J GLY* 3.6 32.1 - - - +
83J VAL* 5.4 0.2 - - + -
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Residues in contact with LYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLU* 4.7 4.9 + - - -
34J TYR* 3.7 31.8 - - + +
41J TYR* 3.0 47.5 + - + +
42J PRO* 4.1 6.5 - - + +
44J ALA* 1.3 74.0 - - - +
46J ALA* 1.3 63.5 + - - +
48J PHE* 3.6 1.0 + - - +
49J GLU* 3.2 48.9 + - + +
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Residues in contact with ALA 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J PRO 3.0 20.3 + - - +
43J ILE 3.6 4.5 - - - +
45J LYS* 1.3 74.3 - - - +
47J ILE* 1.3 59.8 + - - +
49J GLU* 3.8 5.6 - - - +
50J GLY* 3.0 6.4 + - - -
51J GLU* 3.0 29.7 + - - +
54J ASP* 3.4 33.7 - - + -
55J VAL* 3.6 21.5 - - + +
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Residues in contact with ILE 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J ILE* 2.9 32.0 + - + +
44J ALA* 3.1 6.9 + - - +
46J ALA* 1.3 73.9 - - - +
48J PHE* 1.3 59.3 + - - +
50J GLY* 3.1 8.3 + - - +
55J VAL* 4.2 12.1 - - + -
76J ALA 4.4 1.8 - - - +
77J LEU* 3.7 44.2 - - + +
80J GLY 3.6 25.8 - - - +
81J MET* 3.8 10.3 - - - +
84J VAL* 3.9 10.1 - - + -
101J SER* 2.7 38.8 + - - +
104J ALA* 4.9 1.6 - - - -
105J MET* 4.2 18.8 - - + -
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Residues in contact with PHE 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J PRO* 3.5 31.2 - - + -
27J GLU* 4.1 22.4 - - + -
30J ALA* 3.8 12.1 - - + -
34J TYR* 3.3 30.3 - - + +
44J ALA 2.9 12.0 + - - +
45J LYS 3.9 1.3 - - - +
47J ILE* 1.3 77.0 - - - +
49J GLU* 1.3 74.3 + - + +
50J GLY 3.3 0.9 + - - -
80J GLY 5.7 0.2 - - - +
83J VAL* 5.2 2.0 - - + -
84J VAL* 3.9 16.8 - - + -
87J LEU* 3.7 27.8 - - + -
93J ILE* 4.0 17.5 - - + -
97J ASN* 4.8 5.4 - - - +
100J MET* 6.1 0.2 - - - +
101J SER* 3.4 10.8 + - - -
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Residues in contact with GLU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLU* 6.1 0.3 - - - +
45J LYS* 3.2 47.1 + - + +
46J ALA* 4.2 5.6 - - - +
48J PHE* 1.3 90.5 - - + +
50J GLY* 1.3 62.4 + - - +
51J GLU* 3.3 16.2 + - + +
54J ASP* 5.0 7.4 - - - +
100J MET* 4.0 15.7 - - - +
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Residues in contact with GLY 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J ALA 3.0 5.3 + - - -
47J ILE 3.1 14.7 + - - -
48J PHE 3.1 1.0 - - - -
49J GLU* 1.3 78.1 - - - +
51J GLU* 1.3 61.1 + - - +
52J GLU* 3.5 15.7 + - - +
100J MET* 3.9 35.3 - - - +
101J SER 4.2 0.7 - - - -
104J ALA* 3.8 9.9 - - - +
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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