Contacts of the helix formed by residues 43 - 54 (chain X) 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 43 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37X ASP* 5.2 4.3 + - - -
38X SER 5.1 7.8 + - - -
44X SER* 1.3 64.0 + - - +
45X LEU* 3.0 17.4 + - - +
46X ARG* 3.5 13.4 + - - +
47X TRP* 3.6 24.3 + - - -
62X TYR* 4.7 10.1 - - - -
80X GLN* 4.7 21.9 + - - +
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Residues in contact with SER 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X SER* 1.3 76.2 - - - +
45X LEU* 1.3 62.6 + - - +
46X ARG 3.3 0.2 - - - -
47X TRP* 3.1 8.8 + - - +
48X GLU* 3.0 26.1 + - - +
59X VAL* 4.3 12.7 - - - +
62X TYR* 2.8 36.7 + - - -
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Residues in contact with LEU 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X SER* 3.0 11.6 - - - +
44X SER* 1.3 78.0 - - - +
46X ARG* 1.3 63.7 + - - +
48X GLU* 3.4 6.5 + - + +
49X GLU* 3.3 24.0 + - - +
80X GLN* 5.1 17.0 - - + -
81X LYS* 5.2 23.1 - - + +
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Residues in contact with ARG 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X LEU* 4.1 19.9 - - - +
36X CYS 4.4 3.6 + - - -
37X ASP* 2.8 33.2 + - - +
43X SER 3.5 10.1 + - - +
44X SER 3.3 0.6 - - - -
45X LEU* 1.3 78.6 - - - +
47X TRP* 1.3 86.3 + - + +
49X GLU* 3.4 9.3 + - - +
50X VAL* 3.1 25.1 + - + +
77X CYS* 3.3 19.0 + - - +
79X HIS 2.4 32.1 + - - -
80X GLN* 2.7 36.3 + - - +
81X LYS* 5.0 5.4 - - - +
82X LEU* 3.7 30.3 - - + +
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Residues in contact with TRP 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X VAL* 4.1 11.9 - - + -
35X LEU* 3.6 22.9 - - + -
37X ASP* 3.2 35.7 - - - -
43X SER* 3.6 27.6 + - - -
44X SER* 3.1 5.8 + - - +
46X ARG* 1.3 96.7 - - + +
48X GLU* 1.3 60.7 + - - +
50X VAL* 3.2 12.4 + - + +
51X CYS* 2.8 33.3 + - - -
59X VAL* 3.9 22.4 - - + -
62X TYR* 3.6 44.4 - + - -
98X VAL* 3.8 25.8 - - + -
100X VAL* 3.9 21.1 - - + -
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Residues in contact with GLU 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X SER 3.0 15.7 + - - +
45X LEU* 3.7 8.1 - - + +
47X TRP* 1.3 78.2 - - - +
49X GLU* 1.3 61.6 + - - +
51X CYS* 3.3 2.1 + - - +
52X ARG* 3.0 44.6 + - + +
58X SER* 2.8 24.1 + - - -
59X VAL* 3.0 37.8 + - + +
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Residues in contact with GLU 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X LEU 3.3 12.4 + - - +
46X ARG* 3.5 9.4 - - - +
47X TRP 3.3 0.2 - - - -
48X GLU* 1.3 78.4 - - - +
50X VAL* 1.3 59.8 + - + +
52X ARG* 3.3 4.6 + - - +
53X GLU* 2.9 39.0 + - - +
81X LYS* 4.0 32.4 - - + +
82X LEU* 5.9 6.7 - - + +
83X SER* 4.1 22.2 + - - +
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Residues in contact with VAL 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X SER* 3.8 28.5 - - - +
12X ARG 4.9 0.7 - - - +
13X LEU* 3.9 29.6 - - + -
24X VAL* 4.4 11.0 - - + -
46X ARG 3.1 14.2 + - - +
47X TRP* 3.2 22.4 + - + +
49X GLU* 1.3 82.4 - - + +
51X CYS* 1.3 62.1 + - - +
53X GLU* 3.5 1.3 + - - +
54X GLN* 2.9 33.1 + - - +
82X LEU* 3.8 24.2 - - + -
100X VAL* 5.3 3.1 - - + -
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Residues in contact with CYS 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X TRP 2.8 23.4 + - - +
48X GLU 3.7 4.3 - - - +
50X VAL* 1.3 71.4 - - - +
52X ARG* 1.3 63.9 + - - +
54X GLN* 3.1 16.3 + - - +
56X CYS* 3.2 16.8 + - - +
57X GLY 3.2 17.7 - - - +
58X SER* 4.6 0.7 - - - -
59X VAL* 3.7 18.6 - - - +
100X VAL* 3.6 15.5 - - - -
102X CYS* 2.1 49.6 - - - -
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Residues in contact with ARG 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X GLU* 3.0 46.6 + - + +
49X GLU* 4.0 4.5 - - - +
51X CYS* 1.3 77.6 - - - +
53X GLU* 1.3 56.7 + - - +
55X GLN* 2.8 28.3 + - - +
56X CYS 2.8 32.9 + - - -
57X GLY* 4.1 12.1 - - - +
58X SER* 4.6 1.3 - - - +
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Residues in contact with GLU 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X VAL 4.2 5.4 - - - +
10X GLU* 3.4 16.8 - - - +
11X SER* 2.5 50.5 + - - +
49X GLU* 2.9 23.1 + - - +
50X VAL* 3.8 6.9 - - - +
52X ARG* 1.3 71.9 - - - +
54X GLN* 1.3 60.1 + - - +
55X GLN* 3.1 7.7 + - - +
82X LEU* 5.7 2.4 - - - +
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Residues in contact with GLN 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X SER* 3.0 35.1 + - - +
12X ARG* 3.6 23.4 - - - +
13X LEU* 4.2 12.3 + - + -
19X ILE* 4.0 37.6 - - + +
50X VAL* 2.9 27.6 + - - +
51X CYS* 3.1 12.7 + - - +
53X GLU* 1.3 80.2 - - - +
55X GLN* 1.3 70.9 + - - +
56X CYS* 3.7 14.8 - - - -
89Y TRP* 5.8 0.7 - - - -
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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