Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 2R5G
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 PHE 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A CYS* 6.0 0.4 - - - -
32A PHE* 3.2 58.5 - + + -
69A ASN 6.1 0.2 - - - -
70A PRO 4.9 3.8 - - - -
71A PRO* 3.7 27.7 + - + -
81A THR 3.8 0.6 - - - -
82A ASP* 1.3 90.5 - - - +
84A ILE* 1.3 61.1 + - + +
86A ILE* 2.9 34.0 + - - +
87A GLU 3.4 1.2 + - - -
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Residues in contact with ILE 84 (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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32A PHE* 3.4 6.8 - - + -
35A ARG* 4.0 13.7 - - - +
82A ASP* 2.8 8.7 + - - +
83A PHE* 1.3 80.1 - - + +
85A LYS* 1.3 66.1 + - + +
87A GLU* 3.2 34.0 + - + +
88A GLU* 2.9 50.9 + - + +
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Residues in contact with LYS 85 (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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80A LYS* 6.2 0.2 - - - -
81A THR 3.5 14.4 - - - +
82A ASP* 3.0 35.0 + - + +
84A ILE* 1.3 83.4 - - + +
86A ILE* 1.3 57.0 + - - +
88A GLU* 3.8 16.2 - - - +
89A PHE* 3.1 28.4 + - - +
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Residues in contact with ILE 86 (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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36A LEU* 3.8 33.7 - - + -
71A PRO* 3.6 24.2 - - + +
72A PHE* 4.0 5.6 - - - -
73A LEU* 4.0 25.1 - - + -
80A LYS* 3.8 22.9 - - + +
81A THR 3.7 19.7 - - - +
83A PHE* 2.9 20.9 + - - +
85A LYS* 1.3 75.6 - - - +
87A GLU* 1.3 65.9 + - - +
89A PHE* 3.3 6.7 + - + +
90A LEU* 3.0 31.7 + - + +
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Residues in contact with GLU 87 (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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32A PHE* 4.6 2.9 - - + -
35A ARG* 2.8 44.1 + - - +
36A LEU* 3.9 13.8 - - + +
39A ILE* 3.2 27.5 - - + +
83A PHE 3.4 2.6 + - - +
84A ILE* 3.2 25.6 + - + +
86A ILE* 1.3 78.7 - - - +
88A GLU* 1.3 58.4 + - + +
90A LEU* 3.3 4.5 + - - +
91A GLU* 2.9 28.2 + - - +
110A PHE* 4.3 4.9 - - - -
181A LEU* 3.7 36.4 - - + +
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Residues in contact with GLU 88 (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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84A ILE* 2.9 41.5 + - + +
85A LYS* 3.8 18.3 - - - +
87A GLU* 1.3 76.4 - - + +
89A PHE* 1.3 62.5 + - - +
91A GLU* 3.5 5.0 + - - +
92A GLN* 3.0 28.0 + - - +
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Residues in contact with PHE 89 (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 LEU* 4.8 2.2 - - + -
75A TYR* 3.6 46.9 - + + -
78A GLU* 4.8 2.9 - - - -
80A LYS* 3.2 51.1 - - + +
85A LYS 3.1 18.9 + - - +
86A ILE* 3.6 7.0 - - - +
87A GLU 3.3 0.2 - - - -
88A GLU* 1.3 76.8 - - - +
90A LEU* 1.3 68.8 + - + +
92A GLN* 3.4 12.5 + - - +
93A THR* 2.7 58.1 + - + -
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Residues in contact with LEU 90 (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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14A ILE* 4.9 0.4 - - + -
36A LEU* 4.1 21.8 - - + +
39A ILE* 4.1 20.0 - - + -
40A LEU* 3.8 38.6 - - + -
43A LYS* 3.9 3.1 - - - -
73A LEU* 4.2 18.2 - - + -
75A TYR* 4.8 6.1 - - + -
86A ILE* 3.0 28.0 + - + +
87A GLU* 3.3 4.0 + - - +
89A PHE* 1.3 89.2 - - + +
91A GLU* 1.3 60.2 + - - +
93A THR* 4.9 0.7 - - - -
94A LEU* 3.0 48.8 + - + +
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Residues in contact with GLU 91 (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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39A ILE* 5.4 1.1 - - + +
43A LYS* 2.8 29.5 + - - +
87A GLU 2.9 16.7 + - - +
88A GLU* 4.0 5.8 - - - +
90A LEU* 1.3 76.6 - - - +
92A GLN* 1.3 61.8 + - - +
94A LEU 3.6 10.9 - - - +
95A ALA* 4.1 5.7 - - - +
101A HIS* 3.3 16.1 + - - -
102A LEU* 3.2 18.5 + - - +
103A SER* 2.9 44.8 + - - +
181A LEU* 4.2 14.8 - - + +
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Residues in contact with GLN 92 (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 GLU 3.0 19.4 + - - +
89A PHE* 3.7 12.5 - - - +
91A GLU* 1.3 76.8 - - - +
93A THR* 1.3 69.8 + - - +
95A ALA* 3.3 18.5 - - - +
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Residues in contact with THR 93 (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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75A TYR* 3.2 38.0 + - + +
89A PHE* 2.7 50.8 + - + -
90A LEU* 4.5 0.4 - - - -
92A GLN* 1.3 80.7 - - - +
94A LEU* 1.3 62.7 + - - +
95A ALA* 3.3 6.2 + - - +
99A TYR* 4.9 2.9 - - - -
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Residues in contact with LEU 94 (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* 4.1 22.9 - - + -
14A ILE* 4.2 3.4 - - + -
40A LEU* 4.3 3.6 - - + -
43A LYS* 2.7 61.8 + - + +
45A VAL* 4.0 21.5 - - + -
75A TYR* 4.3 8.5 - - + +
90A LEU* 3.0 39.1 + - + +
91A GLU 3.6 1.2 - - - +
93A THR* 1.3 77.3 - - - +
95A ALA* 1.3 56.7 + - - +
99A TYR* 3.5 39.5 - - + +
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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