Contacts of the helix formed by residues 227 - 245 (chain D) in PDB entry 1HYH
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 LEU 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D TRP* 3.5 56.2 - - + +
216D ILE* 3.8 37.2 - - + -
217D VAL* 4.5 13.7 - - + -
220D ALA* 4.0 25.3 - - + +
225D ILE* 3.7 4.1 + - + -
226D ASP* 1.3 73.3 + - - +
228D ALA* 1.3 51.9 + - - +
230D ILE* 3.0 13.2 + - + +
231D GLU* 2.7 33.0 + - - +
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Residues in contact with ALA 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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226D ASP* 3.2 14.6 + - - +
227D LEU* 1.3 76.8 - - - +
229D ALA* 1.3 57.6 + - - +
231D GLU* 3.3 10.9 + - - +
232D GLU* 2.9 24.8 + - - -
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Residues in contact with ALA 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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226D ASP* 3.1 30.6 + - + +
228D ALA* 1.3 74.2 - - - +
230D ILE* 1.3 56.5 + - + +
232D GLU* 3.1 2.9 + - - +
233D GLU* 2.7 35.5 + - - +
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Residues in contact with ILE 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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175D MET* 4.9 2.7 - - + +
178D ALA* 4.0 16.0 - - + +
179D VAL* 3.7 18.4 - - + +
182D ALA* 4.5 17.5 - - + -
206D TRP* 3.6 17.3 - - + -
216D ILE* 4.4 9.4 - - + -
225D ILE* 3.5 35.7 - - + -
226D ASP 3.0 14.6 + - - +
227D LEU* 3.0 22.6 + - + +
229D ALA* 1.3 71.9 - - + +
231D GLU* 1.3 67.1 + - - +
233D GLU* 3.0 18.1 + - - +
234D ALA* 3.0 13.6 + - + +
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Residues in contact with GLU 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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202D GLN 5.1 0.9 - - - +
203D PHE* 4.2 8.3 - - - +
204D VAL* 3.4 41.1 + - + +
206D TRP* 3.1 26.4 + - + -
227D LEU 2.7 15.5 + - - +
228D ALA* 3.6 12.3 - - - +
230D ILE* 1.3 73.5 - - - +
232D GLU* 1.3 61.4 + - - +
234D ALA* 3.5 7.1 + - - +
235D ARG* 3.4 29.2 + - + +
310D LYS* 5.8 2.3 + - - -
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Residues in contact with GLU 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 ALA 2.9 15.0 + - - -
229D ALA* 3.5 3.8 - - - +
231D GLU* 1.3 71.5 - - - +
233D GLU* 1.3 60.3 + - - +
235D ARG* 3.2 7.6 + - - +
236D LYS* 2.8 31.1 + - - +
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Residues in contact with GLU 233 (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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64B ILE* 5.5 3.1 - - - +
177D ARG* 3.5 22.5 + - - +
178D ALA* 3.8 19.5 - - + +
181D GLU* 4.9 6.4 - - + +
229D ALA 2.7 16.3 + - - +
230D ILE* 3.0 13.0 + - - +
232D GLU* 1.3 72.4 - - - +
234D ALA* 1.3 65.7 + - - +
236D LYS* 3.4 17.6 + - - +
237D GLY* 3.1 17.8 + - - -
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Residues in contact with ALA 234 (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 ASP 5.6 0.2 - - - +
174D ARG* 3.8 39.7 - - + +
175D MET* 4.3 8.3 - - + +
177D ARG* 3.9 13.7 + - - +
178D ALA* 4.0 5.4 - - + +
194D ASN* 6.3 0.7 - - - +
230D ILE 3.0 8.4 + - - +
231D GLU* 3.5 13.0 - - - +
233D GLU* 1.3 82.4 - - - +
235D ARG* 1.3 63.4 + - + +
237D GLY* 3.3 7.8 + - - -
238D GLY 3.7 6.6 + - - -
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Residues in contact with ARG 235 (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 ARG* 5.9 1.1 - - - +
202D GLN* 5.6 8.1 - - - +
231D GLU* 3.5 19.1 - - + +
232D GLU* 3.2 10.2 + - - +
234D ALA* 1.3 73.7 - - + +
236D LYS* 1.3 67.5 + - - +
238D GLY* 3.0 13.4 + - - +
239D PHE* 3.3 25.5 + - + -
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Residues in contact with LYS 236 (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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232D GLU 2.8 20.0 + - - +
233D GLU* 3.6 20.0 - - - +
235D ARG* 1.3 72.3 - - - +
237D GLY* 1.4 52.2 + - - +
239D PHE* 2.9 14.3 + - + +
240D THR* 2.7 42.8 + - - +
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Residues in contact with GLY 237 (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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64B ILE* 4.0 17.7 - - - +
68B ASP* 5.8 0.2 - - - -
174D ARG* 5.3 0.7 - - - -
177D ARG* 4.1 13.0 - - - -
233D GLU* 3.1 12.5 + - - -
234D ALA 3.3 4.5 + - - -
235D ARG 3.2 0.4 - - - -
236D LYS* 1.4 78.2 - - - +
238D GLY* 1.3 55.7 + - - +
240D THR* 2.8 25.5 + - - -
241D VAL* 2.9 17.3 + - - +
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Residues in contact with GLY 238 (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 ARG* 3.8 33.2 - - - +
234D ALA 3.7 6.2 + - - -
235D ARG* 3.0 9.0 + - - -
237D GLY* 1.3 73.5 - - - +
239D PHE* 1.3 59.8 + - - +
241D VAL* 3.3 5.7 + - - +
242D LEU* 3.0 35.2 + - - +
248D THR* 4.4 1.0 - - - +
331D SO4 4.9 3.1 - - - -
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Residues in contact with PHE 239 (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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235D ARG* 3.3 30.5 + - + -
236D LYS* 2.9 11.3 + - + +
238D GLY* 1.3 74.3 - - - +
240D THR* 1.3 60.0 + - - +
242D LEU* 3.9 23.7 - - + +
243D ASN* 3.0 31.5 + - - +
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Residues in contact with THR 240 (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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57B ALA 4.8 1.5 - - - +
60B LYS* 4.1 31.9 - - + +
61B ALA* 4.1 2.7 - - - +
64B ILE* 4.3 13.8 - - + +
236D LYS* 2.7 30.6 + - - +
237D GLY* 2.8 12.4 + - - -
239D PHE* 1.3 74.6 - - - +
241D VAL* 1.3 55.9 + - - +
243D ASN* 3.9 9.1 + - - +
244D GLY* 3.0 24.9 + - - -
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Residues in contact with VAL 241 (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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61B ALA* 3.6 26.1 - - - +
64B ILE* 3.7 20.2 - - + -
65B ASP* 3.9 25.1 - - + +
68B ASP* 4.7 3.1 - - - +
174D ARG* 5.2 0.4 - - - +
237D GLY 2.9 18.9 + - - +
238D GLY* 3.6 9.0 - - - +
239D PHE 3.3 0.2 - - - -
240D THR* 1.3 74.9 - - - +
242D LEU* 1.3 65.2 + - - +
244D GLY 3.2 0.7 + - - -
245D LYS* 3.0 30.5 + - + +
247D TYR 3.5 9.9 - - - +
248D THR* 3.5 25.4 - - + -
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Residues in contact with LEU 242 (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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238D GLY 3.0 20.9 + - - +
239D PHE* 3.9 28.9 - - + +
241D VAL* 1.3 76.2 - - - +
243D ASN* 1.3 58.6 + - - +
246D GLY* 2.7 34.2 + - - +
247D TYR* 3.5 32.8 - - - +
248D THR* 4.0 9.9 - - + +
331D SO4 4.3 20.2 - - - +
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Residues in contact with ASN 243 (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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57B ALA* 4.4 12.4 - - - +
239D PHE 3.0 18.5 + - - +
240D THR* 4.1 9.2 + - - +
242D LEU* 1.3 80.1 - - - +
244D GLY* 1.3 64.6 + - - +
246D GLY* 4.7 0.7 + - - -
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Residues in contact with GLY 244 (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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55B ASN* 5.0 2.3 + - - +
57B ALA* 3.2 38.2 - - - +
58B LYS* 3.6 19.6 + - - +
61B ALA* 3.9 2.2 - - - -
240D THR 3.0 14.5 + - - -
241D VAL 3.2 0.6 + - - -
243D ASN* 1.3 78.8 - - - +
245D LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 245 (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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58B LYS* 4.1 17.9 - - + +
61B ALA* 4.1 7.6 - - + -
62B ASP* 2.8 27.9 + - - +
65B ASP* 2.3 35.6 + - - +
241D VAL* 3.0 15.3 + - + +
244D GLY* 1.3 79.7 - - - +
246D GLY* 1.3 59.5 + - - +
247D TYR* 3.1 67.2 - - + +
249D SER* 3.2 14.2 + - - +
250D TYR* 3.3 10.8 - - - -
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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