Contacts of the helix formed by residues 50 - 56 (chain B) in PDB entry 3QTA
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 ASP 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.8 8.9 - - + +
47B GLN* 2.8 38.4 + - - +
49B GLU* 1.3 93.8 - - - +
51B ILE* 1.3 61.9 + - - +
52B ALA 3.3 3.1 + - - -
53B THR* 3.0 33.1 + - + +
54B GLU* 3.7 6.8 + - + +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.0 9.6 - - + -
47B GLN 4.2 0.2 - - - +
48B PRO* 3.2 17.4 + - + +
49B GLU 3.5 1.0 - - - -
50B ASP* 1.3 77.7 - - - +
52B ALA* 1.3 66.3 + - - +
54B GLU* 3.0 16.3 + - - +
55B MSE 3.4 35.1 + - + +
76B LEU* 3.9 14.8 - - + -
147B ALA* 4.1 13.5 - - + +
150B ALA* 4.8 2.7 - - + -
151B LEU* 4.1 22.0 - - + -
160B THR* 3.9 22.2 - - + +
181B PHE* 3.7 29.6 - - + -
183B ILE* 4.7 8.7 - - + -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU 4.7 4.6 + - - +
50B ASP 3.3 0.8 - - - -
51B ILE* 1.3 80.2 - - - +
53B THR* 1.3 66.6 + - + +
55B MSE 3.1 27.9 + - - +
56B GLY* 3.6 5.4 + - - -
143B ALA* 3.9 17.5 - - + +
144B THR* 4.7 8.5 - - - +
147B ALA* 4.0 17.0 - - + +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU 5.6 1.1 - - - +
50B ASP* 3.0 29.3 + - + +
51B ILE 3.2 0.4 - - - -
52B ALA* 1.3 82.8 - - + +
54B GLU* 1.3 65.2 + - - +
55B MSE 3.2 1.0 + - - -
56B GLY* 3.9 7.5 + - - -
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER* 5.7 3.2 - - - -
46B VAL* 4.4 25.4 - - + +
50B ASP* 4.2 9.6 - - + +
51B ILE 3.0 10.8 + - - +
53B THR* 1.3 82.7 + - - +
55B MSE 1.3 59.7 - - - +
56B GLY 3.6 0.4 - - - -
162B VAL* 4.0 13.0 - - + +
179B ARG* 2.8 51.8 + - - +
181B PHE* 3.7 20.6 - - + -
303B GOL 4.4 1.4 + - - -
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Residues in contact with MSE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.5 37.7 - - + +
52B ALA* 3.1 10.0 + - - +
54B GLU* 1.3 80.6 - - - +
56B GLY* 1.3 64.5 + - - +
60B ILE* 3.7 23.8 - - + +
76B LEU* 3.3 33.9 - - + -
78B THR* 4.0 15.7 - - + +
80B GLU* 4.4 1.4 - - - +
143B ALA* 3.8 28.9 - - + +
146B ILE* 4.2 5.6 - - + -
147B ALA* 4.4 6.3 - - + -
181B PHE* 3.9 15.0 - - + -
303B GOL 2.7 30.3 + - - -
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Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 3.6 6.0 + - - -
53B THR 3.9 7.3 + - - -
54B GLU 3.6 1.2 - - - -
55B MSE 1.3 84.5 - - - +
57B GLY* 1.3 64.6 + - - +
58B GLY 4.4 0.3 - - - +
60B ILE* 4.0 8.5 - - - +
80B GLU* 5.7 2.0 - - - -
143B ALA* 3.8 16.0 - - - +
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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