Contacts of the helix formed by residues 105 - 120 (chain A) in PDB entry 1WYN
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 MET 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.2 33.5 - - + +
38A PHE* 4.5 15.9 - - + -
39A GLN* 3.4 38.8 - - + -
99A LEU* 3.2 33.2 - - + -
102A SER* 4.5 11.1 + - - +
104A ASN* 1.3 75.0 + - - +
106A THR* 1.3 63.4 + - + +
107A GLN 3.6 0.7 - - - -
108A VAL* 4.1 13.7 - - + -
109A GLN* 3.4 18.5 + - - +
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Residues in contact with THR 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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12A SER* 3.5 18.0 + - - -
13A LYS* 3.8 8.2 - - - +
14A TYR* 3.9 25.1 - - + -
104A ASN* 3.1 14.4 + - - +
105A MET* 1.3 84.5 - - + +
107A GLN* 1.3 66.8 + - - +
108A VAL 3.3 0.4 - - - -
109A GLN* 3.5 1.4 + - - +
110A VAL* 3.3 30.0 + - - +
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Residues in contact with GLN 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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12A SER* 4.1 19.9 + - - -
91A VAL* 3.7 22.5 + - - +
93A LEU 3.0 25.7 + - - +
94A PHE* 3.9 7.5 - - + +
95A GLU* 5.3 2.9 - - - +
98A ASP* 4.1 10.5 - - - +
104A ASN* 3.4 28.0 + - + +
106A THR* 1.3 80.6 + - - +
108A VAL* 1.3 60.4 + - - +
110A VAL* 3.0 33.0 - - - +
111A SER* 3.1 12.1 + - - -
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Residues in contact with VAL 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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38A PHE* 5.4 0.9 - - + -
42A LEU* 5.0 5.2 - - + -
48A LEU* 5.1 1.6 - - + -
94A PHE* 3.1 51.6 - - + -
98A ASP* 4.0 6.3 - - + -
99A LEU* 3.9 28.3 - - + -
104A ASN 3.4 19.5 - - - +
105A MET* 4.1 13.4 - - + -
106A THR 3.3 0.6 - - - -
107A GLN* 1.3 74.4 - - - +
109A GLN* 1.3 65.9 + - - +
111A SER* 3.5 1.9 - - - -
112A LEU* 3.3 32.2 + - + +
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Residues in contact with GLN 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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13A LYS 4.6 3.6 - - - +
14A TYR* 2.7 41.8 + - + +
15A ASP* 2.9 43.4 + - - +
18A LYS* 4.4 3.8 - - - +
19A GLU* 3.7 20.0 - - - +
22A LEU* 3.3 28.5 - - + +
38A PHE* 5.5 8.8 - - + -
105A MET* 3.4 14.3 + - - +
106A THR* 3.5 7.1 + - - +
107A GLN 3.3 0.4 - - - -
108A VAL* 1.3 81.9 - - - +
110A VAL* 1.3 63.1 + - - +
112A LEU* 3.3 1.5 + - - -
113A LEU* 3.1 25.7 + - + +
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Residues in contact with VAL 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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10A LEU* 4.7 12.3 - - + +
11A LEU 4.5 1.3 - - - +
12A SER* 3.8 8.1 - - - -
13A LYS* 3.2 49.8 - - + +
92A ASP* 5.5 5.6 - - - +
106A THR 3.3 7.9 - - - +
107A GLN* 3.0 33.0 - - - +
109A GLN* 1.3 71.6 - - - +
111A SER* 1.3 79.2 + - - +
113A LEU* 2.8 14.8 + - + +
114A ALA* 2.7 26.3 + - + +
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Residues in contact with SER 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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83A MET* 3.2 26.2 - - - +
88A MET* 3.4 5.2 - - - +
92A ASP 2.7 28.3 + - - -
93A LEU* 3.6 1.4 - - - -
94A PHE* 3.5 15.5 - - - -
107A GLN 3.1 14.6 + - - -
108A VAL 3.5 6.5 - - - -
110A VAL* 1.3 82.8 - - - +
112A LEU* 1.3 59.3 + - - +
114A ALA* 3.2 2.1 + - - -
115A LEU* 2.8 30.3 + - - +
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Residues in contact with LEU 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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22A LEU* 3.4 27.1 - - + -
25A TRP* 4.0 3.0 - - + -
26A ILE* 3.8 21.1 - - + -
38A PHE* 3.9 19.1 - - + -
42A LEU* 4.7 2.0 - - + -
48A LEU* 3.9 26.7 - - + -
51A LEU* 4.3 11.4 - - + -
79A PHE* 4.3 18.8 - - + -
83A MET* 5.4 0.7 - - - -
94A PHE* 5.1 2.5 - - + -
108A VAL* 3.3 19.7 - - + +
109A GLN 3.3 2.8 + - - +
110A VAL 3.1 0.6 - - - -
111A SER* 1.3 74.7 - - - +
113A LEU* 1.3 60.8 + - - +
114A ALA 3.0 2.0 - - - -
115A LEU* 3.9 6.7 - - + +
116A ALA* 2.8 34.7 + - - +
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Residues in contact with LEU 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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8A ASN* 4.0 11.7 + - - -
10A LEU* 4.6 15.4 - - + +
13A LYS* 5.1 8.7 - - + -
18A LYS* 3.7 52.0 - - + +
21A GLU* 4.8 7.0 - - + +
22A LEU* 3.5 24.0 - - + -
109A GLN* 3.1 27.5 + - + +
110A VAL* 2.8 22.5 + - + +
112A LEU* 1.3 74.8 - - - +
114A ALA* 1.3 58.7 + - - +
116A ALA* 4.2 2.7 - - - +
117A GLY* 3.8 12.3 + - - -
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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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8A ASN* 4.7 20.8 - - + +
10A LEU* 5.7 5.8 - - + +
88A MET* 3.6 14.7 - - + +
92A ASP* 3.7 21.5 - - + +
110A VAL* 2.7 14.1 + - + +
111A SER 3.6 4.5 - - - +
113A LEU* 1.3 77.5 - - - +
115A LEU* 1.3 64.5 + - - +
116A ALA 3.3 1.7 + - - -
117A GLY* 3.8 1.4 + - - -
118A LYS* 3.6 20.3 + - - +
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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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25A TRP* 4.1 16.6 - - + -
51A LEU* 4.3 8.5 - - + -
52A MET* 4.0 16.8 - - - -
55A LEU* 4.0 14.6 - - + -
79A PHE* 4.0 29.2 - - + -
83A MET* 4.3 4.0 - - + -
86A TYR* 3.7 26.9 - - + -
88A MET* 3.4 25.1 - - + +
111A SER 2.8 17.4 + - - +
112A LEU* 3.9 5.6 - - + +
114A ALA* 1.3 74.7 - - - +
116A ALA* 1.3 60.3 + - - +
118A LYS* 3.6 5.3 + - - +
119A ALA* 3.0 25.6 + - - +
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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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22A LEU* 5.0 2.7 - - + -
25A TRP* 3.2 45.7 - - + +
112A LEU 2.8 18.0 + - - +
113A LEU* 4.5 4.7 - - - +
115A LEU* 1.3 73.9 - - - +
117A GLY* 1.3 67.7 + - - +
118A LYS 3.0 1.6 - - - -
119A ALA* 2.8 13.7 + - - +
120A LYS* 2.8 19.2 + - + +
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Residues in contact with GLY 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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8A ASN* 4.6 15.7 - - - -
113A LEU 3.8 12.8 + - - -
114A ALA 3.8 2.6 + - - -
115A LEU 3.6 0.2 - - - -
116A ALA* 1.3 78.4 - - - +
118A LYS* 1.3 58.3 + - - +
120A LYS* 3.6 19.3 - - - +
121A THR* 4.3 1.9 + - - -
124A LEU* 5.9 0.2 - - - +
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Residues in contact with LYS 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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2A SER* 4.7 6.0 + - - +
5A SER* 3.3 35.8 + - - +
7A GLY* 6.5 0.7 - - - -
8A ASN* 5.6 1.0 + - - -
86A TYR* 2.6 64.0 + - + -
87A GLY* 3.3 24.0 - - - +
88A MET* 4.2 9.0 - - - +
114A ALA 3.6 12.6 + - - +
115A LEU* 3.8 7.4 - - - +
116A ALA 3.0 0.6 - - - -
117A GLY* 1.3 76.3 - - - +
119A ALA* 1.3 55.2 + - - +
121A THR* 2.6 41.6 + - + +
134A TYR* 5.0 2.2 + - - +
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Residues in contact with ALA 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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25A TRP* 4.0 9.2 - - + +
55A LEU* 3.5 39.9 - - + -
86A TYR* 3.4 14.6 - - + +
115A LEU 3.0 18.4 + - - +
116A ALA 2.8 9.6 + - - +
118A LYS* 1.3 70.1 - - - +
120A LYS* 1.3 65.9 + - - +
122A LYS* 2.7 27.7 + - - +
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Residues in contact with LYS 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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25A TRP* 4.4 26.9 - - - +
116A ALA* 2.8 18.5 + - + +
117A GLY* 3.6 14.8 - - - +
118A LYS 3.2 0.2 - - - -
119A ALA* 1.3 76.0 - - - +
121A THR* 1.3 65.2 + - - +
122A LYS* 5.2 0.2 - - - -
123A GLY* 2.6 21.1 + - - -
124A LEU* 3.5 20.2 + - + +
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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