Contacts of the helix formed by residues 98 - 109 (chain A) in PDB entry 5JZV
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 ASP 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 1.3 71.4 - - - +
99A THR* 1.3 60.9 + - - +
100A ASN* 3.4 4.0 - - + +
101A VAL* 3.0 16.0 + - + +
102A LEU* 2.9 24.9 + - - +
147A ASN* 2.7 32.8 + - - +
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Residues in contact with THR 99 (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 THR 3.4 4.6 + - - -
98A ASP* 1.3 72.4 - - - +
100A ASN* 1.3 56.2 + - - +
102A LEU* 3.9 5.2 - - + +
103A TYR* 2.9 32.8 + - + +
120A ILE* 3.8 32.9 - - + +
123A GLU* 4.8 8.1 - - + +
124A ILE* 4.3 33.5 - - + +
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Residues in contact with ASN 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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98A ASP* 3.4 3.9 - - + +
99A THR* 1.3 78.5 - - - +
101A VAL* 1.3 65.0 + - + +
103A TYR* 3.6 6.5 + - - +
104A GLU* 3.3 40.1 + - - +
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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 THR* 3.7 17.7 - - + -
98A ASP* 3.0 17.9 + - + +
100A ASN* 1.3 80.5 - - + +
102A LEU* 1.3 63.7 + - - +
104A GLU* 3.4 9.0 + - - +
105A ARG* 3.2 35.6 + - + +
147A ASN* 4.0 31.4 - - + +
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Residues in contact with LEU 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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11A THR* 4.3 15.3 - - + -
12A PRO 3.7 9.0 - - - +
13A GLY* 3.4 37.5 - - - +
14A VAL* 3.9 10.1 - - + +
97A THR* 3.8 11.9 - - + +
98A ASP 2.9 15.7 + - - +
99A THR* 3.9 4.9 - - - +
101A VAL* 1.3 76.2 - - - +
103A TYR* 1.4 63.4 + - - +
105A ARG* 3.3 6.1 + - + +
106A LEU* 3.0 33.4 + - + +
119A ASN 4.7 1.6 - - - +
120A ILE* 4.3 11.0 - - + -
123A GLU* 3.8 37.9 - - + -
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Residues in contact with TYR 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 THR* 2.9 19.1 + - + +
100A ASN* 3.8 8.3 - - - +
101A VAL 3.3 0.2 - - - -
102A LEU* 1.4 76.9 - - - +
104A GLU* 1.3 72.1 + - - +
106A LEU* 3.4 1.9 + - - -
107A GLU* 3.0 56.6 + - + +
116A LEU* 3.7 38.2 - - + +
120A ILE* 3.7 31.1 - - + +
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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 ASN* 3.3 30.3 - - - +
101A VAL* 3.4 7.7 + - - +
103A TYR* 1.3 83.1 - - - +
105A ARG* 1.4 64.6 + - + +
107A GLU* 3.1 27.1 - - - +
108A THR* 3.1 29.9 + - - +
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Residues in contact with ARG 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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13A GLY* 3.0 30.1 + - - +
14A VAL 3.2 21.2 + - - -
97A THR* 3.5 6.3 + - - +
101A VAL* 3.2 27.1 + - + +
102A LEU* 3.3 12.1 + - + +
104A GLU* 1.4 75.3 - - + +
106A LEU* 1.3 64.9 + - + +
108A THR* 3.7 5.6 + - - -
109A ARG* 3.3 25.3 + - - +
146A SER 3.2 21.1 + - - -
147A ASN* 3.4 13.1 + - - +
201A ADP 3.3 69.1 + - - +
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Residues in contact with LEU 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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12A PRO 3.6 27.4 - - - +
13A GLY* 3.8 13.7 - - - -
102A LEU* 3.0 30.4 + - + +
105A ARG* 1.3 74.4 - - + +
107A GLU* 1.3 64.6 + - - +
109A ARG* 3.4 34.2 + - - +
111A TYR* 3.2 39.5 + - + +
116A LEU* 3.8 18.8 - - + -
119A ASN* 3.7 30.3 - - + -
120A ILE* 4.8 6.7 - - + -
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Residues in contact with GLU 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 TYR* 3.0 40.0 + - + +
104A GLU* 3.1 27.1 - - - +
105A ARG 3.4 0.2 - - - -
106A LEU* 1.3 75.2 - - - +
108A THR* 1.3 53.4 + - - +
110A GLY* 2.7 29.3 + - - -
111A TYR 3.9 3.3 + - - +
116A LEU* 3.9 20.0 - - + +
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Residues in contact with THR 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 GLU* 3.1 17.1 + - - +
105A ARG* 3.8 5.6 - - - -
107A GLU* 1.3 73.3 - - - +
109A ARG* 1.3 57.8 + - - -
110A GLY* 3.0 6.8 + - - -
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Residues in contact with ARG 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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12A PRO* 4.5 2.6 - - - +
13A GLY 3.8 8.0 - - - +
105A ARG 3.3 14.1 + - - +
106A LEU* 3.5 25.3 - - - +
107A GLU 3.2 1.0 + - - -
108A THR* 1.3 76.4 - - - +
110A GLY* 1.3 59.7 + - - +
111A TYR* 3.3 38.8 + - + -
201A ADP 2.9 69.4 + - - -
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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