Contacts of the helix formed by residues 146 - 155 (chain D) in PDB entry 1VI9
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 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D HIS* 3.5 28.7 + - - -
145D PRO* 1.4 78.5 - - - +
147D LEU* 1.3 64.4 + - - +
148D VAL* 3.2 6.8 + - - +
149D GLU* 3.0 38.3 + - - +
150D LEU* 3.0 17.7 + - - +
181D VAL* 4.4 1.8 - - - -
182D LYS* 3.6 26.3 - - + +
183D HIS* 3.8 23.6 - - + +
298D SO4 5.2 5.3 + - - -
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ASN* 1.3 71.5 - - - +
148D VAL* 1.3 67.8 + - + +
150D LEU* 3.3 10.7 + - + +
151D GLU* 3.0 27.0 + - + +
158D VAL* 3.7 28.0 - - + +
181D VAL* 4.4 4.5 - - + +
183D HIS* 3.0 22.1 + - - +
184D LEU* 3.4 20.4 - - + +
185D ALA* 4.4 7.4 - - + -
186D ARG* 3.9 31.6 - - + +
187D ALA* 3.7 31.4 - - + +
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLY 5.3 1.6 - - - +
117D HIS* 3.6 33.7 - - + +
146D ASN* 3.2 5.2 + - - +
147D LEU* 1.3 79.5 - - + +
149D GLU* 1.3 62.7 + - + +
151D GLU* 3.2 16.7 + - - +
152D ILE* 3.1 39.0 + - + +
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PRO* 3.2 26.8 - - + +
114D VAL* 3.7 5.2 - - - +
115D MSE 3.1 38.4 + - + +
117D HIS* 2.8 24.4 - - + +
145D PRO* 3.6 14.1 - - + +
146D ASN* 3.0 25.7 + - - +
148D VAL* 1.3 73.0 - - - +
150D LEU* 1.3 60.1 + - - +
152D ILE* 3.4 1.7 + - - +
153D LEU* 2.9 35.3 + - - +
182D LYS* 3.0 29.2 + - - -
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Residues in contact with LEU 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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145D PRO* 3.5 15.6 - - + +
146D ASN 3.0 17.1 + - - +
147D LEU* 3.5 8.1 - - + +
149D GLU* 1.3 72.7 - - - +
151D GLU* 1.3 61.5 + - - +
153D LEU* 3.3 3.1 + - - -
154D CYS* 3.0 30.5 + - - -
158D VAL* 4.3 24.0 - - + -
164D ALA* 4.3 12.6 - - + +
167D ALA* 4.0 26.7 - - + -
168D ALA* 4.2 4.0 - - + +
171D LEU* 3.9 26.5 - - + -
181D VAL* 3.9 30.3 - - + -
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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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147D LEU* 3.0 22.0 + - - +
148D VAL* 3.2 17.8 + - - +
150D LEU* 1.3 77.9 - - - +
152D ILE* 1.3 57.9 + - + +
154D CYS* 3.9 2.2 - - - -
155D GLU* 3.0 23.6 + - - -
156D HIS 3.1 22.7 + - - +
157D ALA* 3.5 8.6 - - - +
158D VAL* 2.7 39.4 + - + +
186D ARG* 2.7 31.8 + - - -
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Residues in contact with ILE 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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115D MSE 3.7 29.4 - - + -
129D ALA* 4.8 10.1 - - + -
133D VAL* 3.6 26.9 - - + +
148D VAL* 3.1 30.2 + - + +
149D GLU 3.8 4.3 - - - +
150D LEU 3.3 0.4 - - - -
151D GLU* 1.3 75.5 - - + +
153D LEU* 1.3 65.3 + - - +
155D GLU* 3.5 16.9 + - - +
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Residues in contact with LEU 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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113D PRO* 4.0 17.0 - - + -
115D MSE 3.8 14.6 - - + -
132D HIS* 3.8 9.6 - - + +
133D VAL* 3.6 40.4 - - - +
137D LEU* 4.4 16.0 - - + +
143D ILE* 3.9 20.2 - - + -
145D PRO* 4.1 6.5 - - + -
149D GLU 2.9 23.9 + - - +
150D LEU 3.3 3.3 + - - +
152D ILE* 1.3 78.2 - - - +
154D CYS* 1.3 58.7 + - - +
155D GLU* 4.4 4.9 - - - +
171D LEU* 3.6 38.9 - - + +
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Residues in contact with CYS 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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150D LEU* 3.0 23.5 + - + +
153D LEU* 1.3 74.0 - - - +
155D GLU* 1.3 67.5 + - - +
156D HIS* 3.3 56.2 - - - -
158D VAL* 4.0 4.3 - - - -
167D ALA* 3.8 18.6 - - + +
170D GLU* 3.7 19.2 - - + +
171D LEU* 4.3 12.3 - - + -
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Residues in contact with GLU 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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133D VAL* 4.3 17.4 - - + +
151D GLU 3.0 9.8 + - - -
152D ILE* 3.5 13.7 + - - +
153D LEU 3.3 5.1 - - - +
154D CYS* 1.3 79.9 - - - +
156D HIS* 1.3 58.6 + - - +
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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