Contacts of the helix formed by residues 97 - 109 (chain B) in PDB entry 4O15
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 ASN 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B VAL 4.7 2.0 + - - +
23B TYR* 3.6 52.6 - - + +
95B VAL 3.5 1.8 + - - -
96B PHE* 1.3 76.0 - - - +
98B GLU* 1.3 64.6 + - - +
99B LYS* 3.8 6.9 + - - +
100B GLY* 2.9 30.4 + - - -
101B TRP* 3.3 26.9 + - + +
142B TYR* 5.8 0.2 + - - -
143B TRP* 3.7 25.1 - - + +
147B TRP* 5.7 4.9 - - + -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 4.0 16.3 - - + +
81B GLN* 4.8 4.7 - - - +
84B LYS* 3.0 42.2 + - + +
96B PHE* 2.9 32.2 + - + +
97B ASN* 1.3 72.1 - - - +
99B LYS* 1.3 60.1 + - + +
101B TRP* 3.4 2.8 + - - +
102B ASN* 2.9 50.9 + - - +
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASN* 3.2 6.0 + - - +
98B GLU* 1.3 79.4 - - + +
100B GLY* 1.3 56.8 + - - +
102B ASN* 3.3 10.3 + - - +
103B TYR* 2.9 29.1 + - - +
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN* 2.9 31.6 + - - -
99B LYS* 1.3 76.5 - - - +
101B TRP* 1.3 61.9 + - - +
103B TYR* 3.4 9.1 + - - +
104B ILE* 3.4 18.4 + - - +
140B GLU 5.9 0.2 - - - -
141B CYS* 5.4 0.5 - - - -
143B TRP* 3.7 21.7 - - - -
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Residues in contact with TRP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.4 11.0 - - + -
12B LEU* 3.6 33.0 - - + -
75B VAL* 3.6 36.1 - - + +
80B ILE* 3.8 11.8 - - + +
96B PHE* 3.5 20.4 - + + -
97B ASN* 3.3 26.7 + - + +
98B GLU 3.9 3.1 - - - +
100B GLY* 1.3 75.6 - - - +
102B ASN* 1.3 64.2 + - - +
104B ILE* 3.3 15.7 + - + +
105B LEU* 3.0 21.5 + - - +
112B LEU* 4.1 13.9 - - + -
143B TRP* 3.4 23.5 - + - -
144B LEU* 3.8 15.9 - - + -
147B TRP* 3.4 53.2 - + - -
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LYS* 5.8 1.0 - - - +
80B ILE* 3.2 23.1 - - - +
98B GLU* 2.9 45.7 + - - +
99B LYS* 3.6 9.3 - - - +
101B TRP* 1.3 78.0 - - - +
103B TYR* 1.3 56.8 + - - +
105B LEU* 3.3 9.3 + - - +
106B GLU* 2.8 48.9 + - - +
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS 2.9 12.7 + - - +
100B GLY* 3.4 12.6 - - - +
101B TRP 3.2 0.4 - - - -
102B ASN* 1.3 76.3 - - - +
104B ILE* 1.3 59.8 + - - +
106B GLU* 4.7 5.8 - - + -
107B LYS* 2.8 65.1 + - + +
108B TYR* 4.1 9.9 - + - -
138B ASP* 2.7 34.0 + - - -
140B GLU* 3.7 34.0 - - + +
141B CYS* 4.1 15.0 - - - -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.0 19.1 - - + -
100B GLY 3.4 6.0 + - - +
101B TRP* 3.3 19.6 + - + +
103B TYR* 1.3 77.2 - - - +
105B LEU* 1.3 64.6 + - - +
108B TYR* 3.0 24.0 + - + -
110B GLY 3.1 10.8 + - - -
111B HIS 3.5 27.1 - - - +
112B LEU* 4.6 1.8 - - + -
113B PRO* 4.1 5.6 - - + -
141B CYS* 3.8 19.3 - - - -
143B TRP* 3.9 27.8 - - + -
144B LEU* 3.8 28.5 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 4.0 19.3 - - - +
75B VAL* 3.6 28.2 - - + +
76B THR* 3.9 5.8 - - - -
77B LYS* 3.6 39.9 - - + +
80B ILE* 3.9 11.4 - - + -
101B TRP 3.0 12.9 + - - +
102B ASN* 3.4 14.6 - - - +
104B ILE* 1.3 77.7 - - - +
106B GLU* 1.3 67.5 + - + +
109B ASP* 3.2 24.2 + - - +
110B GLY* 3.4 8.2 + - - +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASN* 2.8 38.2 + - - +
103B TYR* 4.1 4.9 - - + +
105B LEU* 1.3 82.2 - - + +
107B LYS* 1.3 63.1 + - - +
109B ASP 4.3 1.9 + - - -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 2.8 54.8 + - + +
106B GLU* 1.3 74.9 - - - +
108B TYR* 1.3 95.3 + - + +
109B ASP 3.6 0.6 + - - -
138B ASP* 4.2 1.2 + - - -
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 4.1 4.9 - + - -
104B ILE* 3.0 17.2 + - - +
107B LYS* 1.3 110.8 + - + +
109B ASP* 1.3 71.9 + - - +
110B GLY 3.1 0.2 - - - -
111B HIS* 3.0 38.6 + - + +
113B PRO* 4.0 31.4 - - + -
137B THR* 5.2 2.2 + - - -
138B ASP* 2.5 38.4 + - + +
464B ASN* 5.6 10.5 - - + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 3.0 43.1 + - - +
105B LEU* 3.2 14.7 + - - +
106B GLU 4.3 2.4 + - - -
107B LYS 3.6 1.8 - - - -
108B TYR* 1.3 78.2 - - - +
110B GLY* 1.3 56.7 + - - +
111B HIS* 3.0 25.6 + - + +
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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