Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 4LQD
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 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 HIS* 4.1 5.2 - - + -
93A SER* 2.6 32.2 + - - +
95A GLU* 1.3 93.0 - - - +
97A LEU* 1.3 64.8 + - - +
98A VAL* 3.4 2.7 - - - -
99A ALA* 3.0 11.4 + - + +
100A ALA* 2.8 21.3 + - - +
146A LEU* 3.9 18.7 - - + +
148A THR* 2.5 39.2 + - - +
150A GLY 5.2 0.2 + - - -
151A PHE 4.1 0.2 + - - -
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Residues in contact with LEU 97 (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 HIS* 3.6 27.6 + - + -
94A GLU 3.7 13.5 + - - +
95A GLU 3.5 2.0 - - - -
96A ASP* 1.3 75.1 - - - +
98A VAL* 1.3 55.3 + - + +
100A ALA* 2.9 4.5 + - - +
101A GLN* 2.7 57.3 + - + +
133A LEU* 3.8 25.8 - - + -
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Residues in contact with VAL 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 ASP 3.4 0.8 - - - -
97A LEU* 1.3 78.9 - - + +
99A ALA* 1.3 65.3 + - - +
101A GLN* 3.0 20.5 + - + +
102A ASP* 2.8 37.1 + - - +
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Residues in contact with ALA 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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96A ASP* 3.0 16.1 + - + +
98A VAL* 1.3 78.3 - - - +
100A ALA* 1.3 64.9 + - - +
102A ASP* 3.0 13.8 + - - +
103A LEU* 3.0 21.7 + - - +
146A LEU* 4.0 16.2 - - + -
206A PHE* 4.3 8.2 - - + -
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Residues in contact with ALA 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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90A VAL* 3.9 12.3 - - + +
92A HIS* 3.6 32.5 - - + -
96A ASP 2.8 12.5 + - - +
97A LEU 3.3 8.1 - - - +
99A ALA* 1.3 77.7 - - - +
101A GLN* 1.3 57.9 + - - +
103A LEU* 3.0 7.0 + - - +
104A VAL* 2.8 30.5 + - - +
133A LEU* 3.6 15.7 - - + -
146A LEU* 3.8 8.4 - - + +
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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 LEU* 2.7 47.4 + - + +
98A VAL* 3.3 26.3 + - + +
100A ALA* 1.3 72.3 - - - +
102A ASP* 1.3 60.6 + - - +
104A VAL* 3.0 9.3 + - - +
105A SER* 2.8 30.0 + - - -
133A LEU* 4.3 15.2 - - + +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 2.8 32.4 + - - +
99A ALA* 3.0 12.7 + - - +
101A GLN* 1.3 77.0 - - - +
103A LEU* 1.3 52.2 + - - +
105A SER* 3.0 9.5 + - - -
106A TYR* 2.7 35.3 + - - +
206A PHE* 3.9 15.7 - - + -
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Residues in contact with LEU 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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90A VAL* 3.9 16.8 - - + -
99A ALA 3.0 9.3 + - - +
100A ALA* 3.0 9.2 + - - +
102A ASP* 1.3 76.0 - - - +
104A VAL* 1.3 58.9 + - - +
106A TYR* 3.0 2.6 + - + -
107A LEU* 2.8 58.2 + - + +
144A VAL* 3.7 29.6 - - + -
146A LEU* 5.0 4.9 - - + -
178A LEU* 4.2 17.0 - - + -
206A PHE* 3.6 49.3 - - + -
209A VAL* 4.5 5.8 - - + -
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Residues in contact with VAL 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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90A VAL* 3.9 10.5 - - + -
100A ALA 2.8 16.7 + - - +
101A GLN* 3.4 9.2 - - - +
103A LEU* 1.3 74.7 - - - +
105A SER* 1.3 64.7 + - - +
107A LEU* 3.0 10.6 + - - +
108A GLU* 2.9 40.7 + - - +
131A SER* 4.1 19.9 - - - +
132A GLU* 3.8 22.0 - - - +
133A LEU* 3.8 25.1 - - + +
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Residues in contact with SER 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 2.8 12.1 + - - -
102A ASP* 3.3 11.4 - - - -
104A VAL* 1.3 76.5 - - - +
106A TYR* 1.3 64.0 + - - +
108A GLU* 3.0 26.0 + - - +
109A GLY* 3.3 10.7 + - - -
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Residues in contact with TYR 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 ASP 2.7 16.3 + - - +
103A LEU* 3.0 11.4 + - + +
105A SER* 1.3 73.7 - - - +
107A LEU* 1.3 59.7 + - + +
109A GLY* 3.7 3.5 + - - -
203A ASP* 2.8 33.5 + - + -
206A PHE* 3.7 48.7 - + + -
207A ARG* 3.3 22.8 + - - +
210A LYS* 2.8 47.8 + - + -
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Residues in contact with LEU 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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88A VAL* 4.1 22.9 - - + -
90A VAL* 4.2 13.0 - - + -
103A LEU* 2.8 48.2 + - + +
104A VAL* 3.0 4.9 + - - +
106A TYR* 1.3 79.9 - - + +
108A GLU* 1.3 61.2 + - - +
109A GLY 3.3 1.1 + - - -
129A ILE* 3.5 24.4 + - + +
131A SER* 3.6 16.2 - - - +
144A VAL* 4.9 3.1 - - + -
209A VAL* 4.4 5.4 - - + -
210A LYS* 3.8 51.0 + - + +
213A VAL* 4.5 8.7 - - + -
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Residues in contact with GLU 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 VAL* 2.9 23.3 + - - +
105A SER* 3.0 21.4 + - - +
107A LEU* 1.3 77.8 - - - +
109A GLY* 1.3 66.9 + - - +
128A ALA* 4.2 16.5 - - - +
129A ILE 3.9 10.8 + - - +
131A SER* 3.9 27.9 + - - +
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Residues in contact with GLY 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 SER 3.3 9.6 + - - -
106A TYR* 3.7 2.1 + - - -
107A LEU 3.3 2.8 - - - -
108A GLU* 1.3 83.3 - - - +
128A ALA* 5.0 6.4 - - - +
129A ILE 6.2 0.2 - - - -
210A LYS* 3.8 21.1 - - - -
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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