Contacts of the helix formed by residues 50 - 57 (chain A) in PDB entry 1POP
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 GLU 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 4.2 7.6 + - - +
27A ALA* 3.8 12.1 - - + +
28A PHE* 3.6 57.9 - - + +
31A VAL* 3.6 27.9 - - + +
35A GLU* 5.1 0.3 - - - +
48A TYR 4.0 4.2 - - - +
49A SER* 1.3 71.3 - - - +
51A GLN* 1.3 60.7 + - - +
53A LEU* 3.0 7.3 + - - +
54A LEU* 2.9 27.5 + - - +
83A ARG* 2.9 43.5 + - - +
88A TYR* 4.5 7.3 - - + +
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Residues in contact with GLN 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 GLU* 1.3 78.6 + - - +
52A GLU* 1.3 63.1 + - - +
54A LEU* 3.2 11.1 + - - +
55A ASP* 2.9 51.5 + - - +
86A TYR* 3.8 24.7 + - + +
87A PRO 3.3 26.5 - - - +
88A TYR* 3.4 14.2 - - - +
89A GLU* 2.8 34.1 + - - +
90A GLY 3.3 9.5 + - - -
91A VAL 2.9 24.0 + - - -
93A ARG 4.4 0.4 - - - +
96A ARG* 3.8 9.8 - - - +
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Residues in contact with GLU 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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49A SER* 2.8 21.5 + - - +
50A GLU 3.2 0.2 - - - -
51A GLN* 1.3 75.7 - - - +
53A LEU* 1.4 61.0 + - + +
56A CYS* 2.9 38.0 + - + +
79A GLY 5.0 1.6 - - - -
80A ILE* 3.6 9.8 - - + +
81A HIS* 2.8 55.2 + - - +
86A TYR* 3.5 28.9 - - + -
97A SER* 2.8 27.2 + - - +
103A TYR* 3.3 9.7 - - - -
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Residues in contact with LEU 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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26A TRP* 3.5 9.8 - - + -
27A ALA* 4.0 18.8 - - + +
30A ALA* 4.1 5.8 - - + -
31A VAL* 4.0 24.7 - - + -
34A ILE* 5.2 0.4 - - + -
49A SER 3.8 8.7 - - - +
50A GLU 3.0 7.1 + - - +
52A GLU* 1.4 76.9 - - + +
54A LEU* 1.3 64.0 + - - +
56A CYS* 4.5 0.7 - - - +
57A ASP* 3.0 32.0 + - + +
71A ALA* 3.7 29.8 - - + +
74A LEU* 4.8 13.7 - - + -
75A VAL* 3.8 26.2 - - + -
79A GLY 5.5 1.8 - - - +
80A ILE* 4.1 11.7 - - + -
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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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22A CYS* 4.1 11.9 - - - -
24A SER* 4.1 13.7 - - - -
26A TRP* 3.9 14.5 - - + -
27A ALA* 4.5 2.2 - - + +
50A GLU 2.9 11.7 + - - +
51A GLN* 3.2 30.9 + - - +
53A LEU* 1.3 77.0 - - - +
55A ASP* 1.3 60.8 + - - +
57A ASP 4.6 3.8 + - - +
62A GLY* 3.5 42.1 + - - +
63A CYS* 3.7 7.4 - - - +
88A TYR* 3.9 17.0 - - + -
91A VAL 3.9 15.7 - - - +
92A GLN* 3.4 27.1 - - + +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLN* 2.9 28.2 + - - +
52A GLU 4.1 0.4 - - - +
54A LEU* 1.3 74.9 - - - +
56A CYS* 1.3 60.4 + - - +
58A ARG* 3.0 31.1 + - - +
86A TYR* 2.7 30.7 + - - +
92A GLN* 3.8 3.3 - - - -
93A ARG 2.9 40.0 + - - +
94A TYR 3.5 12.3 - - - +
95A CYS* 3.8 7.9 - - - +
96A ARG* 2.9 19.7 + - - -
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Residues in contact with CYS 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 GLU* 2.9 24.8 + - + +
55A ASP* 1.3 77.4 - - - +
57A ASP* 1.3 59.4 + - - +
58A ARG* 3.1 14.5 + - - +
74A LEU* 4.3 22.6 - - + +
86A TYR* 4.1 6.7 - - - -
95A CYS* 2.0 54.0 - - - -
97A SER* 3.3 15.9 - - - +
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Residues in contact with ASP 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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26A TRP* 3.3 15.7 - - + -
53A LEU* 3.0 22.4 + - - +
54A LEU 4.7 4.2 - - - +
55A ASP 3.7 0.6 - - - -
56A CYS* 1.3 75.3 - - - +
58A ARG* 1.3 61.3 + - - +
59A ARG* 3.1 18.9 + - - +
60A SER* 3.0 35.1 + - - +
70A SER* 3.3 34.9 - - - -
71A ALA* 3.4 8.6 + - - -
74A LEU* 4.4 15.1 - - + +
92A GLN* 5.3 1.4 - - - +
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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