Contacts of the helix formed by residues 103 - 114 (chain D) in PDB entry 3WBR
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 SER 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D GLN* 1.3 74.5 - - - +
104D TRP* 1.3 56.0 + - - +
105D THR* 3.8 5.9 + - - -
106D LYS* 3.3 34.4 + - - +
107D SER* 2.8 34.5 + - - -
141D PHE* 3.5 1.8 - - - -
198D CYS 3.5 14.4 - - - -
199D HIS* 3.9 25.2 + - - -
200D VAL 3.7 7.6 - - - -
201D PRO* 4.1 2.6 - - - +
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Residues in contact with TRP 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D SER* 1.3 74.8 - - - +
105D THR* 1.3 65.1 + - - +
107D SER* 3.0 4.3 + - - -
108D GLN* 2.8 47.7 + - + +
118D LEU* 3.4 16.0 - - + +
141D PHE* 3.3 32.0 - + + -
142D LEU 2.7 24.7 + - - -
143D GLY* 4.0 18.6 - - - -
144D LEU 3.8 7.2 + - - -
145D SER* 3.9 24.2 - - - -
180D CYS* 3.3 32.8 - - + -
181D ALA 4.8 0.2 - - - -
198D CYS* 3.0 14.3 + - + +
156E VAL* 3.8 25.6 - - + -
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Residues in contact with THR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D SER* 3.4 6.3 + - - -
104D TRP* 1.3 89.8 - - + +
106D LYS* 1.3 59.0 + - + +
108D GLN* 3.3 4.7 + - - +
109D LYS* 2.9 29.2 + - + +
178D GLU* 5.6 1.6 + - - -
198D CYS* 5.7 3.3 - - - +
199D HIS* 5.1 11.2 + - - -
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLN* 3.5 30.4 + - + +
103D SER* 3.3 26.0 + - - +
105D THR* 1.3 77.3 - - + +
107D SER* 1.3 60.2 + - - +
109D LYS* 3.6 9.4 - - + +
110D ASN* 2.9 28.2 + - - +
186F ARG* 5.9 5.7 - - - +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLN* 3.5 18.8 + - - +
103D SER 2.8 24.2 + - - -
104D TRP* 3.0 7.6 + - - -
106D LYS* 1.3 74.3 - - - +
108D GLN* 1.3 59.6 + - - +
110D ASN* 3.2 9.3 + - - +
111D CYS* 3.0 31.5 + - - -
118D LEU* 3.8 9.9 - - - -
141D PHE* 3.9 4.5 - - - -
202D GLN 4.2 2.6 + - - -
204D SER* 3.7 33.7 + - - -
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D TRP* 2.8 30.4 + - + +
105D THR* 3.6 5.8 - - + +
107D SER* 1.3 72.1 - - - +
109D LYS* 1.3 53.4 + - - +
111D CYS* 3.3 1.9 + - - +
112D SER* 2.8 42.5 + - - -
116D ALA 4.2 2.6 + - - -
117D ASP* 2.8 29.1 + - - +
118D LEU* 2.8 44.0 + - + +
156E VAL* 3.8 24.3 - - + +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D THR* 2.9 18.2 + - + +
106D LYS* 3.6 11.0 - - + +
108D GLN* 1.3 76.3 - - - +
110D ASN* 1.3 57.4 + - - +
112D SER* 3.1 10.6 + - - -
113D VAL* 2.9 55.5 + - + +
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Residues in contact with ASN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 5.4 0.8 - - - -
98D SER* 3.1 29.7 + - - -
102D GLN* 3.8 19.5 + - - +
106D LYS 2.9 19.1 + - - +
107D SER 3.2 7.1 + - - +
109D LYS* 1.3 78.4 - - - +
111D CYS* 1.3 59.2 + - - +
113D VAL* 3.6 10.3 + - - +
114D MET* 3.4 28.5 + - - +
204D SER* 4.9 3.4 + - - -
206D CYS* 4.9 5.2 - - - -
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Residues in contact with CYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D SER 3.0 18.4 + - - -
108D GLN 3.7 5.6 - - - +
110D ASN* 1.3 75.3 - - - +
112D SER* 1.3 57.9 + - - +
114D MET* 3.0 13.5 + - - +
116D ALA* 2.8 29.5 + - - +
117D ASP 3.6 22.7 - - - -
118D LEU* 3.8 17.9 - - - -
204D SER* 5.0 1.6 - - - -
206D CYS* 2.0 56.8 - - + -
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Residues in contact with SER 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLN* 2.8 27.1 + - - -
109D LYS* 3.4 13.7 - - - -
111D CYS* 1.3 78.0 - - - +
113D VAL* 1.3 57.2 + - - +
115D GLY* 3.1 17.7 + - - -
116D ALA 3.2 13.3 + - - -
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LYS* 2.9 48.9 + - + +
110D ASN* 3.8 9.4 - - - +
111D CYS 3.2 0.2 - - - -
112D SER* 1.3 72.0 - - - +
114D MET* 1.3 61.5 + - + +
115D GLY 3.1 8.4 + - - -
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Residues in contact with MET 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PRO* 6.1 0.9 - - + -
87D TRP* 3.8 37.3 - - + +
96D PHE* 4.1 34.5 - - + -
110D ASN* 3.4 26.2 - - - +
111D CYS* 3.0 8.3 + - - +
113D VAL* 1.3 78.1 - - + +
115D GLY* 1.3 61.1 + - - +
116D ALA 3.4 0.9 - - - -
206D CYS* 5.2 2.2 - - - -
208D MET* 3.5 17.0 - - - +
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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