Contacts of the helix formed by residues 250 - 265 (chain C) in PDB entry 5Q1B
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 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C GLU 4.6 1.1 - - - +
249C LEU* 1.3 75.2 - - - +
251C PRO* 1.4 75.1 - - - +
252C ASP* 3.8 8.3 + - - +
253C GLN* 2.9 42.5 + - - +
254C GLN* 3.0 22.0 + - - +
421C LYS* 3.8 11.7 - - - +
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Residues in contact with PRO 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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250C THR* 1.4 86.3 - - - +
252C ASP* 1.4 63.2 + - - +
254C GLN* 3.3 9.0 + - + +
255C THR* 3.0 32.5 + - - -
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Residues in contact with ASP 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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250C THR* 3.3 7.3 + - - +
251C PRO* 1.4 81.1 - - - +
253C GLN* 1.3 58.3 - - + +
255C THR* 3.4 7.6 + - - +
256C LEU* 2.9 28.5 + - - +
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Residues in contact with GLN 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 LEU* 3.5 18.0 - - + -
250C THR* 2.9 33.4 + - - +
252C ASP* 1.3 76.1 - - + +
254C GLN* 1.3 58.9 + - - +
256C LEU* 3.4 9.0 + - + +
257C LEU* 2.9 30.7 + - - +
414C PRO 5.0 0.4 + - - -
417C ASP* 4.1 18.6 + - - +
418C VAL* 3.9 23.6 - - + +
421C LYS* 2.8 42.9 + - - +
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Residues in contact with GLN 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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248C GLU* 5.9 0.4 + - - -
249C LEU* 3.9 29.9 - - + +
250C THR 3.0 15.4 + - - +
251C PRO* 3.6 10.5 - - + +
253C GLN* 1.3 75.4 - - - +
255C THR* 1.4 57.1 + - - +
257C LEU* 3.8 10.8 - - - +
258C HIS* 2.9 65.4 + - + +
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Residues in contact with THR 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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251C PRO 3.0 17.4 + - - -
252C ASP* 3.6 8.7 - - - +
253C GLN 3.3 0.2 - - - -
254C GLN* 1.4 72.8 - - - +
256C LEU* 1.4 59.2 + - - +
258C HIS* 3.4 7.2 + - - +
259C PHE* 3.0 30.1 + - + +
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Residues in contact with LEU 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 ASP 2.9 17.4 + - - +
253C GLN* 3.7 6.5 - - + +
255C THR* 1.4 75.5 - - - +
257C LEU* 1.4 57.4 + - - +
259C PHE* 3.2 10.9 + - + +
260C ILE* 2.9 46.5 + - + +
310C PRO* 3.6 31.9 - - + -
388C LEU* 5.7 0.9 - - + -
414C PRO* 4.6 14.1 - - + +
415C LEU* 3.9 23.8 - - + -
418C VAL* 3.9 23.3 - - + -
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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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249C LEU* 3.8 25.1 - - + -
253C GLN 2.9 21.5 + - - +
254C GLN* 3.8 11.9 - - - +
255C THR 3.4 0.2 - - - -
256C LEU* 1.4 73.3 - - - +
258C HIS* 1.4 61.2 + - + +
260C ILE* 3.2 8.2 + - + +
261C MET* 2.9 32.8 + - + +
384C GLU* 3.9 35.0 - - + +
388C LEU* 4.0 29.2 - - + -
418C VAL* 4.4 8.0 - - + +
422C LEU* 4.0 14.8 - - + -
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Residues in contact with HIS 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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254C GLN* 2.9 49.9 + - + +
255C THR* 3.8 7.0 + - - +
256C LEU 3.4 0.2 - - - -
257C LEU* 1.4 79.2 - - + +
259C PHE* 1.3 57.7 + - - +
261C MET* 3.4 11.3 + - + +
262C ASP* 3.0 36.9 + - - +
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Residues in contact with PHE 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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255C THR* 3.0 20.2 + - + +
256C LEU* 3.5 9.4 - - + +
258C HIS* 1.3 74.1 - - - +
260C ILE* 1.4 73.0 + - + +
262C ASP* 3.5 11.6 + - + +
263C SER* 3.2 24.6 + - - -
308C LYS* 3.1 49.4 - - + -
310C PRO* 5.1 4.5 - - + -
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Residues in contact with ILE 260 (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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256C LEU* 2.9 30.8 + - + +
257C LEU* 3.7 10.1 - - + +
259C PHE* 1.4 80.3 - - + +
261C MET* 1.3 57.9 + - - +
263C SER* 3.4 8.0 - - - -
264C TYR* 2.9 27.2 + - - +
305C PHE* 3.7 11.3 - - + -
308C LYS 5.1 0.9 - - - +
309C LEU* 3.7 27.4 - - + -
310C PRO* 4.0 20.2 - - + -
387C ALA* 3.9 34.3 - - + +
388C LEU* 4.6 10.5 - - + +
391C ALA* 4.9 2.5 - - + -
415C LEU* 4.3 12.6 - - + -
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Residues in contact with MET 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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257C LEU* 2.9 23.3 + - + +
258C HIS* 3.5 15.3 - - + +
259C PHE 3.3 0.2 - - - -
260C ILE* 1.3 73.2 - - - +
262C ASP* 1.3 65.0 + - - +
264C TYR* 3.2 7.4 + - + +
265C ASN* 2.7 47.6 + - - +
383C GLN* 3.8 39.7 - - + +
384C GLU* 3.7 38.1 - - + +
387C ALA* 3.6 25.8 - - + -
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Residues in contact with ASP 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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258C HIS* 3.0 25.0 + - - +
259C PHE* 3.9 11.1 - - + +
260C ILE 3.5 0.2 - - - -
261C MET* 1.3 76.0 - - - +
263C SER* 1.3 62.5 + - - +
265C ASN* 3.2 16.2 + - - +
266C LYS* 3.5 29.9 + - - +
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Residues in contact with SER 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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259C PHE* 3.2 18.4 + - - -
260C ILE* 3.4 7.9 - - - -
262C ASP* 1.3 77.6 - - - +
264C TYR* 1.4 57.8 - - - +
266C LYS* 3.4 25.2 + - - +
267C GLN* 4.7 1.2 + - - +
301C VAL* 5.6 1.7 - - - +
305C PHE* 3.4 32.1 + - - +
308C LYS* 3.4 36.3 - - - +
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Residues in contact with TYR 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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260C ILE 2.9 20.9 + - - +
261C MET* 3.2 15.7 + - + +
263C SER* 1.4 67.2 - - - +
265C ASN* 1.4 60.6 + - - +
266C LYS 3.1 9.5 + - - -
267C GLN* 3.1 52.3 + - - +
305C PHE* 3.8 21.5 - + + -
334C LEU* 5.8 0.7 - - - +
335C ARG* 3.9 11.7 - - - +
338C GLU* 2.7 35.6 + - - -
383C GLN* 4.4 7.0 - - + -
386C TYR* 3.7 8.7 - - - +
387C ALA* 3.6 39.3 - - + -
390C THR* 3.6 27.5 + - + -
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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 MET* 2.7 37.8 + - - +
262C ASP* 3.2 11.5 + - - +
264C TYR* 1.4 73.3 - - - +
266C LYS* 1.4 59.1 + - - +
267C GLN* 3.1 14.4 + - - +
269C MET* 5.5 9.4 - - - +
383C GLN* 3.2 28.9 + - - +
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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