Contacts of the helix formed by residues 111 - 126 (chain A) in PDB entry 1JR9
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.6 3.8 - - - +
106A ASN* 4.4 5.4 - - - -
109A TYR* 2.9 8.7 + - - +
110A GLY* 1.3 74.8 - - - +
112A PHE* 1.3 60.9 + - - +
113A GLU* 3.8 17.5 + - - +
114A LYS* 2.8 31.5 + - - -
115A PHE* 2.9 12.3 + - - +
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Residues in contact with PHE 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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95A GLY 3.8 8.1 - - - -
96A LYS* 3.7 17.9 - - + -
97A PRO* 3.1 46.9 - - + -
105A ILE* 3.9 12.1 - - + -
106A ASN* 4.0 10.0 + - - +
111A SER* 1.3 71.7 - - - +
113A GLU* 1.3 68.6 + - - +
115A PHE* 2.8 22.0 + + - -
116A GLN* 2.7 68.2 + - + +
186A TRP* 4.4 6.3 - + + -
191A TRP* 3.5 24.7 - + - -
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Residues in contact with GLU 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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96A LYS* 5.9 0.3 - - - +
111A SER* 3.3 18.6 + - - +
112A PHE* 1.3 93.1 + - - +
114A LYS* 1.3 61.7 + - - +
116A GLN* 3.5 22.4 + - - +
117A GLU* 3.1 24.1 + - - +
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Residues in contact with LYS 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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109A TYR* 4.1 14.6 - - - -
111A SER* 2.8 21.9 + - - -
113A GLU* 1.3 74.5 - - - +
115A PHE* 1.3 66.4 + - - +
117A GLU* 3.2 17.0 + - - +
118A GLU* 3.2 14.1 + - - +
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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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105A ILE* 3.8 21.5 - - + -
109A TYR* 3.4 42.2 - + + +
111A SER 2.9 4.8 + - - +
112A PHE* 2.8 23.7 + + - +
114A LYS* 1.3 73.3 - - - +
116A GLN* 1.3 63.8 + - - +
118A GLU* 2.7 26.3 + - - +
119A PHE* 2.8 35.0 + + - -
134A LEU* 3.9 27.1 - - + -
143A ILE* 3.3 30.1 - - + -
161A LEU* 4.7 1.6 - - + -
186A TRP* 4.0 19.7 - + - -
191A TRP* 4.0 16.2 - + - -
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Residues in contact with GLN 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 PHE* 2.7 64.6 + - + +
113A GLU* 3.5 24.3 + - - +
115A PHE* 1.3 72.7 - - - +
117A GLU* 1.3 56.1 + - - +
119A PHE* 2.9 2.9 + - - -
120A ALA* 2.8 36.0 + - - +
186A TRP* 3.9 39.9 - - + +
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Residues in contact with GLU 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 GLU 3.1 11.2 + - - +
114A LYS* 3.2 12.6 + - - +
116A GLN* 1.3 79.7 - - - +
118A GLU* 1.3 64.1 + - + +
120A ALA* 4.2 6.3 - - - +
121A ALA* 3.4 21.0 + - - +
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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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109A TYR* 3.7 27.7 - - + -
114A LYS 3.2 11.2 + - - +
115A PHE 2.7 19.2 + - - +
117A GLU* 1.3 75.5 - - - +
119A PHE* 1.3 62.7 + - - +
121A ALA* 3.2 8.6 - - - +
122A ALA* 3.0 20.8 + - - +
143A ILE* 3.9 18.8 - - + +
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Residues in contact with PHE 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* 2.8 35.8 + + + +
116A GLN* 2.9 6.9 + - - +
118A GLU* 1.3 73.9 - - - +
120A ALA* 1.3 55.3 + - - +
122A ALA* 2.7 27.6 + - + +
123A ALA* 2.8 20.5 + - + -
132A ALA* 4.1 34.8 - - + -
133A TRP* 4.1 18.8 - - - -
134A LEU* 4.3 0.9 - - + -
143A ILE* 3.7 13.6 - - + +
161A LEU* 3.2 35.0 - - + -
163A LEU* 4.2 25.4 - - + -
182A ILE* 5.4 1.3 - - + -
185A PHE* 5.0 3.4 - + - -
186A TRP* 3.9 22.0 - + + -
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Residues in contact with ALA 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 GLN 2.8 20.1 + - - +
117A GLU* 4.2 6.5 - - - +
119A PHE* 1.3 73.6 - - - +
121A ALA* 1.3 61.8 + - - +
123A ALA* 3.5 2.8 + - - +
124A ALA* 3.1 24.6 + - - +
182A ILE* 3.8 28.3 - - + +
183A SER* 6.5 0.2 - - - -
186A TRP* 4.7 8.9 - - - +
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Residues in contact with ALA 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 GLU 3.4 14.1 + - - +
118A GLU* 3.2 15.7 + - - +
119A PHE 3.0 0.4 - - - -
120A ALA* 1.3 79.9 - - - +
122A ALA* 1.3 53.1 - - - +
124A ALA* 3.3 6.4 + - - +
125A GLY* 2.8 30.5 + - - -
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Residues in contact with ALA 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 3.0 7.3 + - - +
119A PHE* 2.7 15.4 + - + +
121A ALA* 1.3 67.9 - - - +
123A ALA* 1.3 60.6 + - - +
124A ALA 3.0 1.8 - - - -
125A GLY* 2.9 17.4 + - - +
126A ARG* 3.2 13.5 + - - +
132A ALA* 4.4 10.8 - - + -
143A ILE* 3.7 29.6 - - + -
144A MET 4.7 6.3 - - - +
145A SER* 4.4 7.3 - - - -
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Residues in contact with ALA 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 PHE* 2.8 19.6 + - + +
120A ALA* 3.7 2.0 - - - +
122A ALA* 1.3 73.4 - - - +
124A ALA* 1.3 57.3 + - - +
126A ARG* 4.3 2.5 + - - +
132A ALA* 3.7 19.9 - - + +
163A LEU* 4.0 17.3 - - + -
165A VAL* 3.3 13.7 - - + +
178A ARG* 2.9 23.7 + - - -
182A ILE* 3.6 29.8 - - + -
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Residues in contact with ALA 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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120A ALA 3.1 17.5 + - - +
121A ALA* 3.6 7.2 - - - +
122A ALA 3.0 0.8 - - - -
123A ALA* 1.3 75.4 - - - +
125A GLY* 1.3 65.6 + - - +
126A ARG 3.5 4.3 - - - +
178A ARG* 4.1 11.8 + - + +
179A PRO* 5.1 12.3 - - + -
182A ILE* 4.1 12.3 - - + -
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Residues in contact with GLY 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 ALA 2.8 14.5 + - - -
122A ALA* 2.9 6.4 + - - -
124A ALA* 1.3 79.2 - - - +
126A ARG* 1.3 66.3 + - - +
127A PHE* 3.0 9.2 + - - +
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Residues in contact with ARG 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 ALA 3.2 11.3 + - - +
123A ALA* 4.3 2.0 - - - +
124A ALA 4.1 1.4 - - - +
125A GLY* 1.3 72.9 - - - +
127A PHE* 1.3 74.4 + - - +
129A SER 3.4 22.2 - - - +
130A GLY* 3.8 17.5 - - - -
131A TRP 4.5 3.1 - - - +
145A SER* 2.8 48.9 + - - +
146A THR 4.2 0.2 - - - -
147A PRO* 3.3 34.8 - - - +
165A VAL* 4.3 6.7 - - + -
178A ARG* 2.8 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