Contacts of the helix formed by residues 50 - 57 (chain A) in PDB entry 2PQA
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 THR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A CYS* 1.3 76.6 - - - +
51A ILE* 1.3 65.6 + - - +
52A SER* 3.0 16.9 + - - +
53A GLN* 2.7 36.8 + - - +
54A LEU* 3.2 14.3 + - - +
76A ILE* 3.9 2.0 - - + -
96A ASP* 3.2 5.8 - - - +
98A THR* 3.5 22.9 - - + -
162A VAL* 4.0 5.4 - - + -
113B TYR* 3.4 44.2 - - + +
114B PRO* 4.0 1.2 - - - +
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 1.3 71.6 - - - +
52A SER* 1.3 56.7 + - - +
54A LEU* 3.1 17.3 + - + +
55A LEU* 2.9 28.8 + - + +
76A ILE* 4.2 13.7 - - + -
94A ILE* 3.0 36.8 - - + +
95A ASP* 4.5 0.4 - - - -
96A ASP* 2.8 41.0 + - + +
98A THR* 3.3 1.1 + - - +
99A ALA* 4.3 8.3 - - + -
100A ALA 3.9 16.2 - - - +
102A MET* 3.8 39.9 - - + +
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.0 14.9 + - - -
51A ILE* 1.3 76.7 - - - +
53A GLN* 1.3 56.6 + - - +
55A LEU* 3.1 15.1 + - - +
56A SER* 2.8 29.5 + - - -
98A THR* 3.0 28.5 + - - -
99A ALA* 4.5 2.8 - - - +
114B PRO* 3.0 31.9 + - - +
116B GLY* 4.1 11.7 - - - -
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A CYS* 3.5 8.4 - - + -
50A THR* 2.7 46.1 + - - +
52A SER* 1.3 74.2 + - - +
54A LEU* 1.3 65.2 + - - +
56A SER* 3.1 21.9 + - - +
57A ALA* 3.2 10.9 + - - +
66A ILE* 4.1 10.6 - - + +
162A VAL* 3.2 11.4 - - - +
166A HIS* 3.4 39.7 + - + +
111B GLN 5.2 0.4 + - - -
112B PHE* 2.9 30.3 + - - +
114B PRO* 3.4 21.4 - - + +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A CYS* 4.2 12.8 - - + -
50A THR 3.2 13.2 + - - +
51A ILE* 3.1 17.1 + - + +
53A GLN* 1.3 77.4 - - - +
55A LEU* 1.3 52.6 + - - +
57A ALA* 3.3 11.3 + - + +
66A ILE* 5.8 0.4 - - + -
71A ILE* 4.7 2.9 - - + -
74A VAL* 3.9 34.3 - - + -
76A ILE* 5.0 4.9 - - + -
102A MET* 3.7 32.5 - - + -
132A LEU* 4.1 24.2 - - + +
139A LYS* 2.7 32.7 + - - +
141A LEU* 4.1 18.6 - - + -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 2.9 20.5 + - + +
52A SER* 3.1 9.4 + - - +
54A LEU* 1.3 75.8 - - - +
56A SER* 1.3 57.2 + - - +
57A ALA 3.6 1.0 - - - +
99A ALA* 3.6 30.7 - - + -
100A ALA* 5.4 2.5 - - + +
102A MET* 4.0 20.9 - - + -
139A LYS* 3.0 31.8 + - + +
116B GLY 6.1 0.9 - - - +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A SER 2.8 16.1 + - - -
53A GLN* 3.1 19.6 + - - +
55A LEU* 1.3 69.6 - - - +
57A ALA* 1.3 63.3 + - - +
58A THR* 3.4 9.5 + - - +
65A ARG 4.9 0.2 - - - +
66A ILE* 4.9 8.2 - - - +
114B PRO* 5.6 5.4 - - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN 3.2 11.3 + - - +
54A LEU* 3.4 14.4 - - - +
55A LEU 3.2 2.6 - - - +
56A SER* 1.3 77.2 - - - +
58A THR* 1.3 63.8 + - - +
64A PHE* 4.5 4.7 - - + -
65A ARG 3.5 15.7 - - - +
66A ILE* 4.1 13.2 - - + -
71A ILE* 5.8 1.8 - - + -
132A LEU* 4.4 17.0 - - + -
139A LYS* 2.5 30.6 + - - +
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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