Contacts of the helix formed by residues 184 - 200 (chain D) in PDB entry 1YCH
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 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D VAL* 1.3 77.1 - - + +
185D ALA* 1.3 65.5 + - - +
186D GLY* 2.8 28.8 + - - -
187D LEU* 3.5 33.0 + - + +
188D ILE* 3.1 24.0 + - - +
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Residues in contact with ALA 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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180D ASP 5.9 0.9 - - - -
183D VAL 3.4 5.1 + - - -
184D ASP* 1.3 75.5 + - - +
186D GLY* 1.3 63.1 + - - +
188D ILE* 3.8 4.5 - - - +
189D MET* 3.2 12.8 + - - +
238D ARG* 2.9 39.3 + - - +
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Residues in contact with GLY 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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184D ASP* 2.8 15.9 + - - -
185D ALA* 1.3 75.6 - - - +
187D LEU* 1.3 61.8 + - - -
189D MET* 3.6 2.6 + - - +
190D ASP* 3.2 23.2 + - - +
238D ARG* 4.5 7.6 - - - +
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Residues in contact with LEU 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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33D ARG* 4.2 28.9 - - - +
183D VAL* 5.3 3.8 - - + -
184D ASP* 3.3 33.0 + - + +
186D GLY* 1.3 79.0 - - - +
188D ILE* 1.3 63.2 + - - +
190D ASP* 3.3 6.7 + - - +
191D GLU* 3.1 27.5 + - - +
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Residues in contact with ILE 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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171D GLN* 4.0 19.1 - - + +
173D ILE* 4.8 9.2 - - + -
180D ASP* 5.1 6.3 - - + +
183D VAL* 4.0 19.5 - - + +
184D ASP 3.1 18.9 + - - +
185D ALA* 3.8 9.6 - - - +
187D LEU* 1.3 76.2 - - - +
189D MET* 1.3 64.6 + - - +
191D GLU* 3.5 4.7 + - + +
192D ALA* 3.1 26.0 + - - +
230D ILE* 3.2 49.6 - - + -
232D TRP* 4.0 21.7 - - + -
238D ARG* 4.8 1.3 - - - +
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Residues in contact with MET 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 ALA 3.2 16.9 + - - +
186D GLY* 3.9 4.5 - - - +
188D ILE* 1.3 80.3 - - - +
190D ASP* 1.3 59.1 + - - +
192D ALA* 3.5 5.2 - - - +
193D ALA* 3.1 24.6 + - - +
232D TRP* 4.5 12.3 - - + -
238D ARG* 3.1 71.1 - - + +
239D ILE* 4.5 7.6 - - + +
242D ALA* 4.0 21.1 - - - -
246D TRP* 4.2 13.0 - - + -
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Residues in contact with ASP 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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186D GLY 3.2 17.6 + - - +
187D LEU* 3.6 6.5 - - - +
188D ILE 3.2 0.4 - - - -
189D MET* 1.3 76.7 - - - +
191D GLU* 1.3 67.6 + - - +
192D ALA 3.2 0.2 - - - -
193D ALA* 3.1 8.2 + - - +
194D LYS* 2.9 26.7 + - - +
299D LYS* 3.6 34.7 + - - +
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Residues in contact with GLU 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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29D PHE* 5.6 0.5 - - - -
32D HIS* 6.0 0.9 - - - +
33D ARG* 3.5 35.6 + - - +
171D GLN* 4.0 16.9 - - + +
172D HIS 4.3 14.9 + - - +
173D ILE* 4.3 17.4 - - + +
187D LEU 3.1 18.2 + - - +
188D ILE* 3.8 8.3 - - + +
190D ASP* 1.3 83.5 - - - +
192D ALA* 1.3 63.0 + - - +
194D LYS* 3.3 22.5 + - - +
195D TYR* 3.1 23.2 + - - +
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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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169D PHE 5.6 0.2 - - - +
170D GLY 4.2 6.9 - - - +
171D GLN* 4.0 18.4 - - + +
188D ILE 3.1 17.6 + - - +
189D MET* 3.5 11.2 - - - +
191D GLU* 1.3 78.7 - - - +
193D ALA* 1.3 57.5 + - - +
195D TYR* 3.3 3.5 - - - +
196D TYR* 3.0 28.4 + - - +
232D TRP* 4.5 3.1 - - + -
239D ILE* 4.3 24.2 - - + -
243D TYR* 4.8 2.6 + - + -
246D TRP* 3.9 5.4 - - + -
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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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189D MET 3.1 14.6 + - - +
190D ASP* 3.1 13.9 + - - +
192D ALA* 1.3 73.9 - - - +
194D LYS* 1.3 65.2 + - - +
195D TYR 3.1 1.3 - - - -
196D TYR* 4.0 0.7 - - - +
197D ALA* 2.9 28.1 + - - +
246D TRP* 3.6 28.2 - - + +
299D LYS* 4.3 11.6 - - + +
302D LEU* 4.0 7.3 - - + +
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Residues in contact with LYS 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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29D PHE* 3.7 14.6 - - + -
30D SER* 2.8 39.2 + - - -
32D HIS* 3.8 16.8 + - - +
190D ASP 2.9 9.6 + - - +
191D GLU* 3.3 23.3 + - - +
193D ALA* 1.3 76.0 - - - +
195D TYR* 1.3 61.9 + - - +
197D ALA 3.7 0.2 + - - -
198D ASN* 2.9 40.2 + - - +
295D ASN* 3.7 22.4 - - - +
296D ASP* 3.4 24.8 + - - +
299D LYS* 3.6 26.9 - - + +
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Residues in contact with TYR 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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29D PHE* 4.1 7.8 - - + -
148D HIS* 5.5 0.2 - - - -
167D ASP* 3.2 56.2 + - + +
170D GLY* 3.3 25.6 - - - +
171D GLN* 4.3 1.8 - - - -
172D HIS* 3.5 47.8 - + - +
191D GLU 3.1 12.7 + - - +
192D ALA 3.3 9.4 - - - +
194D LYS* 1.3 75.7 - - - +
196D TYR* 1.3 69.3 + - - +
198D ASN 3.3 0.9 + - - -
199D ILE* 3.0 49.9 + - + +
200D LEU* 4.5 11.4 - - + -
228D HIS* 3.8 8.0 - + - -
243D TYR* 4.2 7.4 - - - -
531D FEO 4.5 0.2 - - - -
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Residues in contact with TYR 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 3.0 16.9 + - - +
193D ALA 4.0 1.8 - - - +
195D TYR* 1.3 75.2 - - - +
197D ALA* 1.3 62.4 + - - +
200D LEU* 2.8 61.1 + - + -
201D MET 3.1 14.9 + - - -
204D SER* 2.9 32.0 + - - -
207D ILE* 3.8 11.0 - - + +
243D TYR* 3.7 33.2 - + - +
246D TRP* 3.6 35.4 - + + -
247D ALA* 3.4 17.9 - - - +
302D LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 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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193D ALA 2.9 19.3 + - - +
194D LYS 4.0 2.5 - - - +
196D TYR* 1.3 77.9 - - - +
198D ASN* 1.3 58.3 + - - +
201D MET* 3.5 20.1 - - - +
298D ILE* 3.5 19.9 - - - +
299D LYS* 3.7 28.0 - - - +
302D LEU* 4.0 24.2 - - + -
332D LEU* 3.9 3.1 - - - +
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Residues in contact with ASN 198 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314C ILE* 6.1 0.7 - - - +
315C ASN* 4.9 4.2 + - - -
721C FMN 6.2 0.3 - - - +
29D PHE* 3.8 20.1 - - + -
194D LYS* 2.9 31.4 + - - +
197D ALA* 1.3 81.6 - - - +
199D ILE* 1.3 62.9 + - - +
295D ASN* 3.3 47.6 + - - +
298D ILE* 3.3 26.9 - - - +
328D ASP* 4.4 4.2 - - - +
332D LEU* 3.4 20.9 - - - +
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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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315C ASN* 5.0 3.3 + - - +
721C FMN 5.1 7.0 - - + -
25D HIS* 4.6 18.4 - - + -
29D PHE* 3.7 28.9 - - + -
148D HIS* 4.2 36.8 - - + +
167D ASP* 6.1 0.7 - - + -
172D HIS* 4.8 3.1 - - + +
195D TYR* 3.0 53.1 + - + +
198D ASN* 1.3 83.8 - - - +
200D LEU* 1.3 73.1 + - + +
201D MET 3.6 0.7 - - - -
202D PRO* 3.5 12.0 - - - +
203D PHE* 3.7 12.3 - - - -
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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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147D LEU* 4.7 20.0 - - + +
148D HIS* 4.7 4.5 - - + +
167D ASP* 6.1 2.0 - - + -
168D ALA* 4.8 12.6 - - + +
195D TYR* 4.5 10.5 - - + -
196D TYR* 2.8 49.9 + - + +
199D ILE* 1.3 85.6 - - + +
201D MET* 1.3 63.6 + - - +
202D PRO* 3.2 4.0 - - - -
203D PHE* 2.9 29.6 + - + +
204D SER 3.6 0.5 + - - -
207D ILE* 4.2 16.3 - - + +
243D TYR* 3.4 34.1 - - + +
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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
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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