Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 1JR9
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 GLY 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 THR* 1.3 79.3 + - - +
100A GLU* 1.3 55.4 + - - -
101A VAL* 3.0 7.2 - - - -
102A ALA* 2.8 30.1 + - - +
103A ASP* 3.4 7.1 + - - +
195A ALA* 5.5 4.7 - - - -
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Residues in contact with GLU 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 GLY* 1.3 70.7 - - - -
101A VAL* 1.3 54.8 + - + +
103A ASP* 3.2 16.7 + - - +
104A LYS* 2.8 39.1 + - - +
198A TYR* 3.9 28.9 - - + -
199A SER* 4.5 11.0 + - - -
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Residues in contact with VAL 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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97A PRO* 5.1 0.2 - - + -
98A THR 3.6 10.3 - - - +
100A GLU* 1.3 80.0 - - + +
102A ALA* 1.3 51.8 + - - +
104A LYS* 3.7 6.8 + - - +
105A ILE* 2.8 52.5 + - + +
134A LEU* 5.2 2.7 - - + -
141A ILE* 5.1 2.6 - - + +
160A ILE* 5.0 7.6 - - + -
191A TRP* 4.7 6.1 - - + +
194A VAL* 3.7 24.5 - - + -
195A ALA* 3.4 32.8 - - + +
198A TYR* 3.5 30.1 - - + -
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Residues in contact with ALA 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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97A PRO* 3.9 19.5 - - + +
98A THR* 3.7 23.8 + - - +
99A GLY 2.8 13.5 + - - +
101A VAL* 1.3 77.0 - - - +
103A ASP* 1.3 72.0 + - - +
105A ILE* 2.9 16.0 + - - +
106A ASN* 3.0 20.4 + - - +
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Residues in contact with ASP 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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99A GLY 3.9 10.5 - - - +
100A GLU* 3.4 15.8 + - - +
102A ALA* 1.3 76.2 - - - +
104A LYS* 1.3 55.3 + - - +
106A ASN* 2.6 37.9 + - - +
107A ASP* 2.8 23.7 + - - +
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Residues in contact with LYS 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 GLU* 2.8 20.5 + - - +
101A VAL* 3.7 7.6 - - - +
103A ASP* 1.3 73.4 - - - +
105A ILE* 1.3 52.7 + - - +
107A ASP* 3.2 19.4 + - + +
108A LYS* 2.7 32.7 + - - +
139A GLY 3.3 26.2 - - - -
140A GLU* 4.8 3.1 - - - +
141A ILE* 3.2 37.7 - - + +
198A TYR* 3.1 24.3 + - + +
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Residues in contact with ILE 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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97A PRO* 3.5 32.3 - - + -
101A VAL* 2.8 30.5 + - + +
102A ALA* 2.9 11.3 + - - +
104A LYS* 1.3 77.5 - - - +
106A ASN* 1.3 56.8 + - - +
108A LYS* 3.3 1.0 + - - +
109A TYR* 3.1 32.6 + - + +
110A GLY 4.0 1.0 + - - -
111A SER 4.6 0.3 - - - +
112A PHE* 3.9 20.4 - - + -
115A PHE* 3.8 38.1 - - + -
134A LEU* 5.2 4.5 - - + -
141A ILE* 4.8 12.1 - - + -
191A TRP* 4.0 17.3 - - + -
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Residues in contact with ASN 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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102A ALA* 3.2 20.7 + - - +
103A ASP* 2.6 25.1 + - - +
105A ILE* 1.3 71.6 - - - +
107A ASP* 1.3 68.4 + - - +
108A LYS 2.9 1.3 - - - -
110A GLY* 2.8 43.0 + - - +
111A SER* 4.3 1.0 - - - +
112A PHE* 4.0 18.4 + - - +
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Residues in contact with ASP 107 (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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103A ASP* 2.8 25.6 + - - +
104A LYS* 3.4 23.7 + - + +
106A ASN* 1.3 77.7 - - - +
108A LYS* 1.3 66.6 + - - +
110A GLY* 4.3 0.3 + - - -
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Residues in contact with LYS 108 (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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104A LYS* 2.7 15.7 + - - +
105A ILE 3.5 3.6 - - - -
106A ASN 2.9 0.8 - - - -
107A ASP* 1.3 83.7 - - - +
109A TYR* 1.3 68.3 + - - +
110A GLY 3.1 5.0 + - - -
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Residues in contact with TYR 109 (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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105A ILE* 3.1 14.9 + - - -
108A LYS* 1.3 77.2 - - - +
110A GLY* 1.3 55.1 + - - +
111A SER* 2.9 13.8 + - - +
114A LYS* 4.1 8.8 - - - -
115A PHE* 3.4 53.0 - + + +
118A GLU* 3.7 30.1 - - + -
134A LEU* 4.6 3.7 - - + +
141A ILE* 4.1 11.9 + - + -
142A GLU* 3.9 9.4 - - - -
143A ILE* 3.4 34.1 + - + +
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Residues in contact with GLY 110 (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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106A ASN* 2.8 40.0 + - - +
107A ASP 5.0 0.4 - - - -
108A LYS 3.1 4.2 + - - -
109A TYR* 1.3 73.7 - - - +
111A SER* 1.3 58.7 + - - -
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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