Contacts of the helix formed by residues 51 - 63 (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 GLU 51 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46L ALA* 3.0 13.8 + - - +
49L GLU* 4.3 20.7 - - + +
50L GLY* 1.3 74.9 - - - +
52L GLU* 1.3 78.1 + - - +
53L ASP* 3.4 3.7 + - + +
54L ASP* 3.2 35.3 + - + +
55L VAL* 3.0 25.7 + - - +
104L ALA* 4.1 0.6 - - - +
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Residues in contact with GLU 52 (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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50L GLY 3.3 14.9 + - - +
51L GLU* 1.3 89.3 - - - +
53L ASP* 1.3 73.8 + - - +
55L VAL* 3.2 5.7 + - - +
56L VAL* 3.2 25.7 + - - +
100L MET 5.1 0.3 - - - +
103L ASP* 4.8 7.3 - - - +
104L ALA* 4.2 25.5 + - - +
107L GLU* 3.0 33.1 - - + +
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Residues in contact with ASP 53 (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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51L GLU* 3.4 4.4 - - + +
52L GLU* 1.3 87.1 + - - +
54L ASP* 1.3 65.2 + - - +
56L VAL* 3.3 9.0 + - - +
57L GLU* 2.9 30.2 + - - +
107L GLU* 5.2 3.8 - - - +
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Residues in contact with ASP 54 (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* 4.6 4.1 - - - +
43L ILE* 5.2 0.5 - - - -
46L ALA* 3.8 18.4 - - + +
49L GLU* 5.1 4.7 - - - +
51L GLU* 3.2 30.4 + - + +
53L ASP* 1.3 81.7 - - - +
55L VAL* 1.3 62.5 + - - +
57L GLU* 4.0 17.6 - - - +
58L GLY* 3.2 18.4 + - - -
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Residues in contact with VAL 55 (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* 4.6 6.1 - - + +
46L ALA* 3.7 12.1 - - + -
47L ILE* 3.7 25.6 - - + +
51L GLU 3.0 19.7 + - - +
52L GLU 3.2 8.5 + - - +
54L ASP* 1.3 76.4 - - - +
56L VAL* 1.3 64.0 + - + +
58L GLY* 4.0 0.3 - - - -
59L LEU* 3.1 25.4 + - + +
77L LEU* 3.9 26.0 - - + -
104L ALA* 3.6 33.4 - - + +
108L GLY* 4.1 11.9 - - - +
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Residues in contact with VAL 56 (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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52L GLU 3.2 11.0 + - - +
53L ASP* 3.6 10.1 - - - +
55L VAL* 1.3 75.5 - - + +
57L GLU* 1.3 67.3 + - + +
59L LEU* 3.1 18.4 + - - +
60L GLN* 3.1 34.7 + - - +
107L GLU* 4.6 23.8 - - + +
108L GLY* 5.4 1.1 - - - -
111L TYR* 3.7 33.3 - - + -
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Residues in contact with GLU 57 (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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53L ASP* 2.9 17.0 + - - +
54L ASP* 4.2 18.7 - - - +
55L VAL 3.5 0.2 - - - -
56L VAL* 1.3 79.4 - - - +
58L GLY* 1.3 61.1 + - - +
60L GLN* 3.5 22.6 + - - +
61L ALA* 3.5 11.8 + - - +
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Residues in contact with GLY 58 (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 4.6 3.3 - - - +
42L PRO* 5.1 11.9 - - - -
43L ILE* 3.5 24.0 - - - +
54L ASP 3.2 14.5 + - - -
55L VAL 4.1 0.4 - - - -
57L GLU* 1.3 77.2 - - - +
59L LEU* 1.3 63.2 + - - +
61L ALA* 3.8 7.8 + - - +
62L ALA* 3.5 14.4 + - - +
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Residues in contact with LEU 59 (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* 3.8 17.9 - - + +
55L VAL* 3.1 24.2 + - + +
56L VAL* 3.1 6.7 + - - +
58L GLY* 1.3 75.6 - - - +
60L GLN* 1.3 62.7 + - - +
62L ALA* 3.1 5.0 + - - +
63L ILE* 2.9 32.7 + - + +
72L LEU* 3.8 34.5 - - + +
76L ALA* 4.9 1.1 - - + -
77L LEU* 4.3 16.8 - - + -
108L GLY* 3.8 35.0 - - - +
111L TYR* 4.1 21.3 - - + -
112L CYS* 4.3 9.2 - - - -
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Residues in contact with GLN 60 (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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56L VAL* 3.1 28.9 + - - +
57L GLU* 3.6 16.6 - - - +
59L LEU* 1.3 71.2 - - - +
61L ALA* 1.3 61.6 + - - +
62L ALA 3.0 5.4 + - - -
63L ILE* 3.2 13.2 + - + +
64L GLU* 3.1 29.3 + - + +
111L TYR* 2.7 31.8 + - + +
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Residues in contact with ALA 61 (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* 4.7 5.2 - - + +
57L GLU 3.5 9.7 + - - +
58L GLY* 4.1 10.1 - - - +
59L LEU 3.5 0.4 - - - -
60L GLN* 1.3 77.5 - - - +
62L ALA* 1.3 56.8 + - - +
64L GLU* 3.7 9.3 - - - +
65L ALA* 3.3 28.4 + - - +
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Residues in contact with ALA 62 (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* 4.8 20.7 - - + +
40L ILE* 6.6 0.2 - - + -
43L ILE* 4.4 6.7 - - + -
58L GLY 3.5 11.2 + - - +
59L LEU* 3.1 12.0 + - - +
60L GLN 3.0 0.6 - - - -
61L ALA* 1.3 75.7 - - - +
63L ILE* 1.3 56.4 + - - +
64L GLU 3.0 4.3 - - - -
66L GLY* 3.1 28.6 + - - -
67L LYS 3.4 5.8 - - - +
72L LEU* 3.8 26.2 - - + -
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Residues in contact with ILE 63 (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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59L LEU* 2.9 33.6 + - + +
60L GLN* 3.5 13.9 - - + +
62L ALA* 1.3 72.5 - - - +
64L GLU* 1.3 56.9 + - + +
66L GLY 3.1 15.3 - - - +
67L LYS* 3.3 26.2 - - - +
68L ASP 3.9 14.6 - - - -
69L PRO* 4.0 11.7 - - + -
72L LEU* 4.0 9.0 - - + -
111L TYR* 4.9 11.0 - - + -
112L CYS* 6.4 1.8 - - - -
115L ASN* 5.2 12.6 - - + +
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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