Contacts of the helix formed by residues 140 - 158 (chain D) in PDB entry 6R7H
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 ASN 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D TYR* 1.3 83.0 - - - +
141D VAL* 1.3 67.5 + - - +
142D ASP* 3.4 10.1 - - + +
143D TYR* 3.6 10.5 + - + +
144D LYS* 3.4 23.0 + - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ASN* 1.3 74.7 - - - +
142D ASP* 1.3 65.8 + - - +
144D LYS* 3.4 1.8 + - - +
145D LEU* 3.0 34.9 + - + +
174D LEU* 4.1 36.3 - - + +
177D GLU* 3.8 25.6 - - + +
178D SER* 5.6 3.8 - - - +
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Residues in contact with ASP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASN* 3.4 6.1 - - + +
141D VAL* 1.3 82.5 + - - +
143D TYR* 1.3 59.5 + - - +
145D LEU* 4.3 7.7 - - - +
146D GLU* 3.3 26.3 + - - +
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Residues in contact with TYR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ALA* 3.6 30.1 + - + +
105D SER* 4.7 1.2 + - - -
108D GLN* 3.9 22.1 - - + +
130D ILE* 5.1 5.1 - - + +
132D LEU* 4.8 6.5 - - + -
139D TYR* 3.7 47.1 - + + -
140D ASN* 3.6 17.0 + - + +
141D VAL 3.2 0.4 - - - -
142D ASP* 1.3 81.2 - - - +
144D LYS* 1.3 60.9 + - + +
146D GLU* 4.2 8.3 - - + +
147D THR* 2.8 40.5 + - + -
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 4.3 30.1 + - + -
133D GLU* 3.6 20.0 + - - -
138D GLN* 4.0 26.9 - - + +
139D TYR* 4.5 21.1 - - + +
140D ASN 3.4 19.7 + - - +
141D VAL* 3.4 0.9 + - - +
143D TYR* 1.3 77.4 - - - +
145D LEU* 1.3 60.1 + - - +
147D THR* 4.0 4.2 - - - +
148D TYR* 3.1 52.8 + - + -
174D LEU* 4.0 30.2 - - + +
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D VAL* 3.0 23.3 + - + +
142D ASP* 4.3 7.9 - - - +
143D TYR 3.4 0.2 - - - -
144D LYS* 1.3 77.2 - - - +
146D GLU* 1.3 61.4 + - - +
148D TYR* 4.1 3.1 - - - +
149D LEU* 3.2 29.6 + - + +
171D ALA* 3.8 35.7 - - + +
174D LEU* 4.9 14.3 - - + +
175D GLN* 4.3 19.3 - - + +
178D SER* 5.5 6.5 - - - +
183D LEU* 5.2 11.0 - - + -
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Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLN* 4.8 7.6 + - - -
142D ASP 3.3 18.2 + - - +
143D TYR* 4.2 9.9 - - - +
145D LEU* 1.3 75.3 - - - +
147D THR* 1.3 66.2 + - - +
149D LEU* 3.5 6.4 + - - +
150D LYS* 3.2 50.9 + - + +
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Residues in contact with THR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLN* 5.8 2.6 - - - +
127D LEU* 4.3 31.8 - - + +
130D ILE* 4.7 6.0 - - + +
132D LEU* 3.9 28.5 - - + -
143D TYR* 2.8 33.6 + - - -
144D LYS* 4.0 5.8 - - - -
146D GLU* 1.3 79.8 - - - +
148D TYR* 1.3 61.7 + - - +
150D LYS* 3.3 8.9 + - - +
151D ILE* 3.3 24.4 + - + +
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Residues in contact with TYR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 3.7 33.1 - - + +
133D GLU* 3.5 30.6 + - - +
144D LYS* 3.1 45.6 + - + +
145D LEU 4.3 1.1 - - - +
147D THR* 1.3 77.4 - - - +
149D LEU* 1.3 60.8 + - - +
151D ILE* 3.6 9.0 + - + +
152D ALA* 3.4 22.0 + - - +
167D TYR* 3.9 35.6 - + + +
168D ILE* 5.3 1.7 - - - +
170D ARG* 3.6 38.1 + - + -
171D ALA* 3.8 32.1 - - + -
174D LEU* 5.5 2.7 - - + -
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU* 3.2 23.6 + - + +
146D GLU* 3.9 7.4 - - - +
147D THR 3.2 0.4 - - - -
148D TYR* 1.3 79.4 - - - +
150D LYS* 1.3 60.9 + - + +
152D ALA* 3.8 6.3 + - + -
153D ARG* 3.3 23.3 + - + +
168D ILE* 5.8 9.2 - - + -
171D ALA* 5.6 1.1 - - + +
183D LEU* 6.3 4.0 - - + -
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLN* 3.9 23.3 - - - +
112D SER* 6.3 1.2 - - - -
115D GLU* 5.1 18.1 + - - +
127D LEU* 4.0 19.1 - - + -
146D GLU* 3.2 40.1 + - + +
147D THR* 3.3 6.9 + - - +
149D LEU* 1.3 79.2 - - + +
151D ILE* 1.3 59.6 + - - +
153D ARG* 3.9 15.9 + - - +
154D LEU* 3.1 39.6 + - + +
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ALA* 4.7 5.6 - - + +
127D LEU* 3.8 44.4 - - + +
128D VAL* 4.4 9.6 - - + +
132D LEU* 5.2 1.1 - - + -
147D THR* 3.3 21.9 + - + +
148D TYR* 3.6 20.4 + - + +
149D LEU 3.4 0.4 - - - -
150D LYS* 1.3 77.8 - - - +
152D ALA* 1.3 61.1 + - - +
154D LEU* 3.5 5.4 + - - +
155D TYR* 3.1 51.2 + - + -
167D TYR* 3.7 29.2 - - + -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR 3.4 13.5 + - - +
149D LEU* 4.3 7.9 - - + +
150D LYS 3.4 0.2 - - - -
151D ILE* 1.3 79.6 - - - +
153D ARG* 1.3 60.0 + - - +
156D LEU* 3.3 24.4 + - - +
163D GLN 5.4 0.2 - - - -
164D ALA* 3.3 33.5 - - + +
165D GLU* 5.5 1.3 - - - +
167D TYR* 5.2 1.3 - - - +
168D ILE* 4.4 22.2 - - + +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLU* 2.4 34.8 + - - +
120D TRP* 5.5 4.0 - - - -
149D LEU* 3.3 19.7 + - + +
150D LYS* 3.9 16.3 + - - +
151D ILE 3.2 0.4 - - - -
152D ALA* 1.3 77.2 - - - +
154D LEU* 1.3 72.7 + - - +
156D LEU* 3.6 8.0 + - + +
157D GLU* 3.5 44.7 + - + +
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 6.0 0.7 - - + -
115D GLU* 4.4 22.0 - - + +
119D ASP 4.4 0.4 - - - +
120D TRP* 3.3 69.8 - - + +
123D ALA* 3.8 37.0 - - + +
124D ALA* 4.0 9.4 - - + +
127D LEU* 4.7 8.3 - - + -
150D LYS* 3.1 28.4 + - + +
151D ILE 4.1 0.7 - - - +
153D ARG* 1.3 81.3 - - - +
155D TYR* 1.3 64.5 + - - +
157D GLU* 3.5 3.5 + - - +
158D ASP* 3.4 10.0 + - - +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D TRP 5.4 0.9 - - - -
121D ARG* 5.1 15.7 - - + -
124D ALA* 3.6 23.8 - - + +
125D GLN* 4.2 16.3 - - + +
128D VAL* 4.2 10.8 - - + +
151D ILE* 3.1 41.8 + - + +
154D LEU* 1.3 75.5 - - - +
156D LEU* 1.3 63.5 + - - +
158D ASP* 3.6 10.9 + - + +
160D ASP* 3.2 34.5 + - + +
163D GLN* 3.4 56.8 + - + -
164D ALA* 3.8 19.5 - - - +
167D TYR* 4.4 10.2 - + - -
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA 3.3 19.6 + - - +
153D ARG* 3.9 9.0 - - + +
154D LEU 3.2 1.0 - - - -
155D TYR* 1.3 77.7 - - - +
157D GLU* 1.3 64.7 + - + +
158D ASP 3.4 0.5 + - - -
159D ASP* 3.4 12.5 + - - +
160D ASP 4.7 1.3 - - - +
161D PRO* 5.2 13.7 - - + -
164D ALA* 3.8 11.6 - - + +
165D GLU* 5.8 3.8 - - - +
193D ARG* 4.7 21.3 - - - +
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D TRP* 3.3 55.6 + - + +
153D ARG* 3.5 39.1 + - + +
154D LEU* 3.5 4.7 + - - +
155D TYR 3.4 0.2 - - - -
156D LEU* 1.3 79.0 - - + +
158D ASP* 1.3 55.5 - - - +
159D ASP* 3.2 11.2 + - - +
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Residues in contact with ASP 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D TRP* 3.5 24.7 + - + +
121D ARG* 3.4 43.2 + - + +
154D LEU 3.4 14.1 + - - +
155D TYR* 3.6 10.0 + - + +
156D LEU 3.2 1.2 - - - -
157D GLU* 1.3 76.5 - - - +
159D ASP* 1.3 66.3 + - - +
160D ASP* 2.9 21.2 - - - +
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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