Contacts of the helix formed by residues 109 - 124 (chain A) in PDB entry 4PJW
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 ASP 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A SER 2.8 19.7 + - - +
108A HIS* 1.3 91.5 + - + +
110A ARG* 1.3 67.8 + - - +
111A ASP* 3.2 21.2 + - - +
112A ILE* 3.5 32.1 - - + +
113A ALA* 3.4 13.3 + - - +
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Residues in contact with ARG 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 TYR* 3.2 53.2 + - + +
107A LYS 5.0 0.6 + - - +
108A HIS 4.2 0.2 - - - -
109A ASP* 1.3 71.9 + - - +
111A ASP* 1.3 60.1 + - - +
113A ALA* 3.3 3.3 + - - +
114A LEU* 2.8 34.1 + - - +
193A ASP* 3.6 35.6 + - - +
195A TYR* 3.9 38.5 - - + +
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Residues in contact with ASP 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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109A ASP* 3.2 11.1 + - - +
110A ARG* 1.3 78.3 - - - +
112A ILE* 1.3 68.1 + - + +
114A LEU* 3.6 2.9 + - - +
115A LEU* 3.2 22.9 + - - +
136A PHE* 3.9 19.6 - - + -
137A ARG* 5.9 2.9 - - - +
195A TYR* 2.4 35.8 + - - -
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Residues in contact with ILE 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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105A SER* 4.7 13.7 - - - +
108A HIS* 5.7 0.7 - - - +
109A ASP* 3.5 38.3 + - + +
111A ASP* 1.3 77.1 - - + +
113A ALA* 1.3 67.8 + - + +
115A LEU* 3.5 8.7 + - - +
116A ASP* 2.8 44.5 + - - +
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Residues in contact with ALA 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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102A TRP* 3.0 28.9 + - + +
105A SER* 4.0 10.3 - - - +
106A TYR* 3.7 26.9 - - + +
109A ASP 3.4 14.3 + - - +
110A ARG 3.3 3.1 + - - +
111A ASP 3.2 0.4 - - - -
112A ILE* 1.3 84.4 - - + +
114A LEU* 1.3 66.3 + - - +
116A ASP* 3.1 7.2 + - - +
117A LEU 2.9 16.8 + - - -
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Residues in contact with LEU 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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102A TRP* 4.1 5.6 - - + -
106A TYR* 4.0 6.3 - - + -
110A ARG 2.8 21.3 + - - +
111A ASP 4.2 2.9 - - - +
113A ALA* 1.3 72.3 - - - +
115A LEU* 1.3 51.9 + - - +
117A LEU* 2.9 23.5 + - + +
118A ILE* 2.7 39.5 + - - +
136A PHE* 4.2 13.2 - - + -
195A TYR* 3.3 39.7 - - + +
196A MSE 3.9 32.5 - - + +
199A THR* 3.6 29.6 - - + +
200A VAL* 4.7 0.2 - - + -
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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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111A ASP 3.2 18.4 + - - +
112A ILE* 3.6 8.1 - - - +
113A ALA 3.2 0.2 - - - -
114A LEU* 1.3 74.7 - - - +
116A ASP* 1.3 66.7 + - - +
118A ILE* 3.3 8.5 + - + -
119A ASN* 2.9 54.2 + - - +
131A VAL* 3.4 24.0 - - + +
132A THR* 3.9 6.1 - - - +
133A ALA* 3.6 34.8 - - + +
136A PHE* 4.0 22.1 - - + -
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Residues in contact with ASP 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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83A MSE 4.6 8.3 + - - -
84A LEU* 4.0 30.7 - - + +
102A TRP* 4.6 3.6 - - + +
112A ILE* 2.8 30.3 + - - +
113A ALA* 3.1 12.8 + - - +
115A LEU* 1.3 80.1 - - - +
117A LEU* 1.3 60.5 + - - +
119A ASN* 3.9 5.9 + - - +
120A PHE* 3.3 20.6 + - - +
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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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84A LEU* 4.7 4.3 - - + -
102A TRP* 3.7 30.9 - - + +
113A ALA 2.9 9.9 + - - +
114A LEU* 2.9 17.1 + - + +
116A ASP* 1.3 77.3 - - - +
118A ILE* 1.3 68.8 + - + +
120A PHE* 3.2 14.1 + - + +
121A PHE* 3.3 28.8 + - + -
178A PHE* 4.2 18.6 - - + -
182A LEU* 4.1 26.2 - - + -
196A MSE 4.9 2.5 - - - -
200A VAL* 3.4 33.4 - - + -
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Residues in contact with ILE 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 LEU* 2.7 22.9 + - + +
115A LEU* 3.5 15.3 - - + +
117A LEU* 1.3 75.1 - - + +
119A ASN* 1.3 63.5 + - - +
121A PHE* 3.1 14.2 + - + +
122A ILE* 3.2 13.6 + - + +
131A VAL* 4.0 27.6 - - + -
136A PHE* 4.1 14.4 - - + -
141A ASN* 6.1 0.4 - - - +
144A ILE* 5.5 5.4 - - + -
199A THR* 3.6 30.7 - - + -
200A VAL* 5.5 4.3 - - + +
203A LEU* 3.7 38.7 - - + +
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Residues in contact with ASN 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* 2.9 36.2 + - - +
116A ASP* 4.1 5.8 - - - +
118A ILE* 1.3 79.3 - - - +
120A PHE* 1.3 54.8 + - - +
122A ILE* 3.2 8.6 + - - +
123A GLN* 2.8 55.0 + - - +
129A GLY 4.6 0.7 - - - +
130A VAL* 3.5 15.1 - - - +
131A VAL* 2.8 48.7 + - - +
148A MSE 4.9 1.0 - - - +
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Residues in contact with PHE 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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84A LEU* 3.8 20.2 - - + -
85A PHE* 3.7 22.9 - - - +
88A VAL* 3.5 34.1 - - + -
116A ASP 3.3 14.1 + - - +
117A LEU* 3.2 11.8 + - + +
118A ILE 3.2 0.2 - - - -
119A ASN* 1.3 77.8 - - - +
121A PHE* 1.3 78.8 + + - +
123A GLN* 3.8 4.9 - - - +
124A CYS* 2.9 60.6 + - - -
175A PHE* 3.9 19.1 - + - -
178A PHE* 3.9 33.0 - + - -
179A ILE* 5.0 1.1 - - + -
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Residues in contact with PHE 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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117A LEU* 3.3 35.2 + - + -
118A ILE* 3.1 8.5 + - + +
120A PHE* 1.3 95.6 - + - +
122A ILE* 1.3 63.6 + - - +
124A CYS* 3.6 8.2 + - - +
125A SER* 3.1 16.6 + - - -
175A PHE* 4.2 6.3 - + - -
178A PHE* 5.8 0.9 - + - -
179A ILE* 3.7 39.0 - - + -
182A LEU* 6.1 1.8 - - + -
200A VAL* 3.7 30.5 - - + -
203A LEU* 4.5 13.0 - - + -
204A LEU* 3.9 23.1 - - + -
207A LEU* 4.9 6.5 - - + +
218A THR* 4.1 5.2 - - + +
219A SER* 6.3 0.2 - - - -
222A ALA* 3.8 17.0 - - + -
226A LEU* 6.2 0.7 - - + -
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Residues in contact with ILE 122 (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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118A ILE* 3.2 14.5 + - + +
119A ASN* 3.2 8.8 + - - +
121A PHE* 1.3 76.9 - - - +
123A GLN* 1.3 60.4 + - + +
125A SER* 2.8 35.0 + - - -
127A CYS* 3.5 23.6 - - + +
131A VAL* 4.2 19.3 - - + -
144A ILE* 5.6 2.7 - - + -
145A ILE* 5.8 1.6 - - + -
148A MSE 3.4 35.0 - - + -
203A LEU* 5.0 8.1 - - + -
207A LEU* 4.1 31.9 - - + -
215A PHE* 4.4 10.1 - - + -
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Residues in contact with GLN 123 (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 MSE 6.0 0.9 - - - -
85A PHE* 3.4 49.9 + - + +
86A GLU* 5.9 1.6 - - - +
119A ASN* 2.8 38.2 + - + +
120A PHE* 4.1 0.4 - - - +
122A ILE* 1.3 75.2 - - + +
124A CYS* 1.3 60.2 + - - +
125A SER 3.0 1.1 - - - -
126A GLY* 3.1 14.4 + - - -
127A CYS 3.6 21.0 - - - +
128A LYS* 5.6 0.7 - - - -
129A GLY 3.9 20.5 + - - +
130A VAL* 3.9 15.2 - - - +
160A PRO* 4.6 0.2 - - - +
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Residues in contact with CYS 124 (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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85A PHE* 3.9 12.1 - - - -
120A PHE* 2.9 62.3 + - - +
121A PHE 3.7 6.7 - - - +
122A ILE 3.1 0.2 - - - -
123A GLN* 1.3 76.0 - - - +
125A SER* 1.3 55.8 + - - +
126A GLY 3.2 1.6 - - - -
160A PRO* 3.2 24.4 - - - +
161A LEU* 5.1 1.6 - - - +
171A PHE* 3.8 17.3 - - + -
175A PHE* 3.5 27.4 - - + -
218A THR* 3.9 9.8 + - + +
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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