Contacts of the helix formed by residues 114 - 128 (chain A) in PDB entry 3U86
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A TYR* 5.1 9.2 - - - -
107A PRO* 5.4 9.1 + - - -
108A ARG* 5.8 0.4 - - - +
112A VAL* 3.7 6.3 + - - -
113A SER* 1.3 78.3 - - - +
115A ARG* 1.3 71.7 + - - +
116A GLU* 3.2 20.0 + - - +
117A LEU* 3.5 18.2 - - - +
118A VAL* 3.0 21.7 + - - +
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Residues in contact with ARG 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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114A SER* 1.3 75.3 + - - +
116A GLU* 1.3 65.9 + - + +
118A VAL* 3.3 2.5 + - + +
119A LYS* 3.0 50.2 + - + +
186A PHE* 3.4 33.2 - - + -
192A GLN* 3.7 24.6 + - - +
193A THR 2.9 30.3 + - - +
194A ALA* 3.9 7.9 - - + +
208A GLY 3.6 17.8 + - - -
209A GLN 3.9 12.7 + - - -
210A THR* 4.0 7.4 + - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 4.0 16.9 + - + -
114A SER* 3.2 10.2 + - - +
115A ARG* 1.3 84.1 - - + +
117A LEU* 1.3 56.0 + - - +
119A LYS* 3.6 23.9 + - - +
120A LYS* 3.1 27.4 + - - +
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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
----------------------------------------------------------
101A VAL* 6.0 2.5 - - + -
103A LEU* 5.0 14.8 - - + -
106A TYR* 3.9 43.9 - - + -
108A ARG* 4.9 10.1 - - + -
113A SER* 4.2 14.8 - - - -
114A SER* 3.5 19.4 + - - +
115A ARG 3.2 0.2 - - - -
116A GLU* 1.3 77.8 - - - +
118A VAL* 1.3 62.3 + - + +
120A LYS* 3.2 6.0 + - + +
121A VAL* 3.1 31.0 + - + +
168A LEU* 5.4 0.4 - - + -
170A LEU* 3.7 41.3 - - + -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 4.5 11.7 - - - -
114A SER 3.0 17.9 - - - +
115A ARG* 3.3 6.2 + - + +
117A LEU* 1.3 76.9 - - + +
119A LYS* 1.3 64.6 + - + +
121A VAL* 3.5 5.2 + - - +
122A SER* 3.0 21.9 + - - -
161A VAL* 5.1 5.6 - - + +
165A CYS* 5.7 2.9 - - - -
170A LEU* 6.0 0.4 - - + -
173A VAL* 4.6 11.7 - - + -
184A VAL* 4.1 26.2 - - + -
186A PHE* 3.8 35.2 - - + -
194A ALA* 4.9 8.3 - - + -
196A VAL* 5.4 5.4 - - + -
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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
----------------------------------------------------------
115A ARG* 3.0 41.1 + - + +
116A GLU* 3.9 23.8 + - - +
118A VAL* 1.3 75.7 - - + +
120A LYS* 1.3 57.6 + - - +
122A SER* 3.0 9.9 - - - -
123A ASP* 2.8 39.5 + - - +
208A GLY* 3.7 39.0 + - - -
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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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100A ALA 3.0 23.0 + - - -
101A VAL* 3.6 28.0 - - + +
102A ASP 5.0 1.4 - - - +
105A LEU* 5.9 3.4 - - - +
106A TYR* 3.6 26.5 + - + +
116A GLU 3.1 15.8 + - - +
117A LEU* 3.2 13.0 + - + +
119A LYS* 1.3 76.0 - - - +
121A VAL* 1.3 63.0 + - + +
123A ASP* 3.0 13.9 + - + +
124A VAL* 2.9 35.8 + - - +
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Residues in contact with VAL 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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97A ILE* 5.3 2.9 - - + -
101A VAL* 4.9 7.6 - - + -
117A LEU* 3.1 30.2 + - + +
118A VAL* 3.9 6.1 - - - +
120A LYS* 1.3 75.8 - - + +
122A SER* 1.3 64.6 + - - +
124A VAL* 3.4 9.5 + - + +
125A ILE* 3.3 20.3 + - + +
161A VAL* 3.9 9.4 - - + +
164A ALA* 3.9 24.7 - - + -
165A CYS* 3.7 29.4 - - - +
168A LEU* 3.8 21.5 - - + -
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL 3.0 15.8 + - - -
119A LYS* 3.0 17.7 + - - -
121A VAL* 1.3 79.2 - - - +
123A ASP* 1.3 55.8 + - - +
125A ILE* 3.2 3.5 + - - +
126A TRP 2.9 23.0 + - - -
161A VAL* 4.0 11.9 - - - +
195A GLU 4.7 1.0 + - - -
196A VAL* 3.8 22.5 - - - +
207A ARG* 2.3 45.3 + - - +
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Residues in contact with ASP 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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119A LYS* 2.8 27.0 + - - +
120A LYS* 3.5 15.6 - - + +
122A SER* 1.3 69.9 - - - +
124A VAL* 1.3 59.3 + - - +
126A TRP* 4.0 6.6 - - - -
127A ASN* 2.6 51.9 + - - +
207A ARG* 3.3 16.8 + - - -
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Residues in contact with VAL 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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96A GLN* 4.8 2.9 - - + +
97A ILE* 3.7 31.2 - - + -
100A ALA* 3.7 25.1 - - + -
101A VAL* 3.7 26.2 - - + -
120A LYS* 2.9 27.7 + - - +
121A VAL* 3.7 9.6 - - + +
122A SER 3.3 0.2 - - - -
123A ASP* 1.3 76.3 - - - +
125A ILE* 1.3 59.4 + - + +
127A ASN* 4.1 2.7 - - - +
128A SER* 2.5 37.2 + - - +
146A PHE* 6.3 0.4 - - + -
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Residues in contact with ILE 125 (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 PHE* 4.7 2.2 - - + -
97A ILE* 4.3 11.0 - - + -
121A VAL 3.3 13.7 + - - +
122A SER 3.2 6.8 + - - +
124A VAL* 1.3 77.3 - - + +
126A TRP* 1.3 65.5 + - - +
128A SER* 3.0 16.8 + - - -
129A LEU* 2.9 17.0 - - + +
146A PHE* 4.0 30.8 - - + -
152A LEU* 4.7 2.5 - - + -
157A VAL* 4.2 18.8 - - + +
160A ALA* 3.9 34.5 - - + +
161A VAL* 3.8 19.3 - - + -
164A ALA* 4.1 13.5 - - + -
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Residues in contact with TRP 126 (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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122A SER 2.9 19.8 + - - +
123A ASP* 3.5 5.4 - - - +
125A ILE* 1.3 75.0 - - - +
127A ASN* 1.3 75.8 + - - +
129A LEU* 2.8 31.8 + - + +
157A VAL* 4.6 7.9 - - + -
196A VAL 4.2 2.9 - - - -
197A THR* 4.1 11.9 - - - -
198A TRP* 3.9 43.7 - + + -
203A ASN* 5.6 2.9 - - + -
205A ASP* 4.5 15.2 + - + -
207A ARG* 3.2 53.4 - - - +
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Residues in contact with ASN 127 (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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123A ASP* 2.6 40.3 + - - +
124A VAL* 4.5 3.1 - - - +
126A TRP* 1.3 88.0 - - - +
128A SER* 1.3 59.8 + - - +
129A LEU 3.4 2.6 + - - +
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Residues in contact with SER 128 (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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96A GLN* 4.4 10.9 + - - -
124A VAL* 2.5 28.2 + - - +
125A ILE 3.0 7.4 + - - -
127A ASN* 1.3 78.7 - - - +
129A LEU* 1.3 59.3 + - - +
146A PHE* 3.7 22.0 - - - -
150A THR* 2.9 18.5 + - - +
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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