Contacts of the helix formed by residues 106 - 120 (chain A) in PDB entry 2W3S
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 CYS 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA* 5.2 10.4 - - + +
100A GLY 5.8 2.5 - - - -
101A SER* 6.2 0.2 - - - -
104A GLY 3.1 0.6 - - - -
105A PHE* 1.3 77.0 - - - +
107A THR* 1.3 68.0 + - - +
108A PRO* 3.4 2.5 - - - -
109A GLY* 3.5 4.2 + - - -
110A PHE* 3.2 45.1 + - + -
132A ASN* 5.2 0.5 + - - -
133A LEU 3.4 20.4 - - - +
134A CYS* 3.6 3.4 - - - -
142A ILE* 5.3 1.6 - - - -
1463A FES 2.3 40.5 - - - -
176B LEU* 4.5 5.8 - - + -
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Residues in contact with THR 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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95A MET* 3.5 27.4 - - + -
100A GLY 5.1 0.2 + - - -
101A SER* 3.2 21.2 - - - -
104A GLY* 2.6 38.5 + - - -
106A CYS* 1.3 74.8 - - - +
108A PRO* 1.4 66.0 - - - +
110A PHE* 3.5 3.8 + - - +
111A ILE* 3.0 37.0 + - + +
15B HIS* 4.0 10.3 - - - +
16B VAL* 4.2 18.8 - - + +
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Residues in contact with PRO 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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34A GLY 3.2 28.3 - - - +
35A THR* 5.1 0.9 - - - -
36A LYS* 4.2 13.5 - - + -
46A ALA 4.8 5.2 - - - +
78A ILE* 3.8 26.1 - - + +
104A GLY 3.4 10.5 - - - +
105A PHE* 3.7 8.1 - - - +
106A CYS 3.6 3.4 - - - -
107A THR* 1.4 90.8 - - - +
109A GLY* 1.3 56.3 + - - +
111A ILE* 3.3 2.9 + - - +
112A VAL* 3.0 34.6 + - - +
15B HIS 4.4 3.8 - - - +
18B GLY* 4.3 14.8 - - - -
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Residues in contact with GLY 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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45A GLY 3.5 21.1 - - - -
46A ALA 4.1 9.8 + - - -
48A THR* 3.4 16.5 - - - +
106A CYS 3.5 5.0 + - - -
107A THR 3.3 0.4 - - - -
108A PRO* 1.3 77.4 - - - +
110A PHE* 1.3 63.0 + - - +
113A SER* 3.0 18.2 + - - -
132A ASN* 3.2 14.7 + - - -
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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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95A MET* 4.3 5.8 - - + -
106A CYS* 3.2 47.9 + - + -
107A THR* 4.0 5.4 - - - +
109A GLY* 1.3 72.5 - - - +
111A ILE* 1.3 55.1 + - - +
113A SER* 3.1 4.3 + - - -
114A MET* 2.5 53.6 + - + +
129A LEU* 4.2 13.0 - - + -
132A ASN* 3.0 45.2 - - + +
133A LEU 4.0 3.6 - - - -
134A CYS* 3.6 13.9 - - + -
139A TYR* 4.0 4.5 - + - -
142A ILE* 3.8 35.2 - - + -
701B PHE* 4.2 17.7 - + - -
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Residues in contact with ILE 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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78A ILE* 3.5 22.2 - - + -
81A ILE* 3.8 17.7 - - + -
91A VAL* 3.6 24.6 - - + +
92A GLN* 3.8 11.2 - - + -
95A MET* 3.7 15.5 - - + -
107A THR* 3.0 28.4 + - + +
108A PRO 3.5 4.0 - - - +
110A PHE* 1.3 75.3 - - - +
112A VAL* 1.3 54.3 + - - +
114A MET* 3.4 8.2 - - + +
115A ALA* 2.7 34.1 + - - +
16B VAL* 3.6 32.3 - - + +
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Residues in contact with VAL 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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48A THR* 3.3 31.9 - - + +
49A VAL* 3.4 25.1 - - - -
50A MET* 3.4 14.2 - - + +
59A ALA* 4.8 0.9 - - + -
76A ARG 4.7 1.3 - - - +
77A THR 4.4 2.0 - - - -
78A ILE* 3.9 30.3 - - + +
81A ILE* 4.4 8.5 - - + -
108A PRO 3.0 17.1 + - - +
109A GLY 3.8 2.5 - - - +
110A PHE 3.2 0.2 - - - -
111A ILE* 1.3 77.6 - - - +
113A SER* 1.3 57.2 + - - +
115A ALA* 3.7 4.4 - - - +
116A ALA* 3.0 29.5 + - - +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.1 21.7 - - - +
59A ALA* 3.8 14.0 - - - +
109A GLY 3.0 13.2 + - - -
110A PHE 3.4 3.6 - - - -
112A VAL* 1.3 76.9 - - - +
114A MET* 1.3 57.5 + - - +
116A ALA* 4.0 1.2 - - - +
117A ALA* 3.1 28.6 + - - +
128A LEU* 4.1 6.1 + - - +
129A LEU* 3.5 23.5 - - - +
132A ASN* 3.1 14.7 + - - -
274A GLN* 3.2 7.4 + - - -
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Residues in contact with MET 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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91A VAL* 3.6 21.5 - - + +
95A MET* 3.5 47.6 - - + +
110A PHE* 2.5 24.8 + - + +
111A ILE* 3.3 34.3 - - + +
113A SER* 1.3 70.3 - - - +
115A ALA* 1.3 59.5 + - - +
117A ALA* 3.5 5.8 + - - +
118A HIS* 2.8 27.4 + - - +
125A TYR* 6.5 0.4 - - + -
129A LEU* 4.2 19.3 - - + -
142A ILE* 4.2 21.1 - - - +
145A ALA* 5.1 2.9 - - - -
146A ALA* 5.0 12.1 - - + -
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Residues in contact with ALA 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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50A MET* 4.9 2.0 - - - -
81A ILE* 3.7 32.8 - - + -
89A HIS* 4.1 19.1 + - + +
91A VAL* 3.9 6.4 - - + +
111A ILE 2.7 20.4 + - - +
112A VAL 3.7 1.8 - - - +
114A MET* 1.3 70.5 - - - +
116A ALA* 1.3 54.5 + - - +
118A HIS* 2.8 10.2 + - - +
119A ASP* 2.7 36.1 + - - +
158A LEU* 4.4 4.6 - - + +
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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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50A MET* 3.8 36.3 - - + -
57A SER* 4.7 1.4 + - - +
58A ARG* 4.3 4.5 - - - -
59A ALA* 3.9 25.1 - - + +
112A VAL 3.0 17.9 + - - +
113A SER 4.1 1.3 - - - +
115A ALA* 1.3 75.5 - - - +
117A ALA* 1.3 62.2 + - - +
119A ASP* 3.4 3.5 + - - +
120A ARG* 3.3 27.0 + - - +
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Residues in contact with ALA 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 SER 3.1 19.7 + - - +
114A MET* 3.6 7.4 - - - +
116A ALA* 1.3 75.2 - - - +
118A HIS* 1.3 65.4 + - - +
120A ARG* 3.1 4.5 + - - +
121A ASP 3.0 3.8 + - - -
122A ARG* 3.0 38.1 + - - +
125A TYR* 5.2 6.1 - - + -
128A LEU* 3.8 33.0 - - + -
129A LEU* 6.1 0.4 - - + -
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Residues in contact with HIS 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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89A HIS* 3.8 28.0 + + + +
90A PRO* 4.4 3.9 - - + +
91A VAL* 4.4 2.7 - - + -
114A MET 2.8 15.0 + - - +
115A ALA 2.8 9.5 + - - +
117A ALA* 1.3 75.6 - - - +
119A ASP* 1.3 61.1 + - - +
121A ASP* 3.1 16.0 + - - +
122A ARG 5.2 1.8 - - - -
149A ALA* 3.0 38.9 + - + -
150A ALA* 4.2 8.4 + - - -
152A GLU* 3.1 24.7 + - - +
153A PRO 3.4 16.8 - - - -
154A PRO* 3.5 24.9 - - + +
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Residues in contact with ASP 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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50A MET* 3.7 10.5 - - + -
52A ARG* 2.9 27.7 + - - -
57A SER* 2.6 24.7 + - - -
89A HIS* 5.8 0.2 + - - -
115A ALA 2.7 19.3 + - - +
116A ALA 3.4 7.2 - - - +
118A HIS* 1.3 74.5 + - - +
120A ARG* 1.3 58.9 + - - +
121A ASP 3.4 1.2 + - - -
154A PRO* 5.0 10.1 - - - +
155A ALA 4.7 2.3 + - - +
158A LEU* 4.4 10.7 - - + +
159A GLN* 4.0 30.0 + - - +
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Residues in contact with ARG 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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55A ALA 6.1 0.2 - - - -
56A GLY* 5.8 1.6 - - - -
57A SER* 3.2 40.7 + - - +
58A ARG* 4.9 5.9 - - - +
116A ALA 3.3 9.2 + - - +
117A ALA* 3.1 4.8 + - - +
119A ASP* 1.3 80.7 - - - +
121A ASP* 1.3 70.9 + - - +
122A ARG* 2.9 55.2 + - + +
128A LEU* 5.5 2.6 - - - +
273A GLU* 4.6 5.5 + - - +
277A GLN* 4.3 20.3 + - - +
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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