Contacts of the helix formed by residues 110 - 121 (chain A) in PDB entry 1WS6
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 PRO 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LYS* 3.8 27.1 - - + +
109A LEU* 1.3 95.3 - - + +
111A VAL* 1.3 66.4 + - - +
112A GLU* 3.8 18.2 - - + +
113A VAL* 3.0 39.1 + - + -
114A PHE 3.1 9.7 + - - -
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Residues in contact with VAL 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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62A PRO* 3.8 11.7 - - + -
63A PHE* 3.7 57.4 - - + +
83A VAL* 4.1 13.5 - - + +
84A GLU* 6.0 0.9 - - - -
85A LYS* 5.8 0.8 - - - +
109A LEU 3.6 0.4 + - - +
110A PRO* 1.3 73.1 - - - +
112A GLU* 1.3 57.7 + - - +
114A PHE* 4.3 2.2 - - + -
115A LEU* 3.1 48.7 + - + +
130A MSE 3.8 23.6 - - + -
141A LEU* 6.0 2.5 - - + -
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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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110A PRO* 3.8 20.3 - - + +
111A VAL* 1.3 79.0 - - - +
113A VAL* 1.3 64.7 + - + +
115A LEU* 5.3 3.8 - - - -
116A PRO* 3.3 21.8 - - - +
141A LEU* 6.5 0.7 - - + -
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Residues in contact with VAL 113 (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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109A LEU* 4.4 12.3 - - + -
110A PRO* 3.0 32.5 + - + +
112A GLU* 1.3 86.4 - - + +
114A PHE* 1.3 68.4 + - - +
116A PRO* 3.0 12.8 - - - +
117A GLU* 3.0 41.8 + - - +
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Residues in contact with PHE 114 (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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60A LEU* 3.9 36.8 - - + -
62A PRO* 5.6 0.2 - - + -
81A VAL* 4.2 11.0 - - + -
83A VAL* 4.0 19.1 - - + -
105A ARG* 5.7 2.9 - - - -
107A VAL* 4.0 34.1 - - + -
109A LEU* 3.2 21.0 - - + +
110A PRO 3.1 9.0 + - - +
111A VAL* 3.3 5.1 + - + +
113A VAL* 1.3 76.4 - - - +
115A LEU* 1.3 69.5 + - + +
117A GLU* 3.2 5.9 + - + +
118A ALA* 2.6 58.9 + - + +
123A GLU* 5.8 3.4 - - + -
125A PHE* 4.5 8.1 - + - -
150A LEU* 4.5 1.1 - - + -
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Residues in contact with LEU 115 (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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60A LEU* 4.7 7.2 - - + -
62A PRO* 5.4 1.8 - - + -
111A VAL* 3.1 32.7 + - + +
112A GLU* 5.4 2.2 - - - -
114A PHE* 1.3 90.4 - - + +
116A PRO* 1.3 72.1 - - + +
118A ALA* 3.6 2.8 - - - +
119A LYS* 3.0 27.9 + - - +
130A MSE 5.5 0.9 - - + -
141A LEU 5.6 0.2 - - - +
144A GLU* 4.1 31.9 - - + +
145A LEU* 4.1 20.4 - - + +
148A SER* 4.5 10.8 - - - +
150A LEU* 3.7 24.9 - - + +
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Residues in contact with PRO 116 (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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112A GLU 3.3 22.7 - - - +
113A VAL* 3.0 14.6 - - - +
115A LEU* 1.3 96.3 - - + +
117A GLU* 1.3 64.6 + - + +
119A LYS* 3.3 16.1 + - - +
120A ALA* 3.2 19.4 + - - +
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Residues in contact with GLU 117 (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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109A LEU* 4.8 9.9 - - - +
113A VAL* 3.0 39.1 + - - +
114A PHE* 3.2 6.4 + - + +
116A PRO* 1.3 79.3 - - + +
118A ALA* 1.3 66.9 + - - +
120A ALA* 3.3 7.7 + - - +
121A GLN* 2.9 40.2 + - + +
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Residues in contact with ALA 118 (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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114A PHE* 2.6 53.2 + - + +
115A LEU 3.6 4.3 - - - +
117A GLU* 1.3 71.8 - - - +
119A LYS* 1.3 64.7 + - - +
121A GLN* 3.1 9.5 + - - -
123A GLU* 3.1 42.6 + - + +
150A LEU* 4.0 12.8 - - + -
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Residues in contact with LYS 119 (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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115A LEU* 3.0 17.4 + - - +
116A PRO* 3.4 15.6 - - - +
117A GLU 3.2 0.2 - - - -
118A ALA* 1.3 76.7 - - - +
120A ALA* 1.3 54.6 + - - +
122A GLY* 2.7 27.5 + - - -
123A GLU 4.8 0.7 - - - +
124A ARG* 4.8 13.0 + - - +
147A ALA 4.4 4.3 - - - -
148A SER* 2.9 43.9 + - - +
150A LEU* 3.7 12.9 - - + +
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Residues in contact with ALA 120 (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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116A PRO 3.2 10.5 + - - +
117A GLU* 3.3 10.7 + - - +
119A LYS* 1.3 78.3 - - - +
121A GLN* 1.3 59.2 + - + +
122A GLY 3.1 3.5 + - - -
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Residues in contact with GLN 121 (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 ARG* 5.3 8.8 + - - +
117A GLU* 2.9 31.9 + - + +
118A ALA* 3.6 7.2 - - - +
119A LYS 3.0 1.4 + - - -
120A ALA* 1.3 77.2 - - + +
122A GLY* 1.3 63.0 + - - +
123A GLU* 3.3 28.9 + - + +
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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