Contacts of the helix formed by residues 196 - 212 (chain D) in PDB entry 3WF4
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 ASP 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D SER* 3.6 12.2 - - - -
150D SER* 2.5 40.0 + - - -
189D TYR* 3.1 25.6 + - - +
194D ALA* 4.0 7.0 - - + +
195D CYS* 1.3 74.1 - - - +
197D PHE* 1.3 55.3 + - - +
198D ASP* 3.2 22.3 + - - +
199D TYR* 3.1 27.5 + - - +
200D LEU* 3.6 3.1 + - - +
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Residues in contact with PHE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D TYR* 6.5 0.2 - + - -
195D CYS* 3.3 27.7 + - - -
196D ASP* 1.3 68.7 + - - +
198D ASP* 1.3 58.9 + - - +
200D LEU* 3.2 13.3 + - + +
201D ARG* 3.0 55.2 + - - +
229D LYS* 3.5 22.4 - - + -
230D CYS* 3.9 17.5 - - - -
232D ALA 3.6 20.2 - - - -
233D LEU* 4.0 19.4 - - + +
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Residues in contact with ASP 198 (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 SER* 4.3 14.1 + - - +
196D ASP* 3.2 11.8 + - - +
197D PHE* 1.3 75.6 - - - +
199D TYR* 1.3 57.9 + - - +
201D ARG* 3.2 28.6 + - - +
202D PHE* 3.0 27.7 + - - +
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Residues in contact with TYR 199 (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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124D PRO* 3.5 9.6 - - + +
148D ARG 3.4 23.3 - - - -
149D SER 3.5 29.2 - - - -
150D SER* 3.9 6.2 - - - +
154D TYR* 2.9 35.3 + + - -
155D LEU* 3.9 11.7 - - + -
158D VAL* 5.2 0.9 - - + -
186D GLU* 2.6 40.1 + - + +
189D TYR* 3.6 19.1 - + - -
196D ASP* 3.1 13.2 + - - +
198D ASP* 1.3 75.1 - - - +
200D LEU* 1.3 67.3 + - + +
202D PHE* 3.1 8.1 + - - +
203D LEU* 3.1 42.5 + - + +
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Residues in contact with LEU 200 (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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185D VAL* 5.1 4.7 - - + +
186D GLU* 4.2 23.3 - - + -
189D TYR* 3.9 32.8 - - + -
196D ASP 3.6 3.1 + - - +
197D PHE* 3.2 13.9 + - + +
199D TYR* 1.3 79.2 - - + +
201D ARG* 1.3 57.2 + - - +
203D LEU* 3.1 9.1 + - + +
204D GLN* 2.9 29.1 + - - +
219D THR* 5.5 2.9 - - + -
230D CYS 3.8 16.8 - - - +
231D GLY 3.7 24.2 - - - +
233D LEU* 4.0 28.7 - - + +
236D LEU* 4.6 7.4 - - + +
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Residues in contact with ARG 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D PHE* 3.0 42.5 + - - +
198D ASP* 3.2 31.6 + - - +
200D LEU* 1.3 73.2 - - - +
202D PHE* 1.3 66.9 + - - +
204D GLN* 3.7 11.1 + - - +
205D LYS* 3.0 25.3 + - - +
233D LEU* 4.0 28.7 - - + +
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Residues in contact with PHE 202 (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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155D LEU* 3.4 54.5 - - + -
158D VAL* 4.5 13.9 - - + -
159D ASP* 3.7 25.1 - - + -
198D ASP 3.0 15.3 + - - +
199D TYR 3.1 9.2 + - - +
201D ARG* 1.3 77.7 - - - +
203D LEU* 1.3 65.9 + - + +
205D LYS* 3.2 21.7 + - - +
206D ARG* 2.9 63.8 + - + +
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Residues in contact with LEU 203 (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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123D GLY 4.6 0.4 - - - +
124D PRO* 4.0 15.0 - - + -
158D VAL* 4.0 24.9 - - + -
162D LEU* 4.4 2.2 - - + -
185D VAL* 3.5 22.9 - - + -
186D GLU* 3.5 32.5 - - + -
199D TYR* 3.1 39.5 + - + +
200D LEU* 3.1 10.5 + - + +
202D PHE* 1.3 81.7 - - + +
204D GLN* 1.3 66.2 + - - +
206D ARG* 3.2 3.2 + - - +
207D PHE* 2.9 40.6 + - + -
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Residues in contact with GLN 204 (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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185D VAL* 4.6 2.2 - - - +
200D LEU 2.9 14.9 + - - +
201D ARG* 3.7 12.5 + - - +
203D LEU* 1.3 77.9 - - - +
205D LYS* 1.3 62.8 + - - +
207D PHE* 3.4 5.6 + - - +
208D ARG* 3.0 38.1 + - + +
217D LEU* 4.3 3.3 - - + +
233D LEU* 3.8 16.8 - - + +
234D GLN 3.8 7.4 + - - -
235D GLY* 3.4 33.4 - - - +
236D LEU* 3.8 22.6 - - + +
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Residues in contact with LYS 205 (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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201D ARG 3.0 18.2 + - - +
202D PHE* 3.6 20.9 - - - +
204D GLN* 1.3 78.3 - - - +
206D ARG* 1.3 78.8 + - - +
208D ARG* 3.3 7.5 + - - +
209D HIS* 2.9 29.7 + - + +
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Residues in contact with ARG 206 (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 ASP* 2.7 35.1 + - - +
162D LEU* 3.9 19.1 - - + -
166D LEU* 4.6 0.7 - - - -
202D PHE* 2.9 46.0 + - + +
203D LEU 3.9 2.0 - - - +
205D LYS* 1.3 90.3 - - - +
207D PHE* 1.3 64.1 + - - +
209D HIS* 3.5 46.4 + - - +
210D HIS* 3.1 42.8 + - + -
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Residues in contact with PHE 207 (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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122D PRO* 3.8 19.5 - - + -
123D GLY 4.0 16.2 - - - -
124D PRO* 5.1 0.2 - - + -
162D LEU* 3.9 34.3 - - + -
166D LEU* 3.8 14.6 - - + -
183D VAL* 3.7 30.1 - - + -
184D GLN 4.0 1.6 - - - -
185D VAL* 3.8 26.2 - - + -
203D LEU* 2.9 43.4 + - + +
204D GLN 3.8 3.6 - - - +
206D ARG* 1.3 75.5 - - - +
208D ARG* 1.3 59.0 + - - +
210D HIS 3.3 0.2 + - - -
211D LEU* 2.9 41.7 + - + +
217D LEU* 3.9 18.8 - - + -
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D GLN* 3.0 35.4 + - + +
205D LYS* 3.6 5.8 - - - +
207D PHE* 1.3 74.9 - - - +
209D HIS* 1.3 60.6 + - - +
212D GLY* 2.8 46.4 + - - -
213D ASP* 3.1 46.8 + - - +
215D VAL* 2.8 37.0 + - - +
216D VAL* 5.0 0.2 - - - +
217D LEU* 3.6 28.8 - - + +
235D GLY 4.3 11.1 + - - -
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Residues in contact with HIS 209 (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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205D LYS* 2.9 17.9 + - + +
206D ARG* 3.5 45.5 + - - +
207D PHE 3.4 0.2 - - - -
208D ARG* 1.3 78.0 - - - +
210D HIS* 1.3 78.9 + + - +
212D GLY* 4.6 1.2 + - - -
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Residues in contact with HIS 210 (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 ASP* 5.1 1.6 + - - -
162D LEU* 4.0 16.3 - - + +
163D GLY* 3.6 27.4 + - - -
166D LEU* 3.5 30.8 - - + +
167D PRO* 3.9 18.9 - - + +
170D LYS* 3.7 26.0 - - - +
206D ARG* 3.1 45.2 + - + +
208D ARG 3.3 0.2 - - - -
209D HIS* 1.3 97.1 + + - +
211D LEU* 1.3 61.8 + - - +
212D GLY 3.6 0.2 - - - -
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Residues in contact with LEU 211 (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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120D LEU* 6.6 0.2 - - + -
166D LEU* 3.6 42.4 - - + +
169D MET* 4.3 9.9 - - + -
170D LYS* 4.1 25.6 - - - +
173D LEU* 3.5 27.8 - - + +
176D ASN* 5.5 0.3 + - - -
183D VAL* 4.2 26.5 - - + -
207D PHE* 2.9 37.8 + - + +
210D HIS* 1.3 76.0 - - - +
212D GLY* 1.3 60.3 + - - +
214D ASP 5.3 0.2 + - - -
215D VAL* 3.7 23.5 + - + +
217D LEU* 4.6 0.7 - - + -
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Residues in contact with GLY 212 (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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170D LYS* 5.4 2.4 - - - +
208D ARG* 2.8 40.7 + - - +
209D HIS 4.5 1.0 + - - -
210D HIS 3.6 1.2 - - - -
211D LEU* 1.3 81.7 - - - +
213D ASP* 1.3 62.4 + - - -
214D ASP 3.5 3.0 + - - -
215D VAL* 3.7 4.0 - - - +
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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