Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 2EX4
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 5.1 3.3 + - - +
20A TRP* 3.5 24.4 - - - +
21A LYS* 4.5 11.4 + - + +
92A ASP* 2.9 14.2 + - - +
93A ILE* 1.3 79.5 - - - +
95A GLU* 1.3 68.2 + - - +
96A ASP* 4.1 9.4 - - + +
97A PHE* 3.1 50.1 + - + +
98A LEU* 3.4 11.1 + - - +
117A CYS* 4.4 1.1 - - - -
1401A SAH 2.8 18.4 + - - -
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Residues in contact with GLU 95 (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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93A ILE 3.5 5.3 + - - -
94A THR* 1.3 72.2 - - - +
96A ASP* 1.3 62.1 + - - +
98A LEU* 3.0 9.0 + - + +
99A VAL* 2.9 41.2 + - + +
117A CYS* 3.8 26.6 - - + +
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Residues in contact with ASP 96 (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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21A LYS* 3.1 40.0 + - + +
25A PRO* 4.6 6.6 - - + +
94A THR* 3.2 9.5 - - + +
95A GLU* 1.3 81.6 - - - +
97A PHE* 1.3 64.2 + - + +
99A VAL* 3.6 8.2 + - - +
100A GLN* 3.1 27.5 + - - +
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Residues in contact with PHE 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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20A TRP* 3.3 41.3 - + - -
21A LYS 5.8 0.4 - - - -
23A ILE* 3.4 24.2 - - + -
25A PRO* 3.8 19.3 - - + -
30A MET* 3.6 27.6 - - + -
72A GLY* 3.6 18.8 - - - +
73A ILE* 3.5 15.7 - - - +
92A ASP* 3.9 2.0 - - - +
94A THR* 3.1 28.5 + - + +
96A ASP* 1.3 78.4 - - + +
98A LEU* 1.3 60.4 + - - +
100A GLN* 3.4 1.7 + - - +
101A ALA 2.8 23.6 + - - -
1401A SAH 3.3 31.6 - - - -
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Residues in contact with LEU 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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72A GLY 4.0 9.9 - - - +
90A MET* 4.1 28.9 - - + +
92A ASP* 3.7 29.6 - - + +
94A THR 3.4 9.6 + - - +
95A GLU* 3.0 7.8 + - + +
97A PHE* 1.3 74.0 - - - +
99A VAL* 1.3 69.3 + - + +
101A ALA* 3.2 17.3 - - - +
102A LYS* 3.5 13.1 + - - +
115A TYR* 3.9 21.5 - - + +
116A PHE 3.6 27.4 - - - +
117A CYS* 3.7 22.4 - - + +
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Residues in contact with VAL 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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95A GLU* 2.9 35.6 + - + +
96A ASP* 3.8 9.6 - - - +
98A LEU* 1.3 76.9 - - + +
100A GLN* 1.3 63.1 + - - +
102A LYS* 3.1 34.5 + - + +
103A THR* 3.9 3.3 + - - -
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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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25A PRO* 3.7 36.3 - - + +
73A ILE* 3.9 12.1 - - + -
96A ASP 3.1 18.4 + - - +
97A PHE 3.6 4.5 - - - +
99A VAL* 1.3 76.6 - - - +
101A ALA* 1.3 64.9 + - - +
103A THR* 2.8 31.2 + - - +
104A TYR* 2.8 28.0 + - + +
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Residues in contact with ALA 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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73A ILE 3.2 30.3 + - - +
90A MET* 3.8 18.8 - - + -
97A PHE 2.8 16.8 + - - +
98A LEU* 3.2 14.4 - - - +
99A VAL 3.2 0.4 - - - -
100A GLN* 1.3 72.1 - - - +
102A LYS* 1.3 57.7 + - - +
104A TYR* 4.1 1.6 - - - -
105A LEU* 2.8 39.7 + - + +
115A TYR* 3.9 9.2 - - + -
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Residues in contact with LYS 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 LEU* 3.6 14.4 - - - +
99A VAL* 3.3 22.4 - - + +
100A GLN 3.1 0.8 - - - -
101A ALA* 1.3 77.5 - - - +
103A THR* 1.3 61.7 + - - +
105A LEU* 4.8 1.5 - - - +
106A GLY* 3.9 13.7 + - - +
109A GLY* 5.9 0.5 - - - -
115A TYR* 3.7 47.2 - - + +
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Residues in contact with THR 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 VAL 3.9 3.1 + - - -
100A GLN* 2.8 28.7 + - - +
102A LYS* 1.3 77.5 - - - +
104A TYR* 1.3 66.1 + - - +
105A LEU 3.2 0.2 - - - -
106A GLY* 3.1 15.6 + - - -
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Residues in contact with TYR 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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27A VAL* 3.2 27.3 - - + +
73A ILE* 3.3 42.4 - - + +
74A GLY 3.7 18.4 - - - -
75A ARG* 4.0 8.6 + - - +
78A LYS* 3.2 52.4 + - + +
79A ARG* 5.5 6.2 - - - -
100A GLN* 2.8 26.9 + - + +
101A ALA 3.9 2.5 - - - +
103A THR* 1.3 75.1 - - - +
105A LEU* 1.3 63.3 + - + +
106A GLY* 3.6 0.7 + - - -
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Residues in contact with LEU 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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73A ILE 4.2 2.7 - - - +
74A GLY* 3.5 26.5 - - - +
77A THR* 4.0 5.8 - - + -
78A LYS* 3.6 35.8 - - + +
82A LEU* 4.4 3.2 - - + +
90A MET* 3.8 19.7 - - + -
101A ALA* 2.8 27.9 + - + +
102A LYS 4.9 0.9 - - - +
104A TYR* 1.3 77.9 - - + +
106A GLY* 1.3 65.3 + - - +
108A GLU* 3.5 9.4 + - - +
109A GLY* 3.2 22.8 + - - +
112A VAL* 3.7 29.6 - - + -
115A TYR* 4.2 5.8 - - - +
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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