Contacts of the helix formed by residues 160 - 174 (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 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D VAL* 4.2 0.2 - - - +
159D ASN* 1.3 81.2 - - - +
161D VAL* 1.3 63.2 + - - +
162D GLU* 3.4 10.2 + - - +
163D GLU* 2.9 53.4 + - - +
164D ALA* 3.0 21.8 + - - +
187D ALA* 3.1 18.0 - - - +
188D GLY 5.4 0.7 - - - +
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Residues in contact with VAL 161 (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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160D ASN* 1.3 69.1 - - - +
162D GLU* 1.3 68.5 + - - +
164D ALA* 2.8 18.7 + - - +
165D VAL* 2.8 13.4 + - + +
184D LEU* 4.5 4.7 - - + -
187D ALA 3.1 13.3 + - - +
188D GLY* 4.3 7.2 - - - -
189D TYR* 3.4 57.6 - - + +
197D LEU* 4.1 15.3 - - + -
206D HIS* 4.4 5.6 - - + -
287D LEU* 3.7 24.9 - - + -
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Residues in contact with GLU 162 (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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160D ASN* 3.4 8.6 + - - +
161D VAL* 1.3 77.7 - - - +
163D GLU* 1.3 59.2 + - + +
165D VAL* 3.1 14.4 + - - +
166D LEU* 3.0 54.7 + - + +
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Residues in contact with GLU 163 (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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156D HIS* 5.1 4.4 - - + -
157D ALA 4.2 4.2 - - - +
158D VAL* 3.8 11.1 - - + +
159D ASN* 2.9 41.6 + - - +
160D ASN* 2.9 38.0 + - - +
162D GLU* 1.3 73.2 - - + +
164D ALA* 1.3 62.0 + - - +
166D LEU* 3.8 16.6 - - + +
167D ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 164 (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* 5.7 0.2 - - + -
150D LEU* 4.3 14.0 - - + +
158D VAL* 3.5 16.7 - - + +
160D ASN 3.0 11.6 + - - +
161D VAL 2.8 10.5 + - - +
163D GLU* 1.3 74.9 - - - +
165D VAL* 1.3 59.8 + - - +
167D ALA* 3.3 1.4 + - - +
168D ALA* 2.8 30.0 + - - +
181D VAL* 4.9 1.2 - - + +
184D LEU* 4.0 17.3 - - + -
187D ALA* 5.0 0.4 - - + -
197D LEU* 3.5 20.5 - - + +
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Residues in contact with VAL 165 (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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161D VAL* 2.8 18.1 + - + +
162D GLU* 3.5 17.9 - - - +
164D ALA* 1.3 77.2 - - - +
166D LEU* 1.3 64.6 + - + +
168D ALA* 3.2 6.5 + - - +
169D ARG* 3.0 54.8 + - - +
197D LEU* 3.9 16.4 - - + -
199D VAL* 4.5 4.3 - - + -
204D ALA* 4.1 24.2 - - + -
287D LEU* 4.1 15.3 - - + -
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Residues in contact with LEU 166 (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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156D HIS* 6.2 1.1 - - + -
162D GLU* 3.0 44.2 + - + +
163D GLU* 3.8 18.2 - - + +
165D VAL* 1.3 79.4 - - + +
167D ALA* 1.3 57.0 + - - +
169D ARG* 3.2 7.8 + - - +
170D GLU* 3.0 37.5 + - - +
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Residues in contact with ALA 167 (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* 4.0 12.1 - - + -
154D CYS* 3.8 16.7 - - - +
156D HIS* 4.2 4.2 - - + -
158D VAL* 3.7 23.1 - - + -
163D GLU 3.0 19.2 + - - +
164D ALA 3.8 2.9 - - - +
166D LEU* 1.3 73.3 - - - +
168D ALA* 1.3 66.0 + - - +
170D GLU* 3.1 23.3 + - - +
171D LEU* 3.1 16.8 + - - +
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Residues in contact with ALA 168 (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* 4.2 2.8 - - - +
164D ALA 2.8 17.9 + - - +
165D VAL 3.6 4.5 - - - +
167D ALA* 1.3 76.2 - - - +
169D ARG* 1.3 57.5 + - - +
171D LEU* 3.0 9.1 + - - +
172D ILE* 2.9 23.6 + - - +
179D VAL* 3.4 29.7 - - + +
181D VAL* 4.8 4.9 - - + -
199D VAL* 3.8 30.3 - - + -
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Residues in contact with ARG 169 (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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165D VAL* 3.0 35.8 + - - +
166D LEU* 3.2 7.1 + - - +
168D ALA* 1.3 73.2 - - - +
170D GLU* 1.3 60.5 + - - +
172D ILE* 3.6 13.9 - - + +
173D ALA* 2.9 28.9 + - - +
199D VAL* 3.8 10.4 - - + +
200D THR 2.8 25.6 + - - -
201D ALA* 3.4 16.4 + - - +
202D ASP 3.6 6.3 + - - -
203D GLU* 3.2 31.3 + - - +
204D ALA* 4.0 4.6 - - - +
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Residues in contact with GLU 170 (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 CYS* 3.7 15.0 - - + +
156D HIS* 2.7 37.5 + - - -
166D LEU* 3.0 27.5 + - - +
167D ALA* 3.1 8.6 + - - +
169D ARG* 1.3 78.0 - - - +
171D LEU* 1.3 62.0 + - + +
173D ALA* 3.5 13.4 - - - +
174D GLN* 3.1 20.6 + - - +
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Residues in contact with LEU 171 (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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137D LEU* 3.8 17.7 - - + +
143D ILE* 3.8 23.3 - - + -
145D PRO* 4.2 5.4 - - + -
150D LEU* 3.9 19.5 - - + -
153D LEU* 3.6 52.5 - - + +
154D CYS* 4.0 9.0 - - + +
167D ALA 3.1 17.3 + - - +
168D ALA 3.0 6.9 + - - +
170D GLU* 1.3 77.2 - - - +
172D ILE* 1.3 67.4 + - - +
174D GLN* 2.9 18.2 + - + +
176D PRO* 3.3 17.0 - - + +
179D VAL* 4.2 10.1 - - + -
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Residues in contact with ILE 172 (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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168D ALA 2.9 18.4 + - - +
169D ARG* 3.3 20.1 + - + +
171D LEU* 1.3 76.3 - - - +
173D ALA* 1.3 57.3 + - - +
175D GLY* 2.9 20.4 + - - -
176D PRO* 3.1 25.6 - - - +
177D GLN* 4.2 10.1 - - - +
179D VAL* 3.6 13.9 - - + -
199D VAL* 3.8 11.0 - - + +
200D THR* 3.6 37.5 - - - +
201D ALA* 3.9 17.5 - - + +
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Residues in contact with ALA 173 (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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169D ARG 2.9 16.8 + - - +
170D GLU* 3.5 10.8 - - - +
171D LEU 3.2 0.2 - - - -
172D ILE* 1.3 77.4 - - - +
174D GLN* 1.3 65.2 + - + +
175D GLY 3.6 0.3 + - - -
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Residues in contact with GLN 174 (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 5.5 0.3 - - - +
137D LEU* 3.7 35.2 - - + +
138D PRO* 3.5 24.6 - - + +
170D GLU 3.1 19.5 + - - +
171D LEU* 2.9 9.1 + - + +
173D ALA* 1.3 81.4 + - - +
175D GLY* 1.3 54.6 + - - +
176D PRO* 4.0 1.3 - - - -
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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