Contacts of the helix formed by residues 113 - 127 (chain A) in PDB entry 4QNR
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 PRO 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A CYS 5.6 0.2 - - - +
68A LEU 6.0 1.1 - - - +
70A GLU* 3.5 52.9 - - + +
73A LEU* 3.7 20.2 - - + -
111A THR 3.3 7.4 - - - +
112A ALA* 1.3 86.8 - - + +
114A MET* 1.3 66.7 + - - +
115A MET 3.1 0.9 - - - +
116A VAL* 3.0 19.3 + - + +
117A GLN* 3.1 9.9 + - - +
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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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112A ALA 3.7 0.2 + - - -
113A PRO* 1.3 73.0 - - - +
115A MET* 1.3 62.1 + - - +
117A GLN* 3.4 20.5 + - - +
118A GLU* 3.1 22.9 + - - +
159A GLY* 3.6 21.3 - - - +
160A THR* 3.4 30.7 - - - +
161A PHE 4.2 2.5 - - - -
162A ARG* 3.6 35.3 + - + +
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Residues in contact with MET 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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70A GLU* 3.5 41.0 + - + +
71A ASN* 5.0 7.0 - - - +
74A ASP* 4.1 31.2 - - + +
113A PRO* 3.1 1.2 - - - +
114A MET* 1.3 79.1 - - - +
116A VAL* 1.3 63.0 + - + +
118A GLU* 3.4 6.3 + - - +
119A LYS* 3.1 41.3 + - + +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A CYS* 6.0 0.9 - - - -
70A GLU 4.6 2.0 - - - +
73A LEU* 4.2 24.0 - - + -
74A ASP* 4.5 13.7 - - + +
77A LEU* 4.0 26.7 - - + -
78A PHE* 4.0 5.6 - - + -
112A ALA* 4.3 9.6 - - + -
113A PRO* 3.0 30.4 + - + +
115A MET* 1.3 90.1 - - + +
117A GLN* 1.3 56.3 + - - +
119A LYS* 3.3 6.9 + - - +
120A LEU* 2.7 37.3 + - + +
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Residues in contact with GLN 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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109A LEU* 6.1 0.4 - - + -
110A ALA 5.0 1.2 + - - -
112A ALA* 2.9 33.1 + - + +
113A PRO 3.1 11.8 + - - +
114A MET* 3.5 20.5 - - - +
115A MET 3.2 0.2 - - - -
116A VAL* 1.3 77.4 - - - +
118A GLU* 1.3 62.5 + - - +
120A LEU* 3.3 6.5 + - + +
121A LEU* 3.0 20.8 + - - +
160A THR 3.4 21.4 + - - -
161A PHE* 3.3 23.6 - - + -
162A ARG* 2.7 40.2 + - - +
165A LEU* 3.7 24.5 - - + +
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Residues in contact with GLU 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 MET 3.1 16.5 + - - +
115A MET* 3.8 5.7 - - - +
116A VAL 3.3 0.2 - - - -
117A GLN* 1.3 75.2 - - - +
119A LYS* 1.3 77.4 + - - +
121A LEU* 3.2 8.7 + - + +
122A ARG* 3.1 52.2 + - - +
162A ARG* 3.6 35.2 - - - +
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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
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74A ASP* 2.7 37.3 + - - +
78A PHE* 3.5 34.1 - - + +
115A MET* 3.1 36.0 + - + +
116A VAL* 3.7 0.7 - - - +
118A GLU* 1.3 87.3 - - - +
120A LEU* 1.3 63.1 + - - +
122A ARG* 3.2 10.3 + - + +
123A VAL* 3.1 25.0 + - + +
130A GLU* 6.1 5.4 - - - -
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Residues in contact with LEU 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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77A LEU* 4.9 4.5 - - + -
78A PHE* 3.8 10.7 - - + -
96A PHE* 3.6 34.1 - - + -
106A LEU* 4.1 22.9 - - + -
109A LEU* 4.2 14.8 - - + -
116A VAL* 2.7 25.8 + - + +
117A GLN* 3.5 5.4 - - - +
119A LYS* 1.3 73.8 - - - +
121A LEU* 1.3 62.4 + - - +
123A VAL* 3.2 3.4 + - - +
124A ILE* 3.0 36.8 + - + +
144A LEU* 4.2 7.6 - - + -
165A LEU* 4.2 21.5 - - + -
169A LEU* 4.7 5.8 - - + -
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Residues in contact with LEU 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 GLN 3.0 12.6 + - - +
118A GLU* 3.2 11.9 + - + +
120A LEU* 1.3 75.8 - - - +
122A ARG* 1.3 60.4 + - + +
124A ILE* 3.2 3.7 + - + +
125A GLU* 2.9 60.1 + - + +
162A ARG* 5.0 2.0 - - - +
164A ASP* 3.3 50.7 - - + +
165A LEU* 4.0 16.1 - - + +
168A ARG* 3.8 25.4 - - + -
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Residues in contact with ARG 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 GLU* 3.1 42.5 + - - +
119A LYS* 3.4 10.1 - - - +
120A LEU 3.2 0.2 - - - -
121A LEU* 1.3 79.7 - - - +
123A VAL* 1.3 58.3 + - + +
125A GLU* 4.9 0.7 - - - -
126A TYR* 2.8 78.7 + - + +
128A GLU 4.8 2.0 - - - +
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Residues in contact with VAL 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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78A PHE* 3.8 14.6 - - + -
96A PHE* 3.9 31.2 - - + -
119A LYS 3.1 15.2 + - - +
120A LEU 3.2 6.2 + - - +
122A ARG* 1.3 77.0 - - + +
124A ILE* 1.3 57.9 + - - +
127A GLY* 2.7 31.2 + - - -
128A GLU 3.9 15.3 - - - +
129A LEU* 3.7 25.1 - - + -
130A GLU 5.8 0.4 - - - +
140A VAL* 4.1 22.2 - - + -
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Residues in contact with ILE 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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31A PRO* 5.3 11.4 - - + -
96A PHE* 5.4 3.1 - - + -
120A LEU* 3.0 31.3 + - + +
121A LEU* 3.6 8.5 - - + +
123A VAL* 1.3 80.3 - - + +
125A GLU* 1.3 60.4 + - + +
127A GLY* 4.3 2.6 + - - -
144A LEU* 3.7 32.3 - - + -
165A LEU* 4.1 11.7 - - + -
168A ARG* 3.7 40.6 + - + +
169A LEU* 3.8 17.5 - - + -
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Residues in contact with GLU 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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121A LEU* 2.9 48.6 + - + +
122A ARG* 4.9 0.4 - - - -
124A ILE* 1.3 80.1 - - - +
126A TYR* 1.3 78.6 + - + +
168A ARG* 3.3 42.5 + - + +
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Residues in contact with TYR 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 ARG* 2.8 66.9 + - + +
125A GLU* 1.3 95.5 - - + +
127A GLY* 1.3 64.3 + - - +
128A GLU* 3.3 23.5 + - + +
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Residues in contact with GLY 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 VAL 2.7 24.6 + - - -
124A ILE 4.3 2.2 + - - -
125A GLU 3.7 1.0 - - - -
126A TYR* 1.3 73.8 - - - +
128A GLU* 1.3 58.8 + - - +
139A GLN* 3.5 5.7 - - - +
140A VAL* 3.0 38.2 + - - +
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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