Contacts of the helix formed by residues 44 - 55 (chain Y) in PDB entry 2OTT
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 SER 44 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45Y LEU* 1.3 66.7 + - - +
46Y ARG* 3.2 13.3 - - - +
47Y TRP* 3.4 40.1 + - - +
48Y GLU* 3.9 14.0 + - - +
59Y VAL* 5.1 4.3 - - - +
62Y TYR* 3.2 28.8 + - - -
80Y GLN* 5.0 3.2 - - - +
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Residues in contact with LEU 45 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Y SER* 1.3 77.5 - - - +
46Y ARG* 1.3 64.3 + - - +
47Y TRP 3.3 0.9 + - - -
48Y GLU* 3.3 27.5 + - + +
49Y GLU* 3.7 6.4 + - - +
80Y GLN* 3.7 19.8 - - + +
81Y LYS* 4.9 19.8 - - + +
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Residues in contact with ARG 46 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y LEU* 3.8 26.9 - - - +
36Y CYS 4.3 9.1 + - - -
37Y ASP* 5.2 5.3 - - - +
44Y SER 3.6 11.4 - - - +
45Y LEU* 1.3 80.1 - - - +
47Y TRP* 1.3 82.5 + - + +
49Y GLU* 3.7 8.8 - - - +
50Y VAL* 3.5 20.3 + - - +
77Y CYS* 3.1 32.2 + - - +
79Y HIS 2.9 25.7 + - - -
80Y GLN* 2.8 32.9 + - - +
81Y LYS* 4.9 6.7 - - - -
82Y LEU* 3.6 31.2 - - + +
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Residues in contact with TRP 47 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Y VAL* 4.2 13.0 - - + -
35Y LEU* 3.6 27.6 - - + -
37Y ASP* 4.1 14.6 + - - -
44Y SER* 3.4 34.3 + - - +
45Y LEU 3.2 0.8 - - - -
46Y ARG* 1.3 100.4 - - + +
48Y GLU* 1.3 58.6 + - - +
49Y GLU 3.3 0.4 - - - -
50Y VAL* 3.3 14.4 + - + +
51Y CYS* 2.9 26.2 + - - -
59Y VAL* 3.4 25.1 - - + +
62Y TYR* 3.6 38.5 - + - -
98Y VAL* 3.5 35.4 - - + -
100Y VAL* 4.0 24.2 - - + -
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Residues in contact with GLU 48 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Y SER 3.9 9.3 + - - +
45Y LEU* 3.3 20.1 + - + +
47Y TRP* 1.3 75.2 - - - +
49Y GLU* 1.3 56.1 + - - +
51Y CYS* 3.0 3.3 + - - +
52Y ARG* 2.7 52.8 + - - +
57Y GLY 4.7 0.9 - - - +
58Y SER* 3.1 29.3 - - - -
59Y VAL* 3.1 40.9 + - - +
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Residues in contact with GLU 49 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y LEU 3.7 6.1 + - - +
46Y ARG* 3.7 12.1 - - - +
48Y GLU* 1.3 79.1 - - - +
50Y VAL* 1.3 52.1 + - + +
52Y ARG* 3.4 28.1 + - - +
53Y GLU* 2.7 41.2 + - + +
81Y LYS* 3.8 22.3 - - - +
82Y LEU* 3.7 14.9 + - - +
83Y SER* 3.0 48.0 + - - -
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Residues in contact with VAL 50 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y SER* 4.0 24.7 - - - +
13Y LEU* 3.9 28.7 - - + -
24Y VAL* 4.5 15.9 - - + -
46Y ARG 3.5 14.5 + - - +
47Y TRP* 3.3 23.8 + - + +
48Y GLU 3.2 0.2 - - - -
49Y GLU* 1.3 78.4 - - + +
51Y CYS* 1.3 60.2 + - - +
53Y GLU* 4.7 0.7 - - - +
54Y GLN* 2.8 40.4 + - - +
82Y LEU* 5.0 13.0 - - + -
100Y VAL* 5.2 4.7 - - + -
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Residues in contact with CYS 51 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Y TRP 2.9 12.4 + - - +
48Y GLU 3.0 5.6 + - - +
50Y VAL* 1.3 70.3 - - - +
52Y ARG* 1.3 67.2 + - - +
54Y GLN* 3.0 13.2 + - - +
56Y CYS 3.1 21.2 + - - -
57Y GLY 3.4 17.0 - - - +
58Y SER* 4.6 0.4 - - - -
59Y VAL* 3.4 32.5 - - + +
100Y VAL* 3.9 8.3 - - - -
102Y CYS* 2.1 48.9 - - + -
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Residues in contact with ARG 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Y GLU* 2.7 37.2 + - - +
49Y GLU* 3.4 41.0 + - - +
51Y CYS* 1.3 71.1 - - - +
53Y GLU* 1.3 56.2 + - - +
55Y GLN* 2.7 28.6 + - - +
56Y CYS 4.1 7.9 - - - -
57Y GLY 3.9 4.4 + - - +
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Residues in contact with GLU 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y VAL 4.7 3.2 - - - +
10Y GLU* 3.3 17.7 - - - +
11Y SER* 2.5 51.6 + - - +
49Y GLU* 2.7 24.6 + - + +
50Y VAL* 4.0 4.6 - - - +
51Y CYS 3.2 0.4 - - - -
52Y ARG* 1.3 72.4 - - - +
54Y GLN* 1.3 60.6 + - - +
55Y GLN* 3.1 6.2 + - - +
82Y LEU* 5.8 0.7 - - - +
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Residues in contact with GLN 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y SER* 3.3 33.7 + - - +
12Y ARG* 3.6 23.7 - - - +
13Y LEU* 4.1 24.9 + - + -
19Y ILE* 4.1 30.2 - - + +
50Y VAL* 2.8 28.6 + - - +
51Y CYS* 3.0 10.1 + - - +
53Y GLU* 1.3 82.0 - - - +
55Y GLN* 1.3 69.5 + - - +
56Y CYS* 3.7 15.3 - - - -
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Residues in contact with GLN 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y CYS* 5.4 0.2 - - - -
52Y ARG* 2.7 19.4 + - - +
53Y GLU 3.1 5.0 - - - +
54Y GLN* 1.3 81.4 - - - +
56Y CYS* 1.3 62.2 + - - +
104Y ASP* 4.4 3.3 - - - +
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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