Contacts of the helix formed by residues 275 - 294 (chain C) in PDB entry 4U1D
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 275 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLN* 4.4 15.9 - - - +
238C ASP* 5.1 9.3 + - - +
274C PRO* 1.3 73.1 - - - +
276C PRO* 1.3 73.8 - - + +
277C SER* 4.2 4.9 - - - +
278C THR* 3.1 31.0 + - + +
279C LEU* 3.0 21.3 + - - +
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Residues in contact with PRO 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PRO 3.3 7.6 - - - +
275C LYS* 1.3 84.4 - - + +
277C SER* 1.3 57.0 + - - +
279C LEU* 4.4 6.7 - - + -
280C ALA* 2.9 31.0 + - - +
309C LEU* 3.7 24.3 - - + +
312C THR* 5.8 1.8 - - - +
313C ASN* 6.4 0.2 - - - +
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LYS* 3.1 6.0 - - - -
276C PRO* 1.3 81.1 - - - +
278C THR* 1.3 69.5 + - - +
280C ALA* 3.3 4.8 + - - +
281C ASN* 3.1 22.0 + - - +
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLN* 5.9 0.3 + - - -
238C ASP* 5.0 16.2 + - - +
241C PHE* 4.5 18.5 - - - +
274C PRO* 4.4 5.9 - - - +
275C LYS* 3.1 39.0 + - + +
277C SER* 1.3 82.4 - - - +
279C LEU* 1.3 60.3 + - - +
281C ASN* 3.6 8.7 + - - +
282C TYR* 3.2 22.3 + - - +
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE* 3.6 28.7 - - + -
267C MET* 4.4 11.0 - - + -
274C PRO* 4.0 26.2 - - + +
275C LYS 3.0 15.8 + - - +
276C PRO* 4.1 2.5 - - + +
278C THR* 1.3 76.8 + - - +
280C ALA* 1.3 65.6 + - - +
281C ASN 3.2 0.2 - - - -
282C TYR* 3.1 10.4 + - + +
283C TYR* 3.0 54.8 + - + +
309C LEU* 3.9 20.2 - - + -
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C PRO 2.9 20.3 + - - +
277C SER* 3.6 6.3 - - - +
279C LEU* 1.3 77.9 - - - +
281C ASN* 1.3 59.3 + - - +
283C TYR* 3.5 2.1 + - - +
284C GLU* 3.1 24.3 + - - +
306C PHE* 3.4 28.2 - - + +
309C LEU* 3.6 18.3 - - + +
310C TYR* 5.9 4.9 - - + +
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Residues in contact with ASN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ASP* 3.6 18.0 + - - +
249C LYS* 6.1 1.2 - - - +
277C SER 3.1 12.7 + - - +
278C THR* 3.7 12.3 - - - +
279C LEU 3.2 0.2 - - - -
280C ALA* 1.3 74.9 - - - +
282C TYR* 1.3 64.4 + - - +
284C GLU* 3.1 15.8 + - - +
285C ASN* 2.9 38.7 + - - +
288C LYS* 6.1 1.9 - - - +
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Residues in contact with TYR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE* 3.3 40.4 - + + -
244C VAL* 4.1 27.6 - - + -
260C ILE* 3.5 27.4 + - + +
263C VAL* 3.8 26.9 - - + +
264C PHE* 5.0 1.6 + - - +
267C MET* 4.7 6.9 - - - -
278C THR 3.2 5.5 + - - +
279C LEU* 3.1 12.5 + - + +
281C ASN* 1.3 79.5 + - - +
283C TYR* 1.3 83.8 + + - +
285C ASN* 3.0 19.9 + - - +
286C LEU* 3.0 44.7 + - + +
354C LEU 5.4 2.3 + - - -
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Residues in contact with TYR 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C MET* 4.5 10.8 - - + +
279C LEU* 3.0 48.0 + - + +
280C ALA* 4.0 2.9 - - - +
282C TYR* 1.3 98.3 - + - +
284C GLU* 1.3 56.9 + - - +
286C LEU* 3.1 13.3 + - + +
287C VAL* 3.1 32.9 + - - +
302C ALA* 3.8 7.5 - - - +
305C LYS* 3.6 65.7 + - + +
306C PHE* 3.8 19.1 - - + -
309C LEU* 4.2 10.3 - - + -
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Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 3.1 15.9 + - - +
281C ASN* 3.1 16.8 + - - +
283C TYR* 1.3 76.2 - - - +
285C ASN* 1.3 57.4 + - - +
287C VAL* 3.0 31.7 - - + +
288C LYS* 3.3 28.1 + - - +
303C TRP* 6.4 2.5 - - + -
306C PHE* 3.7 32.3 - - + -
324C TYR* 5.3 3.6 + - - -
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Residues in contact with ASN 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE 5.1 1.4 + - - -
244C VAL* 4.0 11.3 - - + +
245C ASP* 3.1 46.3 + - - +
248C VAL* 3.9 24.4 - - + +
249C LYS* 5.9 0.2 - - - +
281C ASN* 2.9 24.7 + - - +
282C TYR* 3.0 10.9 + - - +
284C GLU* 1.3 76.3 - - - +
286C LEU* 1.3 61.9 + - - +
287C VAL 3.2 0.4 - - - -
288C LYS* 3.1 25.4 + - - +
289C VAL* 2.9 30.9 + - - +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL* 4.7 6.1 - - + -
260C ILE* 3.5 33.9 - - + -
282C TYR* 3.0 54.5 + - + +
283C TYR* 3.1 16.8 + - + +
285C ASN* 1.3 77.8 - - - +
287C VAL* 1.3 64.1 + - - +
289C VAL* 4.2 4.5 - - + -
290C PHE* 3.0 48.6 + - + -
302C ALA* 3.6 15.5 - - + -
305C LYS* 6.4 0.4 - - + -
355C LEU* 4.3 17.0 - - + -
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C TYR 3.1 16.5 + - - +
284C GLU* 3.0 30.5 - - + +
286C LEU* 1.3 76.3 - - - +
288C LYS* 1.3 66.9 + - + +
291C PHE* 3.4 8.5 + - - +
299C HIS* 2.8 30.6 + - + +
302C ALA* 3.6 5.8 - - + +
303C TRP* 3.5 66.0 - - + +
306C PHE* 5.2 2.0 - - + -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C VAL* 3.8 25.8 - - + -
253C TRP* 4.4 6.3 - - + -
281C ASN* 5.4 1.8 + - - +
284C GLU* 3.3 34.9 + - - +
285C ASN* 3.1 23.3 + - - +
287C VAL* 1.3 80.2 - - + +
289C VAL* 1.3 64.4 + - - +
291C PHE* 3.2 6.2 + - - +
292C VAL* 3.1 29.1 + - + +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL* 5.7 0.9 - - + -
248C VAL* 3.7 23.3 - - + -
253C TRP* 4.0 17.2 - - + +
256C ALA* 4.0 15.7 - - + -
257C TYR* 5.0 12.8 - - + +
260C ILE* 4.0 21.3 - - + -
285C ASN 2.9 20.4 + - - +
286C LEU* 3.7 9.2 - - + +
288C LYS* 1.3 77.1 - - - +
290C PHE* 1.3 74.8 + - + +
292C VAL* 3.3 5.4 + - - +
293C SER* 2.9 30.3 + - - -
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR* 5.0 4.5 - + - -
260C ILE* 4.3 10.1 - - + -
286C LEU* 3.0 37.0 + - + +
289C VAL* 1.3 87.1 - - + +
291C PHE* 1.3 62.8 + - - +
293C SER* 3.7 5.8 - - - -
294C GLY* 3.2 16.1 + - - -
295C ASP* 3.2 24.8 + - - +
298C LEU* 3.5 42.6 - - + -
299C HIS* 3.6 21.6 - - - +
302C ALA* 4.3 0.7 - - + -
351C MET* 3.7 18.8 - - + -
355C LEU* 3.5 43.3 - - + -
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Residues in contact with PHE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL 3.4 18.8 + - - +
288C LYS* 3.2 7.2 + - - +
290C PHE* 1.3 76.5 - - - +
292C VAL* 1.3 68.7 + - + +
293C SER 3.3 0.5 + - - -
294C GLY* 3.4 10.3 + - - -
299C HIS* 3.9 26.0 + + + +
419C GLN* 3.3 44.6 - - + -
420C TYR* 3.8 22.0 - + - -
423C PRO* 5.9 5.6 - - + -
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C TRP* 3.6 60.3 - - + +
288C LYS 3.1 14.1 + - - +
289C VAL 3.6 7.2 - - - +
291C PHE* 1.3 81.3 - - + +
293C SER* 1.3 61.4 + - - +
294C GLY* 3.5 0.5 + - - -
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Residues in contact with SER 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR* 5.2 6.2 - - - -
289C VAL* 2.9 21.3 + - - -
290C PHE* 3.7 15.4 - - - -
291C PHE 3.1 0.4 - - - -
292C VAL* 1.3 79.5 - - - +
294C GLY* 1.3 58.1 + - - +
295C ASP* 2.7 26.4 + - - +
348C HIS* 3.6 21.1 + - - -
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Residues in contact with GLY 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C PHE 3.2 6.1 + - - -
291C PHE* 3.4 6.8 + - - -
292C VAL 3.3 4.0 + - - -
293C SER* 1.3 77.9 - - - +
295C ASP* 1.3 64.3 + - - +
296C PRO* 3.3 12.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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