Contacts of the helix formed by residues 188 - 201 (chain D) in PDB entry 3SWD
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 GLU 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D VAL* 5.2 0.2 - - - +
163D VAL* 3.5 28.8 - - + +
186D ALA* 3.5 22.3 + - - +
187D ARG* 1.3 77.5 + - - +
189D PRO* 1.3 70.9 - - + +
190D GLU* 3.1 9.9 - - + +
191D ILE* 2.8 26.5 + - + +
192D VAL* 3.4 4.5 + - - +
232D ARG* 3.5 23.4 + - - +
298D PRO* 3.8 9.5 - - - +
299D HIS* 2.8 34.2 + - + +
501D EPZ 4.7 7.8 + - - +
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Residues in contact with PRO 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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187D ARG 3.5 1.5 - - - +
188D GLU* 1.3 86.7 - - + +
190D GLU* 1.3 64.0 + - - +
192D VAL* 3.0 27.8 + - + +
193D ASP* 3.0 13.5 + - - +
229D LEU* 4.0 17.0 - - + +
232D ARG* 3.7 27.8 - - - +
255D GLN* 5.8 0.2 - - - +
258D THR* 3.8 20.4 - - - +
299D HIS* 3.6 33.9 - - + +
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 4.5 11.6 - - + +
23D ASN* 3.4 45.6 - - + +
24D ALA* 3.8 10.7 - - + +
27D PRO* 5.4 1.3 - - + -
163D VAL* 6.0 4.0 - - + -
167D VAL* 5.9 0.2 - - - -
188D GLU* 3.1 11.0 - - + +
189D PRO* 1.3 77.4 - - - +
191D ILE* 1.3 60.9 + - + +
193D ASP* 3.8 8.6 - - - +
194D THR* 2.9 31.2 + - - -
229D LEU* 4.7 3.8 - - + +
230D PRO 5.4 0.5 - - - +
232D ARG* 2.8 52.7 + - - +
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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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163D VAL* 4.0 19.7 - - + +
166D THR* 3.7 24.5 - - + -
167D VAL* 3.8 15.0 - - + -
170D MET* 3.8 16.2 - - + +
186D ALA* 3.3 48.5 - - + +
187D ARG 5.0 0.2 - - - -
188D GLU* 2.8 15.6 + - + +
190D GLU* 1.3 75.6 - - + +
192D VAL* 1.3 61.6 + - + +
194D THR* 3.3 6.6 + - - -
195D ALA* 3.0 27.2 + - - +
208D GLN* 5.0 4.5 - - + -
209D GLY 5.3 2.9 - - - +
213D ILE* 4.3 10.3 - - + -
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Residues in contact with VAL 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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187D ARG 4.7 1.3 - - - +
188D GLU 4.1 6.5 - - - +
189D PRO* 3.0 16.0 + - + +
191D ILE* 1.3 78.4 - - - +
193D ASP* 1.3 58.0 + - - +
195D ALA* 3.2 3.8 + - - +
196D ASN* 2.8 46.3 + - - +
208D GLN* 3.8 17.7 - - + +
209D GLY* 3.6 34.8 - - - +
229D LEU* 6.5 0.4 - - + -
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Residues in contact with ASP 193 (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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24D ALA* 4.0 6.4 - - + +
28D ILE* 4.0 3.9 - - + +
189D PRO 3.0 11.5 + - - +
190D GLU* 3.8 8.5 - - - +
191D ILE 3.3 0.2 - - - -
192D VAL* 1.3 79.7 - - - +
194D THR* 1.3 56.2 + - - +
196D ASN* 4.7 1.6 + - - -
197D PHE* 3.1 23.0 + - - +
226D TYR* 2.8 40.7 + - - -
227D ARG 4.5 1.4 - - - +
228D VAL* 3.4 13.5 - - - +
229D LEU* 3.0 54.0 + - + +
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Residues in contact with THR 194 (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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24D ALA 4.5 1.0 + - - -
27D PRO* 3.5 39.4 - - + +
28D ILE* 4.1 15.1 - - + +
31D ALA* 4.6 4.5 - - + -
167D VAL* 4.7 4.5 - - + +
170D MET* 4.2 10.1 - - + -
171D CYS* 4.2 25.6 - - - -
190D GLU 2.9 18.8 + - - -
191D ILE* 3.8 6.4 - - - -
192D VAL 3.3 0.2 - - - -
193D ASP* 1.3 72.4 - - - +
195D ALA* 1.3 65.5 + - - +
197D PHE* 3.3 2.6 + - + +
198D LEU* 3.0 24.0 + - + +
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Residues in contact with ALA 195 (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 MET* 3.8 21.0 - - - +
191D ILE 3.0 14.2 + - - +
192D VAL 3.2 7.4 + - - +
194D THR* 1.3 76.4 - - - +
196D ASN* 1.3 59.2 + - - +
198D LEU* 3.0 4.7 + - - +
199D ILE* 2.9 30.6 + - - +
205D ILE* 4.0 13.4 - - + +
208D GLN* 3.7 32.3 - - + +
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Residues in contact with ASN 196 (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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192D VAL* 2.8 35.6 + - - +
193D ASP* 4.8 1.2 + - - +
195D ALA* 1.3 77.2 - - - +
197D PHE* 1.3 59.7 + - - +
199D ILE* 3.5 11.2 + - - +
200D THR* 3.0 26.2 + - - -
208D GLN* 3.2 22.9 + - - -
226D TYR* 3.3 28.2 + - + +
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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
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28D ILE* 3.7 48.9 - - + -
31D ALA* 3.9 19.3 - - + -
32D ALA* 4.2 10.5 - - - -
39D VAL* 3.6 29.6 - - + -
41D ILE* 4.0 8.1 - - + -
193D ASP 3.1 16.7 + - - +
194D THR 3.7 5.2 - - - +
195D ALA 3.2 0.2 - - - -
196D ASN* 1.3 75.7 - - - +
198D LEU* 1.3 66.3 + - + +
200D THR* 3.2 17.8 + - + -
201D LEU* 3.3 39.0 + - + +
224D GLY 6.0 0.4 - - - -
226D TYR* 3.7 38.9 - - + -
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Residues in contact with LEU 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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31D ALA* 3.8 27.4 - - + +
34D LEU* 3.9 20.4 - - + -
170D MET* 4.4 9.4 - - + -
171D CYS* 3.8 26.7 - - - -
174D THR* 4.0 11.2 - - + -
194D THR* 3.0 18.8 + - + +
195D ALA 3.0 6.3 + - - +
197D PHE* 1.3 77.3 - - + +
199D ILE* 1.3 59.9 + - - +
201D LEU* 2.8 25.9 + - + +
203D ALA* 3.1 21.4 + - + +
205D ILE* 3.8 24.5 - - + -
221D LEU* 4.5 10.3 - - + -
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Residues in contact with ILE 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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195D ALA 2.9 15.1 + - - +
196D ASN* 3.8 14.4 - - - +
197D PHE 3.4 0.2 - - - -
198D LEU* 1.3 74.6 - - - +
200D THR* 1.3 58.9 + - - +
202D GLY* 2.8 21.8 + - - -
203D ALA 3.4 20.9 + - - +
205D ILE* 3.5 35.7 - - + +
208D GLN* 3.6 20.6 - - - +
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Residues in contact with THR 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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196D ASN 3.0 12.7 + - - -
197D PHE* 3.3 15.5 - - + +
199D ILE* 1.3 80.4 - - - +
201D LEU* 1.3 62.4 + - + +
202D GLY 3.5 0.3 + - - -
223D GLY 4.2 5.9 - - - +
224D GLY* 4.8 7.2 - - - -
225D VAL 4.1 27.8 - - - +
226D TYR* 3.8 15.6 - - + -
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Residues in contact with LEU 201 (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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31D ALA 4.9 2.9 - - - +
35D ALA* 3.9 17.5 - - + +
39D VAL* 4.3 11.2 - - + -
197D PHE* 3.6 42.2 - - + +
198D LEU* 2.8 18.2 + - + +
200D THR* 1.3 80.8 - - + +
202D GLY* 1.3 56.0 + - - +
203D ALA 3.6 0.9 - - - -
220D ARG 4.7 0.3 - - - +
221D LEU* 3.6 18.2 - - + +
222D GLY* 3.0 44.4 + - - +
223D GLY* 3.2 32.1 - - - +
224D GLY* 3.9 3.6 - - - +
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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