Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 3QI6
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 TYR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A MET* 3.7 5.6 - - - -
110A ALA* 1.3 70.9 - - - +
112A GLY* 1.3 67.0 + - - +
113A GLY* 3.0 34.0 + - - -
114A THR* 3.0 27.6 + - - +
115A PHE* 3.1 10.0 + - - +
154A GLU* 2.9 27.1 + - - +
158A ASN* 3.3 33.9 - - - +
208A LLP 3.4 60.7 - + + +
368A ARG* 6.1 0.2 - - - -
56B TYR* 5.0 2.3 - - - -
58B ARG* 3.0 23.7 + - - -
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Residues in contact with GLY 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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110A ALA 3.3 5.4 + - - -
111A TYR* 1.3 77.8 - - - +
113A GLY* 1.3 56.3 + - - +
115A PHE* 3.4 7.3 + - - +
116A ARG* 2.9 31.5 + - - +
158A ASN 4.8 1.8 + - - -
352A HIS* 5.5 6.8 - - - -
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Residues in contact with GLY 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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87A MET* 3.1 21.4 - - - +
111A TYR* 3.1 27.9 - - - -
112A GLY* 1.3 73.9 - - - +
114A THR* 1.3 60.8 + - - +
116A ARG* 3.5 4.6 + - - +
117A LEU* 2.9 24.3 + - - +
58B ARG* 5.6 2.2 - - - -
238B GLY* 4.9 1.0 - - - +
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Residues in contact with THR 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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87A MET* 3.9 12.7 - - - +
90A ALA* 4.9 3.4 - - + +
94A LEU* 5.7 0.4 - - + -
106A ILE* 5.8 0.9 - - + -
107A PRO* 6.0 0.2 - - + -
110A ALA* 4.9 8.5 - - + -
111A TYR* 3.0 28.8 + - - +
113A GLY* 1.3 75.0 - - - +
115A PHE* 1.3 65.4 + - - +
117A LEU* 3.3 2.8 + - - +
118A ILE* 3.1 40.5 + - + +
152A TRP* 3.5 46.1 + - + +
154A GLU* 4.8 1.0 + - - -
183A ASP* 4.6 5.9 + - - -
208A LLP 4.7 1.6 - - - -
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Residues in contact with PHE 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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106A ILE* 3.9 12.6 - - + -
110A ALA* 4.7 4.4 - - + +
111A TYR 3.1 9.1 + - - +
112A GLY* 3.9 9.0 - - - +
114A THR* 1.3 82.9 - - - +
116A ARG* 1.3 60.2 + - + +
118A ILE* 3.3 4.6 + - + -
119A ASP* 2.7 52.4 + - + +
129A TYR* 3.4 39.7 - + - -
355A THR* 4.2 20.2 - - - -
358A SER* 3.6 15.9 - - - -
359A GLN* 3.3 49.4 - - + +
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Residues in contact with ARG 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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112A GLY 2.9 21.9 + - - +
113A GLY* 4.0 5.2 - - - +
114A THR 3.3 0.2 - - - -
115A PHE* 1.3 78.2 - - + +
117A LEU* 1.3 57.3 + - - +
119A ASP* 4.8 0.2 - - - -
120A LYS* 2.9 69.5 + - + +
121A VAL* 4.9 0.2 - - - +
352A HIS* 3.4 59.9 + - + +
234B PHE* 3.7 35.7 - - + -
237B ASN* 6.1 3.6 - - - +
238B GLY* 6.4 2.7 - - - -
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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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87A MET* 3.4 26.5 - - + +
90A ALA* 4.4 1.8 - - + -
91A ASP* 3.8 37.9 - - + +
94A LEU* 4.0 13.5 - - + -
113A GLY 2.9 19.3 + - - +
114A THR* 3.3 3.1 + - - +
116A ARG* 1.3 76.2 - - - +
118A ILE* 1.3 57.5 + - - +
121A VAL* 3.0 44.4 + - + +
122A PHE* 3.0 29.2 + - + -
95B ARG* 4.8 0.7 - - - +
234B PHE* 6.2 0.2 - - - -
235B LEU* 5.5 0.7 - - + -
238B GLY* 3.8 25.1 - - - +
239B ALA* 4.4 4.9 - - + +
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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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94A LEU* 3.6 36.1 - - + -
104A VAL* 4.2 9.6 - - + -
106A ILE* 4.0 22.7 - - + -
114A THR* 3.1 39.3 + - + +
115A PHE* 3.9 4.9 - - + +
117A LEU* 1.3 75.7 - - - +
119A ASP* 1.3 64.0 + - - +
122A PHE* 3.3 13.1 + - + +
123A THR* 3.2 27.1 + - + +
127A VAL* 5.6 2.5 - - + +
128A GLU 5.9 0.2 - - - -
129A TYR* 3.9 34.3 - - + -
152A TRP* 4.9 4.3 - - + -
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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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115A PHE* 2.7 49.1 + - + +
116A ARG* 4.4 1.1 - - - +
118A ILE* 1.3 76.3 - - - +
120A LYS* 1.3 79.4 + - + +
123A THR* 2.7 29.0 + - - +
129A TYR* 2.7 30.1 + - - +
358A SER* 4.9 0.7 + - - -
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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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116A ARG* 2.9 57.9 + - + +
119A ASP* 1.3 97.6 + - - +
121A VAL* 1.3 60.8 + - - +
123A THR* 4.4 3.9 + - - -
124A GLY* 4.8 2.8 + - - -
234B PHE* 3.7 25.1 - - + -
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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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117A LEU* 3.0 28.2 + - + +
120A LYS* 1.3 78.6 - - + +
122A PHE* 1.3 71.7 + - + +
123A THR 3.3 1.3 - - - -
124A GLY* 3.1 13.2 + - - -
125A TRP* 3.2 32.7 - - + +
95B ARG* 4.0 24.0 - - + +
234B PHE* 3.8 28.5 - - + +
235B LEU* 4.0 25.6 - - + -
238B GLY* 5.9 1.6 - - - -
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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