Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 5WC9
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 3.8 2.9 + - - -
98A ILE* 1.3 78.6 - - - +
100A ILE* 1.3 65.1 - - - +
101A ALA* 4.0 6.9 + - - +
102A ALA* 3.3 22.3 + - - +
103A LYS* 3.1 19.9 + - - +
128A LEU 5.4 1.0 + - - -
130A LEU* 5.7 1.0 - - - +
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Residues in contact with ILE 100 (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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98A ILE 5.1 0.7 - - - +
99A SER* 1.3 72.6 - - - +
101A ALA* 1.3 62.2 + - - +
103A LYS* 3.5 22.1 + - + +
104A ASP* 3.2 35.8 + - - +
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Residues in contact with ALA 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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99A SER* 3.2 6.8 + - - +
100A ILE* 1.3 80.1 - - - +
102A ALA* 1.3 61.7 + - - +
104A ASP* 3.6 5.9 + - - +
105A ALA* 3.1 21.7 + - - +
108A ARG* 5.1 1.9 + - - -
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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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98A ILE* 3.7 15.0 - - + -
99A SER* 3.2 22.6 + - - +
101A ALA* 1.3 76.2 - - - +
103A LYS* 1.3 53.9 + - - +
105A ALA* 3.0 7.9 + - - +
106A LEU* 2.7 41.0 + - + +
128A LEU* 4.3 18.6 - - + +
130A LEU* 4.3 15.0 - - + -
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Residues in contact with LYS 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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97A THR* 5.2 4.6 - - - +
98A ILE* 3.3 33.5 + - + +
99A SER 3.1 12.1 + - - +
100A ILE* 3.9 21.0 - - + +
101A ALA 3.4 0.2 - - - -
102A ALA* 1.3 75.8 - - - +
104A ASP* 1.3 61.1 + - - +
106A LEU* 3.3 8.3 + - - +
107A GLU* 2.9 33.7 + - - +
138A TRP* 4.4 11.6 - - + +
174C T 4.4 18.3 + - - +
175C C 4.0 24.2 + - - +
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Residues in contact with ASP 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 ILE* 3.2 28.9 + - - +
101A ALA* 4.0 6.0 - - - +
103A LYS* 1.3 80.0 - - - +
105A ALA* 1.3 58.0 + - - +
107A GLU* 3.7 6.2 + - - +
108A ARG* 3.0 42.6 + - - +
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Residues in contact with ALA 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 ALA 3.1 14.5 + - - +
102A ALA* 3.0 12.4 + - - +
104A ASP* 1.3 75.2 - - - +
106A LEU* 1.3 54.3 + - + +
108A ARG* 3.0 24.8 + - - +
109A HIS* 2.7 47.7 + - + -
127A GLU* 5.1 5.4 - - - +
128A LEU* 5.8 4.7 - - + -
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Residues in contact with LEU 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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98A ILE* 4.7 4.5 - - + -
102A ALA* 2.7 28.5 + - + +
103A LYS* 3.8 4.7 - - - +
105A ALA* 1.3 71.2 - - + +
107A GLU* 1.3 51.9 + - - +
109A HIS* 3.0 9.0 + - + +
110A PHE* 2.6 36.0 + - - +
124A MET* 4.6 13.5 - - + -
128A LEU* 5.4 8.1 - - + -
130A LEU* 4.6 18.2 - - + -
135A VAL* 4.1 16.8 - - + -
138A TRP* 3.7 48.9 - - + +
139A PHE* 3.9 26.1 - - + -
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Residues in contact with GLU 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 LYS* 2.9 18.3 + - + +
104A ASP* 3.9 7.9 - - - +
106A LEU* 1.3 75.0 - - - +
108A ARG* 1.3 61.2 + - - +
110A PHE* 3.3 15.6 + - - +
111A GLY* 3.4 10.2 + - - -
138A TRP* 3.8 13.6 - - + -
142A ARG* 2.5 46.3 + - - -
145A ARG* 5.2 1.6 + - - +
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Residues in contact with ARG 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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101A ALA 5.1 1.2 + - - -
104A ASP* 3.0 36.7 + - - +
105A ALA* 3.0 29.0 + - - +
107A GLU* 1.3 76.4 - - - +
109A HIS* 1.3 61.1 + - - +
110A PHE 3.4 0.3 + - - -
111A GLY* 3.5 9.0 + - - -
112A GLU* 4.0 14.9 - - - +
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Residues in contact with HIS 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 ALA* 2.7 30.1 + - + +
106A LEU* 3.4 13.5 - - + +
108A ARG* 1.3 73.8 - - + +
110A PHE* 1.3 62.3 + - - +
112A GLU* 3.3 17.3 + - - +
113A GLN* 3.5 13.6 + - - +
124A MET* 4.0 42.7 - - + +
127A GLU* 2.6 38.6 + - - -
139A PHE* 4.6 3.1 - - + -
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Residues in contact with PHE 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 LEU 2.6 19.3 + - - +
107A GLU* 3.6 13.5 - - - +
108A ARG 3.2 0.6 - - - -
109A HIS* 1.3 75.3 - - - +
111A GLY* 1.3 61.8 + - - +
113A GLN 3.3 10.8 + - - -
114A ASN* 2.9 70.0 - - + +
138A TRP* 4.4 3.1 - + + -
139A PHE* 3.8 22.0 - + + -
142A ARG* 3.5 63.5 - - + -
143A ARG* 4.2 12.3 - - + -
146A GLU* 4.5 9.9 - - + -
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Residues in contact with GLY 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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107A GLU 3.4 9.9 + - - -
108A ARG 3.5 4.1 + - - -
109A HIS 3.3 1.0 - - - -
110A PHE* 1.3 81.0 - - - +
112A GLU* 1.3 65.1 + - - +
113A GLN 3.7 0.3 + - - -
114A ASN* 4.7 3.7 - - - +
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Residues in contact with GLU 112 (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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108A ARG 4.0 13.5 - - - +
109A HIS* 3.3 8.8 + - - +
110A PHE 3.2 0.8 - - - -
111A GLY* 1.3 80.5 - - - +
113A GLN* 1.3 69.2 + - - +
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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