Contacts of the helix formed by residues 147 - 159 (chain D) in PDB entry 2VM8
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 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D HIS* 3.0 20.1 + - - -
146D LYS* 1.3 80.5 - - - +
148D ILE* 1.3 62.7 + - - +
149D GLN 3.4 0.6 + - - -
150D GLU* 3.8 17.2 + - - +
151D GLU* 3.7 21.9 + - - +
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Residues in contact with ILE 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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114D THR 6.0 0.9 - - - +
116D LEU* 4.2 26.0 - - + -
141D ILE* 4.3 4.0 - - + -
143D GLU* 3.2 25.1 - - + +
144D TRP* 3.3 9.0 - - + -
145D HIS* 2.8 53.1 + - + +
147D GLY* 1.3 78.7 - - - +
149D GLN* 1.3 62.6 + - - +
151D GLU* 3.0 14.3 + - - +
152D MET* 2.8 60.6 + - + +
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Residues in contact with GLN 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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144D TRP* 4.3 5.6 - - + -
145D HIS 4.2 2.0 + - - +
146D LYS* 4.7 8.7 - - - +
147D GLY 3.4 0.6 - - - -
148D ILE* 1.3 77.2 - - - +
150D GLU* 1.3 60.2 + - + +
152D MET* 3.3 12.2 + - - +
153D GLU* 2.6 64.2 + - - +
187D VAL* 3.7 35.8 - - + +
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Residues in contact with GLU 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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146D LYS 4.0 15.8 - - - +
147D GLY* 3.8 12.9 + - - +
148D ILE 3.4 0.4 - - - -
149D GLN* 1.3 79.1 - - + +
151D GLU* 1.3 58.8 + - + +
153D GLU* 3.4 12.4 + - - +
154D ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 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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115D SER* 3.4 15.8 - - - -
116D LEU* 3.3 32.1 + - + +
117D LEU* 2.6 55.6 + - + +
145D HIS* 5.6 1.9 - - - -
147D GLY 3.7 14.1 - - - +
148D ILE* 3.0 18.4 + - - +
150D GLU* 1.3 76.6 - - + +
152D MET* 1.3 62.6 - - - +
154D ALA* 3.4 1.1 + - - -
155D LEU* 3.1 30.9 + - - +
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Residues in contact with MET 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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116D LEU* 4.0 7.0 - - + -
141D ILE* 3.0 32.5 - - + -
144D TRP* 3.1 23.3 - - + -
148D ILE* 2.8 41.2 + - + +
149D GLN* 3.7 5.4 - - - +
151D GLU* 1.3 75.2 - - - +
153D GLU* 1.3 57.8 + - - +
155D LEU* 3.4 1.7 + - - -
156D VAL* 3.0 35.9 + - - +
164D PHE* 3.7 29.9 - - + -
184D VAL* 3.9 7.4 - - + -
187D VAL* 3.9 20.2 - - + -
188D ILE* 5.1 3.4 - - - -
191D ILE* 3.8 12.8 - - + -
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Residues in contact with GLU 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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149D GLN* 2.6 63.5 + - + +
150D GLU* 3.6 11.1 + - - +
151D GLU 3.2 0.2 - - - -
152D MET* 1.3 77.1 - - - +
154D ALA* 1.3 57.6 + - - +
156D VAL* 4.0 2.5 - - - +
157D LYS* 3.1 28.9 + - - +
187D VAL* 5.5 0.2 - - + -
191D ILE* 3.6 29.5 - - + +
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Residues in contact with ALA 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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117D LEU* 4.2 15.0 - - + -
150D GLU 3.0 16.9 + - - +
151D GLU* 3.9 4.9 - - - +
152D MET 3.3 0.2 - - - -
153D GLU* 1.3 74.2 - - - +
155D LEU* 1.3 57.4 + - - +
157D LYS* 4.4 2.0 - - - -
158D ASP* 2.7 51.6 + - - +
159D HIS* 3.6 4.9 - - + +
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Residues in contact with LEU 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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116D LEU* 3.9 33.0 - - + +
117D LEU* 3.7 11.9 - - + -
120D PHE* 3.7 32.3 - - + -
139D VAL* 4.2 22.2 - - + -
151D GLU 3.1 20.7 + - - +
152D MET* 3.7 4.9 - - - +
153D GLU 3.3 0.2 - - - -
154D ALA* 1.3 78.4 - - - +
156D VAL* 1.3 56.0 + - - +
159D HIS* 2.9 53.9 + - + +
160D GLY 3.4 5.0 + - - -
161D VAL* 3.4 15.2 + - + -
164D PHE* 4.4 6.5 - - + -
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Residues in contact with VAL 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 MET 3.0 18.5 + - - +
153D GLU* 4.0 4.5 - - - +
155D LEU* 1.3 78.0 - - - +
157D LYS* 1.3 60.0 + - - +
160D GLY* 4.5 6.9 + - - -
161D VAL 3.2 19.0 + - - +
162D ASN* 5.5 0.7 - - - -
164D PHE* 3.5 16.6 - - + -
191D ILE* 3.4 49.8 - - + +
192D GLY 5.7 0.2 - - - -
193D ALA* 4.8 2.9 - - + -
471D ARG 5.3 0.9 - - - +
473D PRO* 3.7 30.7 - - + +
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Residues in contact with LYS 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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153D GLU 3.1 20.2 + - - +
154D ALA* 4.0 2.7 - - - +
156D VAL* 1.3 79.8 - - - +
158D ASP* 1.3 85.0 + - - +
160D GLY 5.1 0.4 + - - -
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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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154D ALA* 2.7 32.0 + - + +
157D LYS* 1.3 107.4 + - - +
159D HIS* 1.3 76.6 + - + +
160D GLY 3.7 2.0 - - - -
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Residues in contact with HIS 159 (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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117D LEU* 4.4 12.2 - - + +
120D PHE* 3.6 29.3 - + + -
121D ASP* 5.6 8.1 - - - -
124D ARG* 5.1 0.7 + - - -
154D ALA* 3.6 22.1 - - - +
155D LEU* 2.9 36.7 + - + +
158D ASP* 1.3 92.7 + - + +
160D GLY* 1.3 60.1 + - - +
161D VAL* 3.2 2.4 + - + -
468D TYR* 2.9 29.8 + - - -
470D PRO* 5.3 0.2 - - - -
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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