Contacts of the helix formed by residues 186 - 200 (chain D) in PDB entry 3SL5
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 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D VAL 5.4 0.7 - - - +
185D PHE* 1.3 74.5 - - - +
187D ASP* 1.3 65.0 + - - +
188D LEU* 3.1 10.3 + - - +
189D GLU* 2.8 40.3 + - - +
190D ILE* 3.1 25.0 + - - +
306D ARG* 4.5 5.6 - - - +
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Residues in contact with ASP 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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131D LEU* 4.2 7.0 - - + +
134D THR* 3.5 21.9 + - + +
135D PHE* 3.5 24.0 - - + -
186D THR* 1.3 74.3 - - - +
188D LEU* 1.3 56.7 + - - +
190D ILE* 3.5 12.9 + - - +
191D LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 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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135D PHE* 3.6 26.9 - - + -
186D THR* 3.0 9.0 + - - +
187D ASP* 1.3 77.0 - - - +
189D GLU* 1.3 60.8 + - - +
190D ILE 3.2 1.1 - - - -
191D LEU* 3.5 7.5 - - + +
192D ALA* 2.9 28.2 + - - +
252D LEU* 3.6 19.7 - - + -
256D GLN* 3.7 38.1 - - + +
259D SER* 3.8 22.4 - - - +
260D LEU* 3.9 9.8 - - + +
263D MET* 4.0 7.6 - - + +
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Residues in contact with GLU 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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185D PHE* 3.2 17.1 - - + -
186D THR* 2.8 35.7 + - - +
188D LEU* 1.3 76.1 - - + +
190D ILE* 1.3 58.8 + - - +
192D ALA* 3.8 1.7 - - - +
193D ALA* 3.0 27.9 + - - +
263D MET* 3.6 29.8 - - + +
303D TYR* 5.6 2.3 - - - -
306D ARG* 2.7 51.4 + - - +
310D LEU* 4.0 19.6 - - + +
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Residues in contact with ILE 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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3D EDO 3.5 30.1 - - - +
129D ARG* 3.7 32.8 - - - +
131D LEU* 4.7 7.2 - - + -
176D LEU* 3.7 17.7 - - + -
185D PHE* 4.1 15.3 - - + +
186D THR 3.1 17.4 + - - +
187D ASP* 3.5 15.3 - - - +
189D GLU* 1.3 75.1 - - - +
191D LEU* 1.3 60.8 + - - +
193D ALA* 3.2 2.3 + - - +
194D ILE* 2.8 48.9 + - + +
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Residues in contact with LEU 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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126D PHE* 3.8 34.5 - - + -
131D LEU* 4.3 12.1 - - + +
135D PHE* 3.7 40.8 - - + -
137D ILE* 5.0 2.2 - - + -
187D ASP 3.0 18.6 + - - +
188D LEU* 3.5 5.6 - - + +
190D ILE* 1.3 78.4 - - - +
192D ALA* 1.3 56.6 + - - +
194D ILE* 4.7 1.1 - - - -
195D PHE* 2.7 33.9 + - + +
249D PHE* 3.9 27.8 - - + -
252D LEU* 4.1 7.9 - - + -
260D LEU* 3.8 14.1 - - + -
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Residues in contact with ALA 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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188D LEU 2.9 19.1 + - - +
189D GLU* 3.9 4.3 - - - +
190D ILE 3.2 0.2 - - - -
191D LEU* 1.3 72.5 - - - +
193D ALA* 1.3 58.3 + - - +
195D PHE 3.1 0.9 + - - -
196D ALA* 2.6 38.5 + - - +
260D LEU* 3.4 19.5 - - + +
263D MET* 3.9 27.1 - - + -
264D VAL* 3.6 16.4 - - + +
267D ILE* 4.3 2.2 - - + -
310D LEU* 5.9 0.2 - - + -
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Residues in contact with ALA 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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172D THR* 3.9 15.6 - - + +
176D LEU* 4.4 8.5 - - + -
189D GLU 3.0 19.2 + - - +
190D ILE 3.8 2.7 - - - +
192D ALA* 1.3 76.8 - - - +
194D ILE* 1.3 61.7 + - - +
196D ALA* 3.5 1.6 + - - +
197D SER* 3.0 28.1 + - - -
267D ILE* 3.7 15.9 - - + +
310D LEU* 4.0 20.6 - - + -
313D MET* 5.2 0.9 - - - -
314D VAL* 4.0 7.2 - - + +
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Residues in contact with ILE 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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122D MET* 3.9 13.0 - - - -
125D ILE* 3.8 17.5 - - + -
126D PHE* 3.8 28.0 - - + -
129D ARG* 3.6 36.6 - - - +
131D LEU* 4.3 5.2 - - + -
169D VAL* 4.2 6.9 - - + +
172D THR* 4.6 7.4 - - + -
173D HIS* 4.6 7.0 - - + +
176D LEU* 3.7 12.8 - - + -
190D ILE* 2.8 27.3 + - + +
191D LEU* 4.0 3.1 - - - +
193D ALA* 1.3 75.2 - - - +
195D PHE* 1.3 65.2 + - - +
197D SER* 3.3 8.6 + - - -
198D ALA* 3.2 18.9 + - - +
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Residues in contact with PHE 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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122D MET* 4.8 9.4 - - + -
126D PHE* 5.8 1.3 - + + -
145D TYR* 3.3 42.6 - + - -
191D LEU* 2.7 25.9 + - + +
192D ALA* 3.6 2.7 - - - +
194D ILE* 1.3 72.6 - - - +
196D ALA* 1.3 66.8 + - - +
198D ALA* 2.9 16.2 + - + +
199D ILE* 3.2 35.5 + - + +
237D GLY 4.1 8.7 - - - -
238D PHE* 4.1 18.6 - + - -
241D LEU* 4.5 5.2 - - + -
248D ILE* 4.1 8.1 - - + -
249D PHE* 3.6 38.8 - + + -
260D LEU* 5.2 0.2 - - + -
264D VAL* 3.6 21.3 - - + -
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Residues in contact with ALA 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 ALA 2.6 20.5 + - - +
193D ALA 3.5 4.0 - - - +
195D PHE* 1.3 74.0 - - - +
197D SER* 1.3 58.4 + - - +
199D ILE* 3.2 2.9 + - - +
200D HIS* 2.8 34.2 + - - +
264D VAL* 4.1 12.3 - - + -
267D ILE* 3.5 38.4 - - + -
268D VAL* 3.9 14.5 - - + +
314D VAL* 5.2 0.4 - - - -
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Residues in contact with SER 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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153D TYR* 4.4 0.2 + - - -
165D ALA* 4.1 4.9 - - - +
168D VAL* 3.8 8.0 - - - +
169D VAL* 3.6 28.3 - - - +
172D THR* 2.8 25.2 + - - +
193D ALA 3.0 12.7 + - - -
194D ILE* 3.6 9.2 - - - -
195D PHE 3.2 0.2 - - - -
196D ALA* 1.3 78.7 - - - +
198D ALA* 1.3 61.7 + - - +
200D HIS* 2.9 31.4 + - - -
314D VAL* 3.7 10.8 - - - +
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Residues in contact with ALA 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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118D LEU* 4.1 5.8 - - + +
122D MET* 3.6 39.0 - - + -
149D LEU* 3.5 20.4 - - + +
153D TYR* 2.6 31.4 + - - -
165D ALA* 4.0 4.0 - - - +
169D VAL* 3.4 9.4 - - + -
194D ILE 3.2 2.2 + - - +
195D PHE* 2.9 10.2 + - + +
197D SER* 1.3 79.3 - - - +
199D ILE* 1.3 55.6 + - + +
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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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145D TYR* 3.3 26.0 - - - +
149D LEU* 3.8 15.0 - - + -
153D TYR* 3.3 3.1 - - - -
195D PHE* 3.6 40.2 - - + +
196D ALA 3.4 9.6 - - - +
198D ALA* 1.3 78.6 - - - +
200D HIS* 1.3 62.1 + - - +
201D ASP 2.8 12.9 + - - -
202D VAL* 2.9 17.9 + - + +
233D HIS* 3.5 4.8 - - - +
234D LEU* 4.0 19.3 - - + -
237D GLY* 4.0 19.5 - - - -
238D PHE* 4.6 2.5 - - + -
264D VAL* 3.7 19.7 - - + -
268D VAL* 4.3 2.7 - - + -
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Residues in contact with HIS 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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153D TYR* 4.6 1.0 + - - -
164D HIS* 3.1 17.3 - + - -
165D ALA* 4.6 4.0 - - - -
168D VAL* 3.5 23.8 - - + +
196D ALA 2.8 19.5 + - - +
197D SER* 2.9 21.6 + - - +
198D ALA 3.4 2.2 - - - -
199D ILE* 1.3 76.8 - - - +
201D ASP* 1.3 69.9 + - + +
202D VAL 3.7 0.2 - - - -
233D HIS* 2.9 20.8 - - - +
268D VAL* 3.9 21.8 - - + +
271D THR* 4.1 20.2 + - + -
314D VAL* 5.0 2.2 - - + -
318D ASP* 3.0 14.6 + - + -
438D ZN 2.2 36.8 - - - -
439D ZN 4.1 1.6 - - - -
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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