Contacts of the helix formed by residues 244 - 257 (chain C) in PDB entry 5HQP
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 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C LYS 4.6 6.1 - - - +
242C GLU 3.4 13.5 + - - +
243C ASP* 1.3 74.0 - - - +
245C GLU* 1.3 66.0 + - - +
246C SER 3.5 1.3 - - - -
247C LEU* 3.4 16.1 + - + +
248C GLU* 3.1 37.7 + - - +
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Residues in contact with GLU 245 (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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243C ASP* 3.1 5.7 + - - +
244C THR* 1.3 78.2 + - - +
246C SER* 1.3 69.1 + - - +
247C LEU 3.1 0.2 + - - -
248C GLU* 3.2 12.2 + - + +
249C ILE* 3.0 48.0 + - + +
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Residues in contact with SER 246 (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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237C LEU* 3.7 4.8 - - - +
239C HIS* 3.4 17.7 - - - +
243C ASP* 2.8 31.2 + - - -
245C GLU* 1.3 81.1 - - - +
247C LEU* 1.3 58.6 + - - +
249C ILE* 3.5 1.1 + - - -
250C PHE* 2.9 28.9 + - - +
290C PRO* 3.4 27.4 - - - -
306C PHE* 3.6 21.5 - - - -
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Residues in contact with LEU 247 (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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216C VAL* 4.6 2.2 - - + -
237C LEU* 3.4 14.1 - - + -
239C HIS* 4.0 23.6 - - + +
244C THR* 3.4 18.3 + - + +
245C GLU 3.1 1.2 - - - -
246C SER* 1.3 81.9 + - - +
248C GLU* 1.3 57.0 + - + +
250C PHE* 3.3 2.4 + - + +
251C GLN* 2.9 53.5 + - + +
269C HIS* 3.6 47.6 - - + +
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Residues in contact with GLU 248 (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 THR* 3.1 32.7 + - - +
245C GLU* 3.5 12.3 - - + +
247C LEU* 1.3 74.8 - - + +
249C ILE* 1.3 66.5 + - + +
250C PHE 3.2 0.9 - - - -
251C GLN* 3.8 12.6 - - - +
252C ASN* 2.9 40.4 + - - +
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Residues in contact with ILE 249 (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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245C GLU* 3.0 45.6 + - + +
246C SER 3.6 4.5 - - - +
248C GLU* 1.3 77.4 - - + +
250C PHE* 1.3 56.6 + - - +
252C ASN* 3.9 5.0 - - - +
253C GLU* 2.9 34.2 + - + +
306C PHE* 4.0 18.6 - - + -
309C VAL* 3.8 28.5 - - + -
310C LEU* 4.2 25.4 - - + -
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Residues in contact with PHE 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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216C VAL* 4.0 30.7 - - + -
235C LEU* 3.9 28.9 - - + -
236C ILE 4.2 0.7 - - - -
237C LEU* 3.7 33.2 - - + -
246C SER 2.9 17.9 + - - +
247C LEU* 3.5 7.6 - - + +
248C GLU 3.2 0.2 - - - -
249C ILE* 1.3 74.5 - - - +
251C GLN* 1.3 66.0 + - - +
253C GLU* 3.2 3.6 + - - +
254C VAL* 2.9 49.4 + - + +
267C PHE* 4.8 2.5 - - + -
268C LEU 3.9 16.4 - - - -
269C HIS* 5.2 0.7 - - + -
292C ILE* 3.9 36.1 - - + -
306C PHE* 5.1 2.7 - - + -
309C VAL* 5.5 2.0 - - + -
315C LEU* 5.0 3.8 - - + -
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Residues in contact with GLN 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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215C LEU* 4.3 3.7 - - + +
216C VAL* 3.5 27.6 + - + +
217C ARG* 5.1 11.0 - - - +
247C LEU* 2.9 47.4 + - + +
248C GLU* 3.8 10.8 - - + +
250C PHE* 1.3 77.7 - - - +
252C ASN* 1.3 64.8 + - - +
254C VAL* 3.4 9.8 - - - +
255C ALA* 2.9 24.7 + - - +
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Residues in contact with ASN 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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248C GLU* 2.9 33.0 + - - +
249C ILE* 3.9 5.0 - - - +
251C GLN* 1.3 77.7 - - - +
253C GLU* 1.3 61.2 + - - +
255C ALA* 3.2 8.5 + - - +
256C ARG* 2.9 44.4 + - - +
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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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249C ILE* 2.9 20.1 + - + +
250C PHE 3.9 2.7 - - - +
252C ASN* 1.3 80.6 - - - +
254C VAL* 1.3 58.8 + - - +
256C ARG* 3.8 26.9 + - - +
257C GLN* 2.8 68.6 + - - +
309C VAL* 3.1 42.4 - - + +
310C LEU* 4.0 22.3 - - - +
311C ILE 4.8 0.2 - - - +
312C PRO* 4.9 3.5 - - - +
315C LEU* 4.2 4.4 - - + +
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Residues in contact with VAL 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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215C LEU* 3.7 16.1 - - + +
216C VAL* 3.7 26.5 - - + -
235C LEU* 5.0 0.4 - - + -
250C PHE* 2.9 37.4 + - + +
251C GLN 3.4 10.1 - - - +
253C GLU* 1.3 73.3 - - - +
255C ALA* 1.3 64.2 + - - +
256C ARG 3.3 0.2 - - - -
258C LEU* 3.2 14.1 + - + +
259C ILE* 3.2 26.2 + - - -
267C PHE* 4.4 16.8 - - + -
315C LEU* 3.6 23.3 - - + -
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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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215C LEU* 3.6 19.1 - - + -
251C GLN 2.9 18.1 + - - +
252C ASN* 3.4 8.5 - - - +
253C GLU 3.2 0.2 - - - -
254C VAL* 1.3 79.3 - - - +
256C ARG* 1.3 62.7 + - + +
259C ILE* 3.5 22.3 - - + +
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Residues in contact with ARG 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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252C ASN* 2.9 28.9 + - - +
253C GLU* 3.3 31.6 + - - +
255C ALA* 1.3 81.4 - - + +
257C GLN* 1.3 65.7 + - + +
259C ILE* 4.9 4.3 + - - +
310C LEU 5.9 1.2 + - - -
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Residues in contact with GLN 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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253C GLU* 2.8 55.2 + - - +
256C ARG* 1.3 79.1 - - + +
258C LEU* 1.3 69.8 + - + +
259C ILE* 3.6 1.9 + - - +
260C SER* 5.0 4.5 + - - -
309C VAL 3.6 2.8 + - - -
311C ILE 3.5 17.6 + - - -
312C PRO* 2.8 26.6 + - + +
315C LEU* 3.2 14.9 + - + +
316C LYS* 2.8 51.0 + - + +
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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