Contacts of the helix formed by residues 50 - 56 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C CYS* 1.3 77.1 - - - +
51C ILE* 1.3 65.5 + - - +
52C SER* 2.7 21.2 + - - +
53C GLN* 3.0 22.9 + - - +
54C LEU* 3.1 21.3 + - - +
76C ILE* 4.5 2.5 - - - -
96C ASP* 3.7 4.7 - - - +
98C THR* 3.6 22.0 - - + -
162C VAL* 4.2 9.6 - - + -
113D TYR* 3.6 42.2 - - + +
114D PRO* 3.8 1.0 - - - +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C THR* 1.3 71.2 - - - +
52C SER* 1.3 51.8 + - - +
54C LEU* 3.3 6.1 + - - +
55C LEU* 2.6 54.0 + - + +
76C ILE* 4.1 29.8 - - + +
77C VAL 5.9 0.7 - - - +
94C ILE* 3.3 29.4 - - + +
95C ASP* 4.3 0.7 - - - -
96C ASP* 2.9 41.9 + - + +
98C THR* 3.9 0.4 - - - +
99C ALA* 4.2 3.1 - - + -
100C ALA 3.9 10.5 - - - +
102C MET* 3.8 29.6 - - + -
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C THR* 2.7 19.2 + - - -
51C ILE* 1.3 73.2 - - - +
53C GLN* 1.3 63.7 + - - +
55C LEU* 3.9 7.3 - - - +
56C SER* 3.2 26.0 + - - -
98C THR* 3.2 27.9 + - - -
99C ALA* 4.4 3.8 - - - -
114D PRO* 2.8 26.5 + - - +
116D GLY 3.5 27.7 - - - +
117D ILE* 4.9 0.5 - - - +
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Residues in contact with GLN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C CYS* 3.4 2.8 - - + -
50C THR* 3.0 37.9 + - - +
52C SER* 1.3 75.2 + - - +
54C LEU* 1.3 65.5 + - - +
56C SER* 3.2 6.0 + - - -
57C ALA 3.1 17.8 + - - -
66C ILE* 3.3 38.1 - - + +
162C VAL* 3.5 5.1 - - - +
166C HIS* 3.0 41.6 + - - -
111D GLN 4.8 1.6 + - - -
112D PHE* 3.1 32.7 + - - +
114D PRO* 3.7 17.8 - - + +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C CYS* 4.2 2.5 - - + -
50C THR 3.1 13.4 + - - +
51C ILE* 3.6 8.1 - - - +
53C GLN* 1.3 74.8 - - - +
55C LEU* 1.3 63.6 + - - +
56C SER 3.1 1.2 + - - -
57C ALA* 3.1 13.8 + - - +
66C ILE* 4.2 14.1 - - + -
71C ILE* 4.5 0.4 - - + -
74C VAL* 3.6 29.4 - - + -
76C ILE* 3.8 26.9 - - + -
102C MET* 4.0 13.5 - - + -
132C LEU* 3.8 31.1 - - + +
139C LYS* 3.2 16.8 + - - +
141C LEU* 3.6 27.8 - - + -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 2.6 29.9 + - + +
52C SER* 3.9 7.0 - - - +
53C GLN 3.4 0.2 - - - -
54C LEU* 1.3 72.1 - - - +
56C SER* 1.3 58.6 + - - +
99C ALA* 3.6 30.5 - - + -
100C ALA* 4.5 7.9 - - + +
101C PRO 5.9 0.7 - - - +
102C MET* 4.3 13.8 - - + +
139C LYS* 3.1 28.7 + - + +
117D ILE* 4.1 29.1 - - + +
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER 3.2 18.3 + - - -
53C GLN* 3.2 6.1 + - - -
54C LEU 3.1 1.0 - - - -
55C LEU* 1.3 75.2 - - - +
57C ALA* 1.3 64.4 + - - +
58C THR* 3.8 6.2 + - - +
65C ARG 4.7 0.5 - - - +
66C ILE* 5.3 5.2 - - - +
114D PRO* 5.8 2.4 - - - +
117D ILE* 3.7 34.3 - - - -
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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