Contacts of the helix formed by residues 215 - 232 (chain D) in PDB entry 1S9C
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 HIS 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D ALA* 3.8 29.1 - - + +
188D TYR* 3.5 30.9 - + + +
189D ARG* 3.7 13.0 - - + +
193D ASP* 3.2 44.8 + - + +
198D HIS* 3.2 51.4 + + + +
214D LEU* 1.3 75.9 - - - +
216D GLY* 1.3 67.1 + - - +
217D LEU* 4.2 3.1 - - + +
218D CYS* 2.9 17.9 + - + +
219D THR* 3.4 7.3 + - - -
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Residues in contact with GLY 216 (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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198D HIS* 4.8 2.4 - - - -
214D LEU 3.4 3.9 + - - -
215D HIS* 1.3 71.7 - - - +
217D LEU* 1.3 61.8 + - - +
218D CYS 3.1 0.3 + - - -
219D THR* 3.2 8.4 + - - -
220D PHE 3.0 17.7 + - - -
246D PHE* 3.4 31.1 - - - -
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Residues in contact with LEU 217 (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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30D TYR* 4.4 2.9 + - - -
62D VAL* 3.2 36.6 - - + -
63D ILE* 6.3 0.2 - - + -
66D GLN* 3.3 28.5 - - + +
89D HIS* 4.1 22.9 - - + +
92D GLN* 3.9 15.5 - - + -
142D PHE* 4.9 1.6 - - + -
188D TYR* 3.4 23.6 + - + +
215D HIS* 3.1 2.5 - - + +
216D GLY* 1.3 74.9 - - - +
218D CYS* 1.3 57.3 + - - +
220D PHE* 3.2 16.7 - - + +
221D GLY* 2.9 21.5 + - - -
246D PHE* 3.8 19.2 - - + -
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Residues in contact with CYS 218 (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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33D GLY 3.3 27.1 - - - -
34D VAL* 3.7 2.8 - - - +
184D GLN* 3.9 14.1 - - - -
188D TYR* 3.8 32.8 - - + -
214D LEU* 4.0 16.2 - - + -
215D HIS* 2.9 12.6 + - + +
217D LEU* 1.3 74.9 - - - +
219D THR* 1.3 67.2 + - - +
220D PHE 3.0 1.1 - - - -
221D GLY* 3.0 2.8 + - - +
222D PHE* 2.9 42.7 + - - -
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Residues in contact with THR 219 (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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214D LEU* 3.9 11.1 + - - +
215D HIS 3.4 9.1 + - - -
216D GLY* 3.2 9.6 + - - -
218D CYS* 1.3 77.1 - - - +
220D PHE* 1.3 62.9 + - - +
222D PHE* 3.1 5.1 + - - +
223D SER* 3.0 23.4 + - - -
250D VAL* 3.9 15.3 - - + +
256D LEU* 3.6 38.4 - - + -
271D THR* 4.0 5.2 - - + -
280D VAL* 3.9 16.2 - - + -
281D ILE* 3.8 18.2 - - + -
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Residues in contact with PHE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 5.1 0.7 - - - -
59D THR* 3.6 24.2 - - + -
62D VAL* 3.7 21.3 - - + -
92D GLN* 4.0 20.6 - - + -
94D LEU* 5.3 0.7 - - + -
216D GLY 3.0 13.2 + - - +
217D LEU* 3.2 25.4 - - + +
219D THR* 1.3 77.5 - - - +
221D GLY* 1.3 58.4 + - - +
223D SER* 3.4 1.6 + - - -
224D ALA* 2.9 34.1 + - + +
242D VAL* 3.1 34.1 - - + -
244D ALA* 3.6 33.4 - - + -
246D PHE* 4.1 11.9 - + + -
269D PHE* 5.2 5.9 - + - -
281D ILE* 3.7 10.9 - - + +
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Residues in contact with GLY 221 (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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30D TYR* 3.9 10.3 - - - -
34D VAL* 3.3 25.3 - - - +
59D THR* 4.0 9.4 + - - -
217D LEU 2.9 14.1 + - - -
218D CYS 3.0 0.8 + - - -
220D PHE* 1.3 77.5 - - - +
222D PHE* 1.3 52.5 + - - +
224D ALA* 3.7 1.4 - - - +
225D ARG* 2.8 37.2 + - - +
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Residues in contact with PHE 222 (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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34D VAL* 3.3 17.2 - - - +
35D GLY* 3.7 18.8 - - - -
178D ASP* 3.7 35.7 - - + -
179D THR 4.8 6.1 - - - -
180D THR* 4.4 11.9 - - - -
184D GLN* 3.6 35.7 - - + -
214D LEU* 5.1 1.1 - - + -
218D CYS* 2.9 39.4 + - - -
219D THR* 3.2 7.4 - - - +
221D GLY* 1.3 73.6 - - - +
223D SER* 1.3 66.8 + - - +
225D ARG* 2.9 29.8 + - - +
226D ARG* 2.9 18.0 + - - +
256D LEU* 3.6 20.9 - - + -
258D THR* 5.6 0.9 - - - +
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Residues in contact with SER 223 (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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219D THR 3.0 10.2 + - - -
220D PHE 4.0 1.8 - - - -
222D PHE* 1.3 80.0 - - - +
224D ALA* 1.3 64.8 + - - +
226D ARG* 3.0 5.3 + - - +
227D VAL* 2.9 28.2 + - - +
258D THR* 2.6 37.6 + - - +
269D PHE* 3.6 21.1 - - - -
271D THR* 2.8 25.0 + - - +
281D ILE* 5.0 0.9 - - - -
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Residues in contact with ALA 224 (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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59D THR* 3.5 29.8 - - + +
220D PHE* 2.9 22.2 + - + +
221D GLY 3.8 1.6 - - - +
223D SER* 1.3 75.1 - - - +
225D ARG* 1.3 63.6 + - - +
227D VAL* 3.2 10.0 + - - +
228D LEU* 3.0 22.9 + - - +
239D PHE* 3.9 16.8 - - + -
242D VAL* 4.9 4.9 - - + -
269D PHE* 4.9 8.4 - - + -
286D VAL* 6.0 1.1 - - - -
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Residues in contact with ARG 225 (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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34D VAL* 2.4 35.4 + - + -
35D GLY* 3.0 24.3 + - - -
36D ALA* 3.6 20.2 - - - +
43D ASP* 4.4 11.6 + - - +
46D PHE* 5.4 4.7 - - + -
57D LEU* 4.1 35.2 - - + -
59D THR* 5.7 0.2 + - - -
178D ASP* 3.2 25.3 + - - -
221D GLY 2.8 18.9 + - - +
222D PHE* 3.1 23.5 - - - +
224D ALA* 1.3 72.7 - - - +
226D ARG* 1.3 73.0 + - - +
228D LEU* 3.3 11.9 - - + +
229D GLN* 3.1 26.2 + - - +
234D ASN* 4.6 1.3 + - - +
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Residues in contact with ARG 226 (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 LEU* 3.3 42.1 - - + +
177D THR 3.0 24.5 + - - +
178D ASP* 2.6 32.3 + - - +
222D PHE 2.9 18.4 + - - +
223D SER* 3.4 9.4 - - - +
225D ARG* 1.3 86.4 - - - +
227D VAL* 1.3 66.9 + - - +
229D GLN* 2.4 40.3 + - - +
230D GLN* 2.8 26.9 + - - +
258D THR* 4.8 7.0 - - - +
260D MET* 4.5 7.4 - - + -
173G ASP* 4.5 5.3 + - - +
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Residues in contact with VAL 227 (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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223D SER 2.9 20.0 + - - +
224D ALA* 3.6 7.9 - - - +
226D ARG* 1.3 74.7 - - - +
228D LEU* 1.3 65.1 + - - +
230D GLN 3.1 0.2 + - - -
231D PHE* 2.9 26.8 + - + -
232D ALA* 4.0 0.7 + - - +
258D THR* 4.8 0.7 - - + -
260D MET* 3.8 27.8 - - + -
267D ILE* 3.9 22.7 - - + -
269D PHE* 4.2 19.1 - - + -
286D VAL* 3.1 42.2 - - + -
288D LEU* 5.2 2.9 - - + -
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Residues in contact with LEU 228 (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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46D PHE* 3.9 28.3 - - + -
57D LEU* 3.9 17.3 - - + -
58D PRO* 4.3 11.0 - - + -
224D ALA 3.0 12.1 + - - +
225D ARG* 3.3 12.1 - - + +
226D ARG 3.1 0.2 - - - -
227D VAL* 1.3 78.9 - - - +
229D GLN* 1.3 59.8 + - - +
232D ALA* 3.3 25.0 + - + +
234D ASN* 3.1 25.8 + - - +
235D ASP 3.9 31.2 - - - +
236D VAL* 4.1 5.4 - - + +
239D PHE* 4.0 25.7 - - + -
288D LEU* 5.7 0.7 - - - -
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Residues in contact with GLN 229 (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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40D ASP* 3.9 19.6 + - - +
42D LYS* 5.7 1.8 - - - +
43D ASP* 4.3 9.3 + - - -
176D LEU* 4.3 1.9 - - + +
225D ARG* 3.1 11.6 + - - +
226D ARG* 2.4 51.4 + - - +
228D LEU* 1.3 80.4 - - - +
230D GLN* 1.3 71.5 + - + +
233D ASP* 4.0 12.1 + - - -
234D ASN* 2.9 33.4 + - - +
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Residues in contact with GLN 230 (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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174D ALA* 3.7 18.2 - - + +
176D LEU* 3.8 22.6 - - + +
226D ARG 2.8 16.5 + - - +
229D GLN* 1.3 83.8 + - - +
231D PHE* 1.3 93.1 + - + +
232D ALA 3.7 0.2 - - - -
233D ASP 4.9 0.6 + - - -
260D MET* 4.2 7.2 - - + -
176G LEU* 4.0 2.8 - - - +
230G GLN* 3.2 37.7 + - - +
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Residues in contact with PHE 231 (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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173D ASP* 4.6 10.1 - - + -
174D ALA* 4.3 14.6 - - + -
227D VAL* 2.9 10.5 + - + +
230D GLN* 1.3 104.2 - - + +
232D ALA* 1.3 60.4 + - - +
233D ASP* 3.8 0.9 - - - -
238D ARG* 3.9 9.8 + - - -
260D MET* 3.6 31.4 - - + -
262D LYS* 3.8 32.5 - - + -
267D ILE* 3.5 43.1 - - + -
288D LEU* 3.2 15.0 - - + +
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Residues in contact with ALA 232 (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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228D LEU* 3.3 25.2 + - + +
231D PHE* 1.3 79.9 - - - +
233D ASP* 1.3 74.9 + - - +
234D ASN 3.2 1.1 - - - -
235D ASP* 2.9 19.6 + - - +
238D ARG* 3.5 27.9 + - + +
288D LEU* 3.9 25.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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