Contacts of the helix formed by residues 249 - 265 (chain C) in PDB entry 4HRE
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 LYS 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C VAL* 1.3 77.9 - - - +
250C GLY* 1.3 68.2 + - - +
252C LEU* 3.6 10.6 + - - +
253C GLU* 3.1 27.9 + - - +
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Residues in contact with GLY 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C LYS* 1.3 81.9 - - - +
251C ASP* 1.3 59.7 + - - -
253C GLU* 3.4 8.6 + - - +
254C ASN* 3.1 25.8 + - - +
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Residues in contact with ASP 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 3.7 34.8 - - - +
126C ASP* 5.5 0.3 - - - +
129C ILE* 4.8 1.2 - - - +
167C PHE* 3.7 33.5 - - + -
250C GLY* 1.3 71.6 - - - -
252C LEU* 1.3 61.0 + - - +
253C GLU 3.2 0.4 - - - -
254C ASN* 3.5 15.8 + - + +
255C ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ASP* 3.5 57.2 - - + +
167C PHE* 3.7 13.3 - - + +
170C LEU* 4.5 5.8 - - + -
210C VAL* 4.1 17.3 - - + -
248C VAL* 4.3 17.0 - - + -
249C LYS 3.6 9.6 + - - +
251C ASP* 1.3 77.9 - - - +
253C GLU* 1.3 56.0 + - - +
255C ALA* 3.2 4.0 + - - +
256C PHE* 3.0 59.9 + - + -
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 4.2 10.2 - - + +
245C LYS* 3.8 24.7 - - - +
248C VAL* 3.7 23.7 - - - +
249C LYS* 3.1 38.2 + - - +
250C GLY 3.5 7.1 + - - +
252C LEU* 1.3 76.6 - - - +
254C ASN* 1.3 66.4 + - - +
256C PHE* 4.1 0.3 - - - +
257C LEU* 3.0 39.6 + - + +
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Residues in contact with ASN 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ASP* 3.6 24.8 + - - +
129C ILE* 3.8 11.5 - - + +
250C GLY 3.1 11.9 + - - +
251C ASP* 3.3 18.0 + - - +
253C GLU* 1.3 79.0 - - - +
255C ALA* 1.3 58.7 + - - +
257C LEU* 3.8 6.3 - - - +
258C ASN* 2.5 51.2 + - - -
273C ARG* 5.5 1.0 + - - -
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ILE* 3.7 17.0 - - + +
133C CYS* 3.7 3.7 - - - -
167C PHE* 3.9 18.2 - - + -
170C LEU* 3.6 22.4 - - + -
171C MET* 4.5 4.5 - - - -
251C ASP 2.9 18.5 + - - +
252C LEU 3.5 4.0 - - - +
254C ASN* 1.3 73.1 - - - +
256C PHE* 1.3 61.9 + - - +
258C ASN* 3.1 4.5 + - - +
259C LEU* 2.8 30.2 + - - +
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU* 3.9 21.5 - - + +
210C VAL* 4.3 9.6 - - + -
213C TRP* 3.8 41.5 - + + -
214C ILE* 3.8 20.2 - - + -
217C MET* 3.6 38.4 - - + -
244C ILE* 3.7 24.2 - - + -
248C VAL* 4.7 5.2 - - + -
252C LEU* 3.0 49.6 + - + +
255C ALA* 1.3 75.5 - - - +
257C LEU* 1.3 61.8 + - - +
259C LEU* 3.3 7.7 + - + +
260C VAL* 2.9 29.6 + - - +
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LEU* 3.6 44.4 - - + +
244C ILE* 4.1 14.4 - - + -
245C LYS* 4.1 28.5 - - + -
253C GLU* 3.0 33.9 + - + +
254C ASN* 3.8 6.1 - - - +
256C PHE* 1.3 77.1 - - - +
258C ASN* 1.3 64.8 + - - +
260C VAL* 3.2 1.9 + - - +
261C GLN* 3.1 36.7 + - - +
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Residues in contact with ASN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ILE* 3.3 26.2 - - + +
133C CYS* 4.0 6.1 - - + -
254C ASN* 2.5 43.9 + - - -
255C ALA 3.4 6.5 - - - +
257C LEU* 1.3 75.6 - - - +
259C LEU* 1.3 63.2 + - - +
261C GLN* 3.4 6.1 + - - +
262C CYS* 3.2 26.0 + - - -
269C TYR* 2.3 45.1 + - + +
273C ARG* 3.5 15.0 + - - +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C CYS* 3.8 30.2 - - - +
170C LEU* 4.3 14.1 - - + -
174C LEU* 3.9 39.0 - - + -
179C ARG* 4.1 5.8 - - - +
217C MET* 4.0 29.6 - - + +
255C ALA 2.8 19.2 + - - +
256C PHE* 3.7 13.5 - - + +
258C ASN* 1.3 73.3 - - - +
260C VAL* 1.3 63.5 + - - +
262C CYS* 3.4 3.3 + - - +
263C ILE* 3.2 46.0 + - + +
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Residues in contact with VAL 260 (chain C).
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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217C MET* 4.1 23.1 - - - -
229C PHE* 3.8 16.2 - - + -
240C MET* 4.2 11.7 - - + -
241C LEU* 3.6 23.3 - - + -
244C ILE* 3.4 19.3 - - + -
256C PHE 2.9 20.6 + - - +
259C LEU* 1.3 76.0 - - + +
261C GLN* 1.3 62.1 + - - +
263C ILE* 3.3 4.6 + - - +
264C GLN* 3.0 48.1 + - - +
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Residues in contact with GLN 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LEU* 4.2 23.2 - - + +
257C LEU* 3.1 28.4 + - - +
258C ASN* 3.8 4.1 + - - +
260C VAL* 1.3 74.7 - - - +
262C CYS* 1.3 55.7 + - - +
264C GLN* 3.0 9.4 + - - +
265C ASN 2.7 39.0 + - - +
268C LEU* 6.1 0.2 - - - +
269C TYR* 3.7 35.1 - - + -
272C ASP* 3.9 20.6 - - - +
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Residues in contact with CYS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C CYS* 3.9 27.6 - - - +
134C SER* 3.9 11.9 - - - -
222C VAL* 5.4 0.7 - - - +
258C ASN 3.2 18.7 + - - -
259C LEU 3.7 7.0 - - - +
261C GLN* 1.3 76.1 - - - +
263C ILE* 1.3 64.8 + - + +
266C LYS* 3.3 48.0 + - + +
269C TYR* 3.6 31.8 - - - +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ARG* 4.5 4.9 - - - +
217C MET* 4.2 6.3 - - + +
222C VAL* 3.4 37.2 - - + +
225C LEU* 3.5 47.3 - - + -
226C GLN* 2.9 25.3 + - + +
229C PHE* 4.1 18.6 - - + -
259C LEU* 3.2 39.6 + - + +
260C VAL* 3.6 6.1 - - - +
261C GLN 3.1 0.6 - - - -
262C CYS* 1.3 80.9 - - + +
264C GLN* 1.3 59.2 + - - +
265C ASN* 4.7 0.2 - - - -
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Residues in contact with GLN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C GLN* 3.1 25.3 + - + +
229C PHE* 3.8 29.7 - - + +
239C ASP* 6.0 1.6 + - - +
240C MET* 4.4 7.7 - - - +
241C LEU* 4.3 18.0 - - - +
260C VAL* 3.0 40.9 + - - +
261C GLN* 3.6 6.6 - - - +
263C ILE* 1.3 76.7 - - - +
265C ASN* 1.3 61.2 + - - +
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C GLN* 2.7 21.2 + - - +
264C GLN* 1.3 77.6 - - - +
266C LYS* 1.3 57.7 + - - +
267C PRO* 3.0 13.7 - - - +
268C LEU* 2.5 49.0 + - + +
269C TYR* 3.1 19.9 + - - +
306C GLU* 3.2 27.3 + - - -
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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