Contacts of the helix formed by residues 105 - 119 (chain A) in PDB entry 1WYI
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A GLY 3.2 6.1 + - - -
104A GLU* 1.3 75.3 - - - +
106A ASP* 1.3 54.9 + - - +
107A GLU* 3.6 9.5 + - - +
108A LEU* 3.1 25.6 + - - +
109A ILE* 2.8 35.7 + - - +
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Residues in contact with ASP 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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99A ARG* 2.7 34.9 + - - +
105A SER* 1.3 70.7 - - - +
107A GLU* 1.3 56.9 + - - +
109A ILE* 4.0 6.3 - - - +
110A GLY* 2.5 35.3 + - - -
145A GLU* 5.4 2.1 - - - +
146A GLN* 3.9 22.2 + - - +
149A VAL* 3.4 28.5 - - + +
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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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105A SER* 3.2 8.6 + - - +
106A ASP* 1.3 80.0 - - - +
108A LEU* 1.3 58.2 + - - +
110A GLY* 3.2 1.6 + - - -
111A GLN* 2.6 51.5 + - + +
149A VAL* 5.2 2.0 - - - -
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Residues in contact with LEU 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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67A TYR* 4.1 15.0 - - + +
68A LYS* 3.9 26.0 - - + +
104A GLU* 3.2 27.8 - - + +
105A SER* 3.1 15.8 + - - +
107A GLU* 1.3 79.4 + - - +
109A ILE* 1.3 64.9 + - - +
111A GLN* 2.8 14.9 + - - +
112A LYS* 3.0 58.3 + - + +
102B PHE* 6.3 0.9 - - + -
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Residues in contact with ILE 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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93A LEU* 5.1 1.5 - - + +
94A GLY* 3.5 26.7 - - - +
98A ARG* 5.7 0.2 - - + -
99A ARG* 3.4 55.6 - - + +
104A GLU* 3.9 24.2 - - + +
105A SER 2.8 20.7 + - - +
106A ASP* 3.6 6.5 - - - +
108A LEU* 1.3 79.0 - - - +
110A GLY* 1.3 63.6 + - - +
112A LYS* 3.2 8.3 + - + +
113A VAL* 3.0 39.1 + - + +
149A VAL* 5.2 2.0 - - + -
150A ILE* 5.0 9.0 - - + -
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Residues in contact with GLY 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 ASP 2.5 21.1 + - - -
107A GLU 3.6 2.2 - - - -
109A ILE* 1.3 73.3 - - - +
111A GLN* 1.3 58.1 + - - +
113A VAL* 3.7 4.2 - - - +
114A ALA 3.2 10.6 + - - -
149A VAL* 3.6 11.0 - - - -
150A ILE* 5.7 0.2 - - - -
153A ASN* 2.7 48.6 - - - +
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Residues in contact with GLN 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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68A LYS* 3.6 43.0 + - + +
107A GLU* 2.6 41.2 + - + +
108A LEU* 2.8 22.1 + - - +
110A GLY* 1.3 77.8 - - - +
112A LYS* 1.3 59.3 + - - +
114A ALA* 3.6 5.5 + - - +
115A HIS* 3.0 28.2 + - - +
153A ASN* 4.8 1.8 - - - +
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Residues in contact with LYS 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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65A ASN* 3.1 16.2 + - - +
66A CYS* 2.9 25.7 + - - +
67A TYR* 4.3 12.3 - - - +
68A LYS* 4.0 17.5 - - - +
77A GLU* 4.9 3.4 + - - -
93A LEU* 3.8 25.4 - - + -
94A GLY 6.1 0.2 - - - +
104A GLU* 2.4 42.2 + - - +
108A LEU* 3.0 45.2 + - + +
109A ILE* 3.2 10.5 + - + +
111A GLN* 1.3 73.9 - - - +
113A VAL* 1.3 57.6 + - - +
115A HIS* 3.7 0.2 - - - +
116A ALA* 2.6 38.6 + - - +
102B PHE* 6.3 0.4 - - - -
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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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93A LEU* 3.7 23.3 - - + +
109A ILE* 3.0 34.0 + - + +
110A GLY* 3.7 8.1 - - - +
112A LYS* 1.3 74.6 - - - +
114A ALA* 1.3 60.9 + - - +
116A ALA* 3.9 0.8 - - - +
117A LEU* 2.9 40.6 + - + +
123A VAL* 4.6 10.5 - - + -
125A ALA* 5.2 2.5 - - + -
150A ILE* 4.2 18.8 - - + +
153A ASN* 3.9 18.6 - - + +
154A VAL* 3.9 19.7 - - + -
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Residues in contact with ALA 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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110A GLY 3.2 5.5 + - - +
111A GLN* 4.0 5.4 - - - +
113A VAL* 1.3 80.5 - - - +
115A HIS* 1.3 57.0 + - - +
117A LEU* 3.9 2.3 - - - +
118A ALA* 2.9 28.6 + - - +
153A ASN* 3.4 39.9 - - + +
155A LYS* 6.1 1.4 - - - +
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Residues in contact with HIS 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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67A TYR 4.0 0.4 + - - +
68A LYS* 3.0 28.2 - - - +
69A VAL* 3.5 19.5 - - - -
70A THR* 3.3 28.1 + - - +
80A PRO* 3.3 23.5 - - + +
111A GLN 3.0 19.3 + - - +
112A LYS 3.7 2.5 - - - +
114A ALA* 1.3 75.1 - - - +
116A ALA* 1.3 68.0 + - - +
118A ALA* 2.9 9.7 + - + +
119A GLU* 2.8 46.2 + - + +
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Residues in contact with ALA 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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66A CYS* 4.5 1.8 - - - -
80A PRO* 3.8 20.2 - - + +
91A VAL* 4.0 14.4 - - + -
93A LEU* 4.0 11.0 - - + -
112A LYS 2.6 22.1 + - - +
113A VAL 3.9 0.7 - - - +
115A HIS* 1.3 74.0 + - - +
117A LEU* 1.3 63.4 + - - +
119A GLU* 3.0 11.1 + - - +
121A LEU* 3.1 20.3 + - - +
123A VAL* 3.7 21.1 - - + -
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Residues in contact with LEU 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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113A VAL* 2.9 24.8 + - + +
114A ALA* 3.9 3.8 - - - +
116A ALA* 1.3 74.2 - - - +
118A ALA* 1.3 66.1 + - - +
120A GLY* 2.8 16.1 + - - -
121A LEU 3.4 18.3 + - - +
123A VAL* 3.4 15.9 - - + -
153A ASN 3.7 8.7 - - - +
154A VAL* 3.4 41.1 - - + -
155A LYS* 4.9 7.9 - - + +
156A ASP* 4.5 4.7 - - + +
159A LYS* 3.8 28.9 - - + +
160A VAL* 4.4 3.8 - - + -
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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 ALA 2.9 20.0 + - - +
115A HIS* 2.9 10.8 + - + +
117A LEU* 1.3 76.1 - - - +
119A GLU* 1.3 59.1 + - + +
120A GLY* 3.1 4.9 + - - -
155A LYS* 6.4 3.1 - - + +
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Residues in contact with GLU 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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70A THR* 3.1 29.6 - - - +
80A PRO* 3.6 17.7 - - + -
81A GLY* 4.0 17.4 - - - -
84A LYS* 2.7 49.9 + - + +
115A HIS* 2.8 35.8 + - + +
116A ALA 3.3 9.6 - - - +
117A LEU 3.0 0.2 - - - -
118A ALA* 1.3 76.1 - - + +
120A GLY* 1.3 55.8 + - - +
121A LEU 4.7 0.2 - - - +
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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