Contacts of the helix formed by residues 100 - 111 (chain A) in PDB entry 3WH3
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LYS* 1.3 73.2 - - - +
101A TRP* 1.3 56.0 + - - +
102A ALA* 3.6 5.1 + - - +
103A LEU* 3.1 33.2 + - - +
104A SER* 2.7 34.7 + - - -
138A PHE* 3.6 1.8 - - - -
198A PHE* 3.8 26.0 - - - -
199A LEU 3.3 12.1 - - - -
200A ASN* 3.6 5.7 + - - -
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Residues in contact with TRP 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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100A SER* 1.3 71.0 - - - +
102A ALA* 1.3 72.8 + - + +
104A SER* 3.0 4.3 + - - -
105A LEU* 2.9 43.4 + - + +
115A LEU* 3.4 21.3 - - + -
138A PHE* 3.4 22.9 - + + -
139A ILE 3.2 21.3 - - - -
141A LEU 3.6 30.5 - - - -
142A SER* 3.8 17.7 - - - -
153A VAL* 3.8 18.6 - - + -
177A GLU* 3.4 25.9 + - - -
179A CYS* 3.3 23.8 - - + -
197A CYS* 2.8 31.1 + - + +
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Residues in contact with ALA 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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100A SER* 3.3 4.5 + - - +
101A TRP* 1.3 89.7 - - + +
103A LEU* 1.3 70.9 + - + +
105A LEU* 3.2 12.6 + - + +
106A LYS* 3.0 24.3 + - - +
198A PHE* 6.0 0.2 - - - +
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Residues in contact with LEU 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 LYS* 3.5 25.5 - - + +
100A SER* 3.1 23.2 + - - +
102A ALA* 1.3 85.7 - - + +
104A SER* 1.3 59.4 + - - +
106A LYS* 3.5 23.2 - - + +
107A ASN* 2.9 27.5 + - - +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 3.7 9.2 + - - +
100A SER 2.7 24.5 + - - -
101A TRP 3.3 6.7 - - - -
103A LEU* 1.3 75.4 - - - +
105A LEU* 1.3 64.6 + - - +
107A ASN* 3.2 0.9 + - - +
108A CYS* 2.9 30.5 + - - -
115A LEU* 4.3 8.7 - - - -
138A PHE* 3.5 19.4 - - - -
201A TYR 4.6 1.2 + - - -
203A ARG* 3.6 33.6 - - - +
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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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101A TRP* 2.9 43.1 + - + +
102A ALA* 3.3 12.1 - - + +
104A SER* 1.3 74.4 - - - +
106A LYS* 1.3 64.5 + - - +
108A CYS* 4.0 2.2 - - - +
109A SER* 3.0 26.0 + - - -
115A LEU* 3.6 29.6 - - + +
153A VAL* 4.0 20.6 - - + -
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Residues in contact with LYS 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 ALA 3.0 12.9 + - - +
103A LEU* 3.5 27.1 - - + +
104A SER 3.2 0.2 - - - -
105A LEU* 1.3 77.6 - - - +
107A ASN* 1.3 57.7 + - - +
109A SER* 3.3 6.2 + - - -
110A ALA* 2.9 29.3 + - + +
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Residues in contact with ASN 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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93A PHE* 4.7 1.0 - - - -
99A LYS* 3.9 13.4 - - - +
103A LEU 2.9 17.1 + - - +
104A SER 3.8 0.7 - - - +
106A LYS* 1.3 76.0 - - - +
108A CYS* 1.3 66.6 + - - +
110A ALA* 3.2 8.8 + - - +
111A MET* 3.1 44.1 + - - +
203A ARG* 2.8 43.2 + - - +
205A CYS* 4.3 3.1 - - - -
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Residues in contact with CYS 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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104A SER 2.9 20.0 + - - +
105A LEU* 4.0 3.4 - - - +
107A ASN* 1.3 74.9 - - - +
109A SER* 1.3 61.1 + - - +
111A MET* 3.0 10.1 + - - -
112A GLY 3.2 0.2 + - - -
113A ALA* 2.8 35.4 + - - +
114A HIS* 3.7 11.4 - - - -
115A LEU* 3.7 24.0 - - - +
203A ARG* 4.3 2.5 - - - -
205A CYS* 2.0 55.0 - - - -
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Residues in contact with SER 109 (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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105A LEU 3.0 19.5 + - - -
106A LYS* 3.4 7.4 - - - -
108A CYS* 1.3 77.5 - - - +
110A ALA* 1.3 56.6 + - - +
112A GLY* 2.9 20.3 + - - -
113A ALA 3.3 9.8 + - - -
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Residues in contact with ALA 110 (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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106A LYS* 2.9 20.8 + - + +
107A ASN* 3.2 12.1 + - - +
109A SER* 1.3 75.0 - - - +
111A MET* 1.3 61.4 + - + +
112A GLY 3.3 1.0 + - - -
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Residues in contact with MET 111 (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 TRP* 3.5 43.5 - - + +
93A PHE* 4.3 24.5 - - + -
107A ASN* 3.1 34.7 + - - +
108A CYS* 3.0 10.1 + - - +
110A ALA* 1.3 81.0 - - + +
112A GLY* 1.3 60.7 + - - +
113A ALA* 3.3 1.6 + - - +
205A CYS* 5.4 1.3 - - - -
207A MET* 3.8 14.4 - - - +
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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