Contacts of the helix formed by residues 96 - 111 (chain A) in PDB entry 1GV5
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LYS* 6.2 0.9 - - - +
94A PRO 4.6 5.2 - - - +
95A TRP* 1.3 77.7 - - - +
97A LYS* 1.3 67.9 + - - +
98A GLU* 3.5 18.1 + - - +
99A GLU* 3.1 36.2 + - - +
100A ASP* 3.1 24.3 + - - -
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Residues in contact with LYS 97 (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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95A TRP 5.8 0.7 - - - +
96A THR* 1.3 75.4 - - - +
98A GLU* 1.3 75.0 + - - +
100A ASP* 3.4 11.1 + - - +
101A GLN* 3.0 23.7 + - - +
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Residues in contact with GLU 98 (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 THR* 3.5 20.1 + - - +
97A LYS* 1.3 88.8 + - - +
99A GLU* 1.3 65.2 + - + +
101A GLN* 3.3 6.7 + - - +
102A ARG* 3.0 31.9 + - + +
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Residues in contact with GLU 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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92A LYS* 3.4 29.1 + - - +
94A PRO 3.9 1.4 - - - +
95A TRP* 3.5 14.8 - - + -
96A THR* 3.1 37.8 + - - +
98A GLU* 1.3 77.2 - - + +
100A ASP* 1.3 63.1 + - - +
102A ARG* 3.1 11.7 + - - +
103A VAL* 2.9 28.1 + - - +
122A LEU* 4.7 10.8 - - + +
123A LYS 4.3 0.5 - - - +
125A ARG* 2.8 53.0 + - - +
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Residues in contact with ASP 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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95A TRP* 3.8 6.5 - - - +
96A THR 3.1 18.1 + - - +
97A LYS* 3.6 12.4 - - - +
99A GLU* 1.3 76.5 - - - +
101A GLN* 1.3 62.4 + - - +
103A VAL* 3.3 4.6 + - - +
104A ILE* 3.1 29.3 + - + +
133A ARG* 2.8 52.4 + - - +
137A HIS* 4.0 6.6 - - - -
138A LEU* 3.9 20.5 - - + +
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Residues in contact with GLN 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 LYS 3.0 17.6 + - - +
98A GLU* 3.7 7.2 - - - +
99A GLU 3.2 0.2 - - - -
100A ASP* 1.3 75.2 - - - +
102A ARG* 1.3 65.1 + - + +
104A ILE* 3.3 29.4 + - - +
105A LYS* 3.1 53.1 + - + +
108A GLN* 5.6 0.6 - - - +
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Residues in contact with ARG 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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98A GLU* 3.0 23.2 + - + +
99A GLU* 3.1 9.8 + - - +
101A GLN* 1.3 74.6 - - + +
103A VAL* 1.3 60.7 + - - +
105A LYS* 3.2 9.0 + - + +
106A LEU* 2.9 40.6 + - + +
121A HIS* 2.9 44.4 + - - +
122A LEU* 3.7 25.4 - - + +
123A LYS* 5.1 1.8 - - - +
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Residues in contact with VAL 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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95A TRP* 3.5 28.7 - - + -
99A GLU 2.9 19.8 + - - +
100A ASP* 3.6 7.4 - - - +
102A ARG* 1.3 75.6 - - - +
104A ILE* 1.3 64.7 + - - +
106A LEU* 3.2 7.7 + - - +
107A VAL* 2.9 37.6 + - + +
115A TRP* 5.1 2.9 - - + -
118A ILE* 5.2 3.1 - - + -
122A LEU* 3.7 17.0 - - + -
130A CYS* 4.6 17.7 - - + +
133A ARG* 5.2 0.4 - - + -
134A TRP* 4.5 5.2 - - + -
138A LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 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 ASP* 3.1 16.5 + - + +
101A GLN* 3.5 28.9 - - - +
102A ARG 3.2 0.2 - - - -
103A VAL* 1.3 78.2 - - - +
105A LYS* 1.3 61.9 + - - +
107A VAL* 3.4 2.6 + - - +
108A GLN* 3.1 43.6 + - + +
134A TRP* 4.6 18.6 - - + -
138A LEU* 4.4 23.6 - - + +
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Residues in contact with LYS 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 GLN* 3.1 50.0 + - + +
102A ARG* 3.2 11.0 + - + +
104A ILE* 1.3 74.8 - - - +
106A LEU* 1.3 64.2 + - + +
108A GLN* 3.3 18.0 + - - +
109A LYS* 3.1 20.8 + - - +
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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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102A ARG* 2.9 30.6 + - + +
103A VAL 3.8 3.4 - - - +
105A LYS* 1.3 75.2 - - + +
107A VAL* 1.3 62.0 + - - +
109A LYS* 3.2 8.0 + - + +
110A TYR* 2.8 53.7 + - + +
118A ILE* 3.8 32.3 - - + +
121A HIS* 3.8 43.5 - - + +
122A LEU* 4.3 13.7 - - + -
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Residues in contact with VAL 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 VAL* 2.9 24.6 + - + +
104A ILE 3.8 3.8 - - - +
106A LEU* 1.3 72.4 - - - +
108A GLN* 1.3 63.1 + - + +
111A GLY* 2.7 32.2 + - - -
112A PRO* 3.6 26.9 - - + +
115A TRP* 4.0 16.8 - - + -
118A ILE* 4.0 16.8 - - + -
134A TRP* 3.9 43.3 - - + -
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Residues in contact with GLN 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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101A GLN* 5.6 0.6 - - - +
104A ILE* 3.1 40.6 + - + +
105A LYS* 3.4 17.4 - - - +
106A LEU 3.2 0.2 - - - -
107A VAL* 1.3 80.7 - - + +
109A LYS* 1.3 60.7 + - - +
111A GLY* 4.5 0.9 + - - -
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Residues in contact with LYS 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 LYS 3.1 13.1 + - - +
106A LEU* 3.6 12.8 - - + +
107A VAL 3.2 0.2 - - - -
108A GLN* 1.3 81.2 - - - +
110A TYR* 1.3 102.3 + - + +
121A HIS* 5.1 4.2 + - - -
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Residues in contact with TYR 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 LEU* 2.8 33.2 + - + +
109A LYS* 1.3 117.4 + - + +
111A GLY* 1.3 61.8 + - - +
113A LYS* 3.8 1.7 - - - +
114A ARG* 2.9 48.9 + - + +
117A VAL* 3.7 25.1 - - + +
118A ILE* 4.0 23.3 - - + -
121A HIS* 3.5 31.0 + + - -
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Residues in contact with GLY 111 (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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107A VAL* 2.7 24.8 + - - -
108A GLN 4.5 1.7 + - - -
109A LYS 3.6 1.0 - - - -
110A TYR* 1.3 74.6 - - - +
112A PRO* 1.3 63.6 - - - +
113A LYS* 2.5 34.8 + - - +
118A ILE* 3.8 8.7 - - - +
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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