Contacts of the helix formed by residues 99 - 106 (chain A) in PDB entry 5KZX
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ILE* 1.3 77.4 - - - +
100A GLN* 1.3 60.2 + - - +
101A GLU* 3.6 7.5 + - - +
102A GLN* 2.9 41.1 + - - +
103A CYS* 2.9 28.8 + - - +
110A TYR* 4.4 3.6 - - - -
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Residues in contact with GLN 100 (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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99A THR* 1.3 74.1 - - - +
101A GLU* 1.3 58.5 + - - +
103A CYS* 3.4 1.2 + - - +
104A GLU* 2.9 57.6 + - - +
110A TYR* 3.4 56.9 + - + +
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Residues in contact with GLU 101 (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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99A THR* 3.3 7.6 + - - +
100A GLN* 1.3 78.6 - - - +
102A GLN* 1.3 59.6 + - + +
104A GLU* 3.3 9.1 + - - +
105A ALA* 2.9 29.3 + - + +
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Residues in contact with GLN 102 (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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96A LYS* 4.5 13.9 - - - +
97A ALA 4.2 3.3 - - - +
98A ILE* 3.5 22.3 - - + +
99A THR* 2.9 40.2 + - - +
101A GLU* 1.3 75.0 - - + +
103A CYS* 1.3 64.1 + - - +
105A ALA* 3.3 7.9 + - - +
106A ARG* 3.0 27.9 + - - +
1023A SO4 4.2 15.9 + - - +
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Residues in contact with CYS 103 (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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98A ILE* 3.6 11.3 - - + +
99A THR 2.9 18.1 + - - +
100A GLN 3.5 5.6 - - - +
102A GLN* 1.3 74.5 - - - +
104A GLU* 1.3 63.1 + - - +
106A ARG* 3.1 15.7 + - - +
108A CYS* 3.2 21.1 + - - +
109A CYS 3.4 25.4 - - - -
110A TYR* 4.0 10.3 - - + -
127A CYS* 2.1 49.4 - - + -
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Residues in contact with GLU 104 (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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100A GLN* 2.9 54.0 + - + +
101A GLU* 3.8 6.6 - - - +
103A CYS* 1.3 75.4 - - - +
105A ALA* 1.3 58.7 + - - +
107A GLY* 3.0 19.4 + - - -
108A CYS 3.5 16.3 - - - +
110A TYR* 4.3 11.7 + - + +
1026A EDO 4.5 13.8 + - - +
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Residues in contact with ALA 105 (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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101A GLU* 2.9 19.9 + - + +
102A GLN* 3.8 8.5 - - - +
103A CYS 3.3 0.2 - - - -
104A GLU* 1.3 71.2 - - - +
106A ARG* 1.3 60.1 + - - +
107A GLY 3.1 6.4 + - - -
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Residues in contact with ARG 106 (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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92A CYS* 2.8 44.5 + - - -
93A ALA* 3.6 6.5 - - - +
95A ASP* 2.9 39.4 + - - -
96A LYS* 3.9 8.5 - - - +
98A ILE* 3.7 23.0 - - - +
102A GLN 3.0 14.6 + - - +
103A CYS 3.1 9.4 + - - +
105A ALA* 1.3 74.4 - - - +
107A GLY* 1.3 58.4 + - - +
133A TYR* 3.4 19.9 + - - -
134A PRO* 5.7 0.3 - - - +
159A PHE* 3.4 32.5 - - + +
1023A SO4 3.0 43.8 + - - +
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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