Contacts of the helix formed by residues 176 - 188 (chain D) in PDB entry 3NY5
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D GLY 4.1 3.3 + - - +
175D VAL* 1.3 77.0 - - - +
177D VAL* 1.3 54.7 + - - +
178D ARG* 3.5 6.8 - - - +
179D ASP* 2.8 39.4 + - - +
180D SER* 2.7 36.3 + - - -
210D TRP 3.7 11.4 - - - -
211D ASP* 3.7 28.5 - - + +
212D THR 3.2 6.7 - - - -
213D ASP* 5.6 0.4 - - - -
214D ILE 4.4 0.4 - - - -
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Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D THR* 1.3 70.0 - - - +
178D ARG* 1.3 67.3 + - - +
180D SER* 3.1 7.7 + - - -
181D LEU* 2.9 38.1 + - + +
197D VAL* 4.2 11.2 - - + -
208D ILE* 3.9 12.3 - - + -
209D GLY 4.4 0.7 - - - +
210D TRP* 3.5 29.8 + - + +
212D THR* 2.9 37.2 + - - +
214D ILE* 4.3 11.9 - - + -
217D LEU* 4.0 11.7 - - + -
222D LEU* 4.1 12.8 - - + -
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Residues in contact with ARG 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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176D THR* 3.5 7.2 - - - +
177D VAL* 1.3 76.6 - - - +
179D ASP* 1.3 72.9 + - - +
181D LEU* 3.1 1.4 + - - +
182D LYS* 3.0 29.3 + - - +
192D PRO* 3.6 27.5 - - + +
193D GLU* 3.8 34.3 + - - +
210D TRP* 2.9 56.1 + - + +
211D ASP* 3.9 24.1 + - - -
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Residues in contact with ASP 179 (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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175D VAL* 4.1 14.9 - - + +
176D THR* 2.8 29.1 + - - +
178D ARG* 1.3 80.1 - - - +
180D SER* 1.3 60.7 + - - +
181D LEU 3.4 0.3 + - - -
182D LYS* 3.0 41.8 + - - +
183D LYS 5.1 0.5 + - - -
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D VAL* 3.5 38.9 - - - +
170D PRO* 4.5 5.0 + - - +
175D VAL* 3.6 8.8 - - - +
176D THR 2.7 21.4 + - - -
177D VAL 3.1 4.9 + - - -
179D ASP* 1.3 76.7 - - - +
181D LEU* 1.3 62.5 + - - +
183D LYS* 5.0 5.2 + - - +
184D ALA* 5.5 1.4 + - - +
214D ILE* 3.5 26.5 - - - +
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Residues in contact with LEU 181 (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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159D VAL* 3.5 39.9 - - + -
161D LEU* 4.8 2.9 - - + -
167D THR* 4.0 9.6 - - + -
169D VAL* 3.7 15.7 - - + -
177D VAL* 2.9 36.2 + - + +
178D ARG 3.8 1.3 - - - +
180D SER* 1.3 79.4 - - - +
182D LYS* 1.3 65.2 + - - +
183D LYS 3.3 3.0 + - - -
184D ALA* 3.3 9.4 + - + +
185D LEU* 3.0 30.8 + - + +
197D VAL* 4.8 0.4 - - + -
210D TRP* 4.0 11.2 - - + -
214D ILE* 5.9 0.2 - - + -
222D LEU* 4.8 5.4 - - + -
224D VAL* 3.8 25.6 - - + -
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Residues in contact with LYS 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ARG* 3.0 21.3 + - - +
179D ASP* 3.0 35.6 + - - +
180D SER 3.5 1.4 - - - -
181D LEU* 1.3 76.9 - - - +
183D LYS* 1.3 58.6 + - - +
185D LEU* 3.4 5.0 + - - +
186D MSE 2.9 33.8 + - + +
190D LEU 4.8 0.7 - - - +
192D PRO* 4.9 16.5 - - + +
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Residues in contact with LYS 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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220C GLU* 3.7 22.7 + - - -
179D ASP 5.1 1.0 + - - -
180D SER 5.0 5.2 + - - +
181D LEU 3.3 0.6 - - - -
182D LYS* 1.3 77.5 - - - +
184D ALA* 1.3 69.1 + - - +
186D MSE 3.2 7.4 + - + +
187D MSE 3.1 44.1 + - + +
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Residues in contact with ALA 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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161D LEU* 4.2 5.4 - - + -
167D THR* 4.0 31.4 - - + +
169D VAL* 5.9 1.1 - - + -
180D SER 5.5 1.3 + - - +
181D LEU* 3.3 15.9 + - + +
183D LYS* 1.3 83.1 - - - +
185D LEU* 1.3 63.1 - - - +
187D MSE 3.6 16.5 + - + +
188D ARG* 3.0 37.7 + - - +
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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
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161D LEU* 4.3 15.9 - - + -
162D PRO* 4.9 1.6 - - + -
181D LEU* 3.0 24.8 + - + +
182D LYS* 3.9 3.4 - - - +
183D LYS 3.2 0.2 - - - -
184D ALA* 1.3 75.7 - - + +
186D MSE 1.3 59.6 + - - +
188D ARG* 2.9 18.6 + - - +
189D GLY 3.2 0.2 + - - -
190D LEU* 2.8 59.1 + - + +
191D ILE* 4.1 3.8 - - - -
192D PRO* 3.9 35.0 - - + -
195D CYS* 4.4 5.4 - - - -
210D TRP* 4.1 17.7 - - + -
224D VAL* 4.0 19.1 - - + -
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Residues in contact with MSE 186 (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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182D LYS* 2.9 21.8 + - + +
183D LYS* 3.2 7.4 + - + +
185D LEU* 1.3 76.6 - - - +
187D MSE 1.3 60.8 - - + +
189D GLY* 3.2 22.7 + - - -
190D LEU 3.4 15.2 + - - +
191D ILE* 4.5 15.3 - - + -
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Residues in contact with MSE 187 (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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152C MSE 3.8 29.3 + - + +
158C ARG* 6.0 0.2 - - - -
218C THR 3.9 7.4 - - - +
219C GLY* 3.7 40.8 - - - +
220C GLU* 6.0 1.3 - - + +
167D THR* 6.1 0.7 - - - +
183D LYS* 3.1 29.0 + - + +
184D ALA* 3.7 14.8 - - + +
185D LEU 3.1 0.2 - - - -
186D MSE 1.3 77.1 - - + +
188D ARG* 1.3 92.9 + - + +
189D GLY 3.3 1.6 + - - -
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Residues in contact with ARG 188 (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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152C MSE 4.3 20.2 - - + +
153C GLN* 6.0 1.7 - - + +
218C THR* 3.3 28.2 + - - +
161D LEU* 3.6 36.4 - - - +
162D PRO* 5.2 4.7 + - - -
165D GLN* 2.8 36.8 + - - +
166D ARG 4.0 4.6 + - - -
167D THR* 5.4 1.2 - - - -
184D ALA* 3.0 25.2 + - - +
185D LEU* 2.9 10.6 + - - +
187D MSE 1.3 102.6 - - - +
189D GLY* 1.3 59.8 + - - +
190D LEU* 3.4 22.3 - - + +
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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