Contacts of the helix formed by residues 98 - 108 (chain A) in PDB entry 1WKB
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ARG* 2.9 36.2 + - + +
96A ASN* 3.2 6.2 - - + -
97A ARG* 1.3 74.7 - - - +
99A PRO* 1.3 78.0 - - - +
100A LYS* 3.6 10.3 + - - +
101A THR* 2.6 38.0 + - - +
102A ILE* 2.9 23.9 + - - +
199A MET 5.2 3.9 - - - +
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Residues in contact with PRO 99 (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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97A ARG 3.1 8.7 - - - +
98A ASP* 1.3 90.7 - - - +
100A LYS* 1.3 63.4 + - - +
102A ILE* 3.7 7.5 - - + +
103A TRP* 2.9 26.2 + - - +
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Residues in contact with LYS 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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93A ARG* 5.5 3.8 - - - +
98A ASP* 3.4 10.8 + - - +
99A PRO* 1.3 79.8 - - - +
101A THR* 1.3 63.9 + - - +
103A TRP* 3.4 7.5 + - + +
104A ILE* 3.0 40.1 + - + +
654A SER* 2.8 41.9 - - - +
902A SO4 4.0 4.3 + - - -
903A SO4 4.3 19.3 - - - +
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Residues in contact with THR 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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90A ILE* 4.1 7.9 - - + -
93A ARG* 3.3 32.0 + - + -
94A ILE* 3.7 28.0 - - + -
98A ASP* 2.6 30.0 + - - -
100A LYS* 1.3 72.9 - - - +
102A ILE* 1.3 67.6 + - - +
104A ILE* 3.2 9.0 + - - +
105A TYR* 3.0 44.9 + - + -
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Residues in contact with ILE 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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94A ILE* 5.1 9.2 - - + -
97A ARG* 3.1 53.4 - - + +
98A ASP 2.9 13.8 + - - +
99A PRO* 3.7 7.2 - - + +
101A THR* 1.3 75.4 - - - +
103A TRP* 1.3 58.0 + - - +
105A TYR* 3.2 3.2 + - - +
106A ARG* 2.8 50.1 + - + +
116A LEU* 4.2 13.0 - - + -
117A TRP* 4.2 23.3 - - + -
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Residues in contact with TRP 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 PRO 2.9 18.6 + - - +
100A LYS* 3.7 7.0 - - + +
102A ILE* 1.3 79.9 - - - +
104A ILE* 1.3 69.0 + - + +
106A ARG* 4.5 4.5 - - + +
107A ASP* 2.8 64.8 + - + +
108A VAL* 4.2 3.4 - - + -
653A LYS 3.4 22.9 - - - -
654A SER* 3.6 14.6 - - - -
655A LYS 4.1 3.8 - - - -
656A GLY* 3.6 25.4 - - - -
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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 LYS* 3.0 50.5 + - + +
101A THR* 3.2 9.6 + - - +
103A TRP* 1.3 86.0 - - + +
105A TYR* 1.3 66.7 + - + +
108A VAL* 3.0 29.2 + - + +
109A TYR* 3.0 31.7 + - + -
653A LYS* 3.8 51.1 - - + +
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Residues in contact with TYR 105 (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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46A SER* 2.6 30.1 + - - -
90A ILE* 3.4 44.7 - - + +
94A ILE* 5.1 0.7 - - + -
101A THR* 3.0 34.0 + - + +
102A ILE 3.9 1.3 - - - +
104A ILE* 1.3 89.4 - - + +
106A ARG* 1.3 58.5 + - - +
109A TYR* 3.4 25.5 - + - -
110A LYS 3.2 8.0 + - - -
111A VAL* 2.9 30.3 + - + +
116A LEU* 3.6 25.4 - - + -
119A PHE* 4.2 14.6 - + - -
125A ILE* 5.3 1.3 - - + -
129A PHE* 3.7 21.5 - + - -
653A LYS* 6.4 0.2 - - + -
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Residues in contact with ARG 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 ILE* 2.8 32.7 + - + +
103A TRP* 4.0 4.9 - - + +
105A TYR* 1.3 75.8 - - - +
107A ASP* 1.3 60.5 + - + +
110A LYS* 3.0 28.5 - - - +
111A VAL 2.8 29.7 + - - +
112A PRO* 3.6 4.8 - - - +
113A GLU* 3.3 40.9 + - - +
116A LEU* 3.7 18.8 - - + +
117A TRP* 5.8 1.6 - - - -
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Residues in contact with ASP 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 TRP* 2.8 62.9 + - + +
106A ARG* 1.3 75.0 - - + +
108A VAL* 1.3 66.5 + - - +
110A LYS* 3.6 19.1 + - - +
656A GLY* 4.7 5.2 - - - +
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Residues in contact with VAL 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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103A TRP* 4.2 7.6 - - + -
104A ILE* 3.0 16.5 + - + +
107A ASP* 1.3 83.9 - - - +
109A TYR* 1.3 78.3 + - + +
110A LYS* 3.4 6.0 + - - +
653A LYS* 3.7 28.0 - - + +
656A GLY* 3.7 22.2 - - - +
658A VAL* 3.2 37.6 - - + +
660A ASN* 2.9 22.7 + - - -
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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