Contacts of the helix formed by residues 112 - 135 (chain A) in PDB entry 6RLR
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 GLY 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A SER* 1.3 60.9 + - - -
114A LYS* 3.3 4.3 - - - -
115A ASP* 3.3 21.5 + - - +
116A GLU* 3.0 38.7 + - - +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY* 1.3 67.6 - - - -
114A LYS* 1.3 65.7 + - - +
116A GLU* 3.2 15.5 + - - +
117A VAL* 3.0 32.6 + - - +
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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
----------------------------------------------------------
112A GLY* 4.3 1.5 - - - -
113A SER* 1.3 76.7 - - - +
115A ASP* 1.3 68.2 + - - +
117A VAL* 3.2 7.3 + - - +
118A ILE* 3.0 39.5 + - + +
189D PHE* 2.6 42.6 + - + +
190D ASP* 4.1 20.7 - - - +
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Residues in contact with ASP 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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112A GLY* 3.3 22.1 + - - +
114A LYS* 1.3 84.8 - - - +
116A GLU* 1.3 56.3 + - + +
118A ILE* 3.6 16.3 + - - +
119A LYS* 3.2 27.7 + - - +
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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
----------------------------------------------------------
112A GLY 3.0 23.0 + - - +
113A SER* 3.4 16.2 + - - +
114A LYS 3.2 0.2 - - - -
115A ASP* 1.3 74.1 - - + +
117A VAL* 1.3 60.4 + - + +
119A LYS* 3.4 12.1 + - + +
120A GLU* 3.0 28.3 + - - +
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Residues in contact with VAL 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 SER* 3.0 27.3 + - - +
114A LYS* 3.2 5.1 + - - +
116A GLU* 1.3 72.8 - - + +
118A ILE* 1.3 67.8 + - - +
120A GLU* 3.1 9.1 + - + +
121A VAL* 3.0 30.3 + - + +
189D PHE* 3.8 30.5 - - + -
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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 LYS* 3.0 33.8 + - + +
115A ASP* 3.7 16.8 - - - +
117A VAL* 1.3 76.0 - - - +
119A LYS* 1.3 57.7 + - - +
121A VAL* 3.2 2.6 + - - +
122A GLN* 2.9 52.9 + - + +
185D ILE* 3.9 2.1 - - + +
186D LYS* 4.3 29.4 - - + +
189D PHE* 3.6 42.8 - - + -
190D ASP* 5.1 4.7 - - + +
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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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115A ASP 3.2 15.0 + - - +
116A GLU* 3.7 10.1 - - + +
117A VAL 3.2 0.2 - - - -
118A ILE* 1.3 79.2 - - - +
120A GLU* 1.3 55.7 + - - +
122A GLN* 3.3 12.3 + - - +
123A GLU* 2.8 59.1 + - + +
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Residues in contact with GLU 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 GLU 3.0 14.7 + - - +
117A VAL* 3.4 13.2 - - + +
119A LYS* 1.3 78.9 - - - +
121A VAL* 1.3 59.6 + - + +
123A GLU* 3.4 5.6 + - - +
124A PHE* 3.0 29.3 + - + +
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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 VAL* 3.0 28.4 + - + +
120A GLU* 1.3 75.3 - - + +
122A GLN* 1.3 66.8 + - - +
124A PHE* 3.1 11.1 + - + +
125A TYR* 2.9 22.5 + - - +
146D ILE* 6.3 3.6 - - + -
150D LEU* 5.8 2.5 - - + -
185D ILE* 3.5 34.8 - - + -
189D PHE* 4.7 10.3 - - + -
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Residues in contact with GLN 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* 2.9 38.4 + - - +
119A LYS* 3.6 10.3 - - - +
121A VAL* 1.3 77.5 - - - +
123A GLU* 1.3 65.0 + - - +
125A TYR* 3.4 4.5 + - - +
126A LYS* 3.0 41.1 + - - +
182D PRO* 2.8 39.9 + - + +
185D ILE* 3.7 21.5 - - + -
186D LYS* 4.1 8.3 - - - +
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Residues in contact with GLU 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 45.2 + - + +
120A GLU* 4.0 4.9 - - - +
122A GLN* 1.3 74.0 - - - +
124A PHE* 1.3 61.4 + - - +
126A LYS* 3.8 31.1 + - - +
127A ASP* 2.9 48.4 + - - +
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Residues in contact with PHE 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 GLU* 3.0 18.5 + - + +
121A VAL* 3.5 10.3 - - + +
123A GLU* 1.3 76.2 - - - +
125A TYR* 1.3 56.7 + - - +
127A ASP* 3.8 6.0 - - + +
128A THR* 2.8 52.3 + - + -
142D THR* 3.6 31.4 - - + -
146D ILE* 4.3 15.3 - - + -
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Residues in contact with TYR 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 VAL 2.9 12.1 + - - +
122A GLN 3.5 8.5 - - - +
124A PHE* 1.3 82.1 - - - +
126A LYS* 1.3 58.5 + - - +
128A THR* 3.7 3.6 - - - -
129A TYR* 2.9 46.0 + + - +
143D LEU* 3.5 25.3 - - + +
146D ILE* 4.0 21.5 - - + -
147D HIS* 2.5 34.1 + + - -
154D GLY* 3.0 30.6 + - - -
155D LEU* 3.9 22.0 - - + -
163D ILE* 3.9 0.2 - - - +
181D CYS* 3.6 26.7 - - + -
182D PRO* 4.2 4.9 - - + -
185D ILE* 3.9 12.8 - - + -
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Residues in contact with LYS 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 GLN* 3.0 27.0 + - - +
123A GLU* 3.8 30.7 + - - +
125A TYR* 1.3 79.0 - - - +
127A ASP* 1.3 61.7 + - - +
129A TYR* 3.5 4.3 + - - +
130A ASN* 3.0 42.4 + - - +
155D LEU* 3.9 22.4 - - + -
182D PRO* 3.8 28.9 - - + +
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Residues in contact with ASP 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 GLU* 2.9 34.6 + - - +
124A PHE* 3.8 6.0 - - + +
126A LYS* 1.3 75.5 - - - +
128A THR* 1.3 65.4 + - - +
130A ASN* 3.3 6.9 + - - +
131A LYS* 3.0 37.4 + - + +
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Residues in contact with THR 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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124A PHE* 2.8 41.3 + - - -
125A TYR* 3.8 3.8 - - - -
127A ASP* 1.3 75.4 - - - +
129A TYR* 1.3 63.4 + - - +
131A LYS* 3.3 9.3 + - - +
132A LEU* 3.0 22.2 + - - +
139D GLN* 3.6 32.6 - - + +
142D THR* 4.4 11.4 - - + -
143D LEU* 3.6 26.9 - - + -
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Residues in contact with TYR 129 (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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125A TYR* 2.9 37.7 + + + +
126A LYS* 3.5 4.9 - - - +
128A THR* 1.3 75.1 - - - +
130A ASN* 1.3 70.3 + - - +
132A LEU* 3.2 5.7 + - - +
133A LYS* 2.9 31.6 + - + +
143D LEU* 3.7 11.8 - - + +
154D GLY* 3.9 15.7 - - - -
155D LEU* 3.4 37.2 + - + +
158D GLY 4.8 1.0 + - - -
160D GLU* 2.5 47.2 + - - +
162D PHE* 3.7 14.7 - + - -
163D ILE* 3.1 37.9 - - + -
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Residues in contact with ASN 130 (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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126A LYS* 3.0 30.9 + - - +
127A ASP* 4.0 6.0 + - - +
129A TYR* 1.3 88.5 - - - +
131A LYS* 1.3 65.2 + - - +
133A LYS* 3.2 14.4 + - - +
134A THR* 2.9 35.8 + - + +
155D LEU* 4.7 6.9 - - - +
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Residues in contact with LYS 131 (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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127A ASP* 3.0 26.4 + - + +
128A THR* 3.5 9.9 - - - +
130A ASN* 1.3 74.8 - - - +
132A LEU* 1.3 57.6 + - - +
134A THR* 4.2 3.8 - - - -
135A LYS* 2.9 39.1 + - + +
136A ASP* 3.3 4.0 + - - +
139D GLN* 3.6 31.1 - - - +
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Residues in contact with LEU 132 (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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128A THR 3.0 12.5 + - - +
129A TYR 3.5 8.1 - - - +
131A LYS* 1.3 75.6 - - - +
133A LYS* 1.3 62.3 + - - +
136A ASP* 3.3 36.3 + - + +
137A GLU* 3.0 31.1 + - - +
140A ARG* 6.3 1.3 - - - -
136D ASP* 4.1 2.7 - - + +
139D GLN* 4.5 3.1 + - + -
140D ARG* 4.0 38.8 - - + +
143D LEU* 3.5 25.8 - - + -
162D PHE* 3.9 22.7 - - + +
163D ILE* 4.6 1.6 - - + -
166D ILE* 4.3 12.3 - - + -
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Residues in contact with LYS 133 (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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129A TYR* 2.9 16.4 + - + +
130A ASN* 3.2 18.4 + - - +
132A LEU* 1.3 80.0 - - - +
134A THR* 1.3 68.3 + - + +
137A GLU* 3.6 15.1 - - - +
138A PRO* 3.6 4.9 - - - +
160D GLU* 2.8 43.0 + - - +
162D PHE* 3.5 34.3 - - + -
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Residues in contact with THR 134 (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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130A ASN* 2.9 22.6 + - + +
131A LYS* 3.7 3.6 + - - -
133A LYS* 1.3 88.2 - - + +
135A LYS* 1.3 68.6 + - - +
138A PRO* 3.0 24.6 - - - +
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Residues in contact with LYS 135 (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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131A LYS* 2.9 17.4 + - + +
134A THR* 1.3 83.8 + - - +
136A ASP* 1.3 69.4 + - - +
138A PRO* 3.9 5.2 - - - +
139A GLN* 3.2 49.3 + - - +
131D LYS* 3.8 31.3 - - - +
135D LYS* 4.2 23.3 - - + +
136D ASP* 4.3 1.1 - - - +
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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