Contacts of the helix formed by residues 177 - 192 (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 THR 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B ASP* 4.5 6.1 - - - -
175D GLN* 5.6 3.8 - - - +
176D LEU* 1.3 78.2 - - - +
178D ASP* 1.3 60.8 + - - +
179D CYS* 3.0 28.1 - - - -
180D GLN* 2.9 23.6 + - - +
181D ILE* 3.0 28.1 + - - +
238D ARG* 6.3 0.2 - - - +
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Residues in contact with ASP 178 (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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178B ASP* 5.6 0.9 - - - +
201B ASN* 3.4 18.0 + - - +
203B ASP* 3.9 21.5 + - + +
204B ILE* 5.1 3.1 - - + +
238B ARG* 4.7 5.4 + - - -
168D MET* 4.8 0.3 - - - +
177D THR* 1.3 73.5 - - - +
179D CYS* 1.3 54.8 - - - +
181D ILE* 3.3 7.9 + - - +
182D TYR* 2.7 35.6 + - - +
238D ARG* 3.0 52.5 + - - +
242D ILE* 3.6 18.1 - - + +
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Residues in contact with CYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LYS* 3.9 24.5 - - - +
203B ASP* 3.7 26.1 + - + +
207B GLU* 4.2 14.4 - - - +
177D THR* 3.0 23.8 - - - -
178D ASP* 1.3 78.1 - - - +
180D GLN* 1.3 67.2 + - - +
182D TYR* 3.3 10.0 + - - +
183D GLU* 3.0 34.7 + - + +
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Residues in contact with GLN 180 (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* 3.7 46.1 + - + +
175D GLN 4.2 2.6 - - - +
176D LEU* 3.1 23.8 - - + +
177D THR* 2.9 44.4 + - - +
179D CYS* 1.3 83.4 - - - +
181D ILE* 1.3 51.0 + - - +
183D GLU* 2.9 7.1 + - - +
184D VAL* 2.7 40.0 + - - +
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Residues in contact with ILE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D VAL* 4.3 15.3 - - + -
167D TYR 4.3 5.8 - - - +
168D MET* 3.7 31.9 - - + -
176D LEU* 3.8 22.9 - - + +
177D THR 3.0 20.5 + - - +
178D ASP* 3.6 14.4 - - - +
180D GLN* 1.3 72.1 - - - +
182D TYR* 1.3 58.9 + - - +
184D VAL* 4.2 7.4 - - - -
185D LEU* 2.8 59.5 + - + +
197D VAL* 5.2 4.3 - - + -
238D ARG* 5.6 0.7 - - - +
239D ALA* 5.8 4.0 - - + -
242D ILE* 3.6 19.7 - - + -
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Residues in contact with TYR 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 4.3 18.2 - - + -
207B GLU* 3.5 47.8 + - + -
208B GLU* 2.3 41.4 + - + -
211B ARG* 3.6 16.9 - - - +
178D ASP 2.7 18.3 + - - +
179D CYS* 3.3 13.9 + - - +
181D ILE* 1.3 71.6 - - - +
183D GLU* 1.3 61.4 + - + +
186D SER* 2.9 45.0 + - - -
242D ILE* 3.5 19.4 - - + +
245D GLN* 4.9 1.8 - - + -
246D THR* 3.7 21.5 - - + +
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Residues in contact with GLU 183 (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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207B GLU* 4.2 20.7 - - - +
144D TRP* 3.1 29.4 + - + +
179D CYS* 3.0 18.6 + - - +
180D GLN* 2.9 11.2 + - - +
182D TYR* 1.3 79.4 - - + +
184D VAL* 1.3 62.5 + - - +
186D SER* 4.1 4.8 - - - -
187D VAL* 3.0 30.7 + - + +
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Residues in contact with VAL 184 (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 ILE* 4.1 1.6 - - + -
144D TRP* 3.6 29.4 - - + -
152D MET* 3.9 24.5 - - + -
166D VAL* 3.9 20.0 - - + -
176D LEU* 3.9 18.2 - - + -
180D GLN 2.7 28.9 + - - +
181D ILE* 3.9 3.8 - - - +
183D GLU* 1.3 72.5 - - - +
185D LEU* 1.3 57.6 + - + +
187D VAL* 3.0 2.9 + - - +
188D ILE* 2.7 51.0 + - + +
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D VAL* 4.7 9.9 - - + -
181D ILE* 2.8 43.2 + - + +
182D TYR 3.9 2.7 - - - +
184D VAL* 1.3 83.1 - - + +
186D SER* 1.3 56.2 + - - +
188D ILE* 4.4 2.2 - - + -
189D ARG* 2.9 23.7 + - - +
195D ALA* 3.9 26.0 - - + -
197D VAL* 6.2 0.7 - - + -
239D ALA* 4.6 2.9 - - + +
242D ILE* 4.2 10.1 - - + -
243D ALA* 3.8 37.0 - - + +
246D THR* 3.8 12.6 - - - +
248D CYS* 3.1 22.1 - - + +
250D LEU* 4.7 7.9 - - + -
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Residues in contact with SER 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D TYR* 2.9 36.5 + - - -
183D GLU* 4.1 5.6 - - - -
185D LEU* 1.3 73.0 - - - +
187D VAL* 1.3 67.1 + - - +
189D ARG* 3.4 29.2 + - - +
190D ASP* 3.1 28.9 + - - -
246D THR* 3.9 9.3 - - - +
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Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D TRP* 3.8 15.5 - - + -
149D GLN* 3.7 42.4 - - + +
152D MET* 3.9 24.9 - - + -
183D GLU* 3.0 20.1 + - + +
184D VAL* 3.0 9.8 + - - +
186D SER* 1.3 79.6 - - - +
188D ILE* 1.3 63.4 + - - +
190D ASP* 3.1 16.9 + - - +
191D ILE* 3.1 26.6 + - + +
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Residues in contact with ILE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ILE* 5.0 0.2 - - + -
152D MET* 5.1 3.6 - - - -
164D PHE* 3.9 40.6 - - + +
166D VAL* 5.4 2.2 - - + -
184D VAL* 2.7 40.2 + - + +
185D LEU* 3.9 4.9 - - + +
187D VAL* 1.3 71.7 - - - +
189D ARG* 1.3 63.2 + - - +
191D ILE* 3.4 10.3 + - + +
192D GLY 3.2 4.3 + - - -
193D ALA* 3.2 54.6 + - + +
194D ILE 3.6 7.0 - - - +
195D ALA* 3.9 20.6 - - + -
248D CYS* 3.6 14.4 - - - -
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Residues in contact with ARG 189 (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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211B ARG* 6.0 4.0 - - - +
185D LEU 2.9 17.9 + - - +
186D SER* 3.4 30.7 + - - +
187D VAL 3.3 0.2 - - - -
188D ILE* 1.3 79.6 - - - +
190D ASP* 1.3 96.6 + - - +
191D ILE 3.4 0.2 + - - -
192D GLY* 3.4 4.5 + - - -
246D THR* 3.1 30.0 + - - +
247D ASN* 3.5 22.4 - - - +
248D CYS* 3.6 10.3 - - + -
474D PHE* 4.1 3.5 - - - -
479D TYR* 3.4 23.9 + - - -
482D ILE* 4.3 11.7 - - + -
486D SER* 5.2 5.6 + - - +
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Residues in contact with ASP 190 (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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186D SER 3.1 9.5 + - - +
187D VAL* 3.1 8.6 + - - +
189D ARG* 1.3 118.4 + - - +
191D ILE* 1.3 62.9 + - + +
474D PHE* 3.7 12.1 - - - -
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Residues in contact with ILE 191 (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* 3.8 25.4 - - + +
153D GLU* 3.6 32.1 - - + +
156D VAL* 3.4 37.7 - - + +
164D PHE* 3.9 10.3 - - + -
187D VAL* 3.1 24.2 + - + +
188D ILE* 3.5 15.0 - - + +
190D ASP* 1.3 80.0 - - + +
192D GLY* 1.3 56.6 + - - +
193D ALA* 4.1 4.5 - - + -
473D PRO* 3.2 19.4 - - - +
474D PHE* 3.6 7.5 - - - -
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Residues in contact with GLY 192 (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 VAL* 5.7 0.2 - - - -
162D ASN* 4.4 2.1 - - - +
188D ILE 3.2 3.4 + - - -
189D ARG 3.4 4.6 + - - -
191D ILE* 1.3 78.9 - - - +
193D ALA* 1.3 59.5 + - - +
473D PRO* 3.5 8.5 - - - +
474D PHE* 2.9 51.0 + - - -
475D PRO* 3.7 4.9 - - - +
479D TYR* 3.4 16.1 - - - -
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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