Contacts of the helix formed by residues 280 - 300 (chain C) in PDB entry 3U1K
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 SER 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C THR 3.6 2.3 + - - -
279C PRO* 1.3 74.7 - - - +
281C PRO* 1.3 73.1 - - - +
282C GLU* 3.6 7.9 + - - +
283C ILE* 2.8 36.4 + - - +
284C VAL* 3.1 18.5 + - - +
335C GLU* 2.8 17.8 + - - -
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Residues in contact with PRO 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PRO 3.4 4.0 - - - +
280C SER* 1.3 86.9 - - - +
282C GLU* 1.3 56.8 + - - +
284C VAL* 3.8 7.1 - - + +
285C LYS* 2.9 32.6 + - - +
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C SER* 3.0 9.2 + - - +
281C PRO* 1.3 83.1 - - - +
283C ILE* 1.3 60.2 + - - +
285C LYS* 3.6 6.5 + - + +
286C TYR* 3.3 21.5 + - - +
327C LYS* 6.0 0.7 - - - -
328C PHE* 4.0 26.3 - - + -
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PRO* 5.0 0.7 - - + -
280C SER* 2.8 21.8 + - - +
282C GLU* 1.3 76.9 - - + +
284C VAL* 1.3 58.1 + - - +
286C TYR* 4.0 0.7 - - - +
287C THR* 2.5 44.5 + - - +
324C LEU* 3.5 20.9 - - + -
328C PHE* 3.9 37.2 - - + -
331C ALA* 5.2 4.9 - - + -
335C GLU* 4.4 18.2 - - + +
336C ILE* 4.0 17.5 - - + -
339C SER* 3.0 35.2 - - - +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PRO* 3.6 34.3 - - + +
280C SER 3.1 18.7 + - - +
281C PRO* 3.9 7.2 - - + +
283C ILE* 1.3 77.6 - - - +
285C LYS* 1.3 57.1 + - - +
287C THR* 3.3 2.7 + - - -
288C HIS* 2.8 29.8 + - + +
339C SER* 3.5 14.1 - - - +
342C VAL* 4.5 17.0 - - + -
343C VAL* 3.7 14.3 - - + +
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Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PRO 2.9 18.0 + - - +
282C GLU* 3.8 7.4 - - - +
283C ILE 3.3 0.2 - - - -
284C VAL* 1.3 78.8 - - - +
286C TYR* 1.3 58.2 + - - +
288C HIS* 3.2 9.3 + - + +
289C LYS* 2.8 57.5 + - + +
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLU 3.3 14.4 + - - +
283C ILE 4.0 1.6 - - - +
284C VAL 3.4 0.2 - - - -
285C LYS* 1.3 78.0 - - - +
287C THR* 1.3 57.4 + - - +
289C LYS* 3.4 18.9 + - + +
290C LEU* 2.9 59.3 + - + +
323C GLN* 4.8 8.3 + - - +
324C LEU* 3.6 18.4 - - + -
327C LYS* 4.0 42.9 - - + +
328C PHE* 3.9 17.5 - + + -
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Residues in contact with THR 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ILE* 2.5 32.0 + - - +
284C VAL 3.5 3.6 - - - -
286C TYR* 1.3 75.8 - - - +
288C HIS* 1.3 57.0 + - - +
290C LEU* 3.1 2.8 + - - +
291C ALA* 2.9 32.1 + - + +
320C THR* 5.5 0.9 - - - +
324C LEU* 3.5 21.3 - - + +
336C ILE 5.6 0.2 - - - +
339C SER* 2.7 14.9 + - - +
340C PHE* 3.9 37.0 - - + +
343C VAL* 3.7 17.9 - - + -
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Residues in contact with HIS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C VAL* 2.8 23.5 + - + +
285C LYS* 3.4 10.3 - - + +
287C THR* 1.3 72.5 - - - +
289C LYS* 1.3 66.7 + - + +
292C MET* 3.0 65.3 + - + +
343C VAL* 3.6 20.7 - - + +
346C GLU* 3.0 33.5 + - - -
347C VAL* 4.3 2.5 - - + -
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Residues in contact with LYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LYS* 2.8 56.1 + - + +
286C TYR* 3.7 17.3 - - + +
288C HIS* 1.3 77.1 - - + +
290C LEU* 1.3 64.4 + - - +
292C MET* 4.5 15.4 + - + +
293C GLU* 5.5 3.1 + - - +
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C TYR* 2.9 50.4 + - + +
287C THR* 3.6 5.6 - - - +
289C LYS* 1.3 79.7 - - - +
291C ALA* 1.3 59.3 + - - +
293C GLU* 5.3 2.5 + - - +
294C ARG* 4.6 11.8 + - - -
320C THR* 4.3 14.2 - - + +
323C GLN* 3.8 45.5 - - + +
324C LEU* 4.2 11.2 - - + -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C THR* 2.9 16.0 + - + +
290C LEU* 1.3 77.4 - - - +
292C MET* 1.3 66.1 + - - +
293C GLU 3.2 2.7 - - - -
294C ARG* 3.1 8.3 + - - +
295C LEU* 3.0 35.8 + - + +
316C ILE* 3.9 22.7 - - + -
320C THR* 4.1 11.9 - - + +
340C PHE* 4.2 9.4 - - + -
343C VAL* 4.7 2.7 - - + -
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Residues in contact with MET 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C HIS* 3.0 60.6 + - + +
289C LYS* 4.6 10.3 - - + +
290C LEU 3.8 0.6 - - - -
291C ALA* 1.3 76.7 - - - +
293C GLU* 1.3 76.4 + - + +
295C LEU* 3.7 2.0 - - - +
296C TYR* 2.8 33.1 + - - +
343C VAL* 4.9 0.6 - - - +
347C VAL* 4.0 18.2 - - + +
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LYS 5.5 3.1 + - - +
290C LEU 5.3 2.0 + - - +
291C ALA 3.2 1.0 - - - -
292C MET* 1.3 97.5 - - + +
294C ARG* 1.3 61.0 + - + +
296C TYR* 3.3 6.6 + - - +
297C ALA* 2.9 27.7 + - - +
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Residues in contact with ARG 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU 4.6 14.3 + - - -
291C ALA 3.1 6.0 + - - +
293C GLU* 1.3 81.0 - - + +
295C LEU* 1.3 62.9 + - - +
297C ALA* 3.3 9.1 + - - +
298C VAL* 3.0 26.0 + - - +
315C LYS* 4.8 3.2 - - - +
316C ILE* 3.6 41.7 - - + +
319C ASP* 3.0 37.6 + - - +
320C THR* 5.1 5.3 - - - +
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Residues in contact with LEU 295 (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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291C ALA* 3.0 29.2 + - + +
292C MET 3.8 2.9 - - - +
294C ARG* 1.3 72.7 - - - +
296C TYR* 1.3 65.7 + - - +
298C VAL* 3.1 4.5 + - - +
299C PHE* 2.9 38.5 + - + -
313C VAL* 4.4 12.3 - - + -
316C ILE* 3.9 18.8 - - + -
340C PHE* 4.0 21.3 - - + -
343C VAL* 3.7 23.3 - - + +
344C ALA* 3.6 34.8 - - + +
347C VAL* 3.9 15.0 - - + -
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Residues in contact with TYR 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C MET 2.8 18.7 + - - +
293C GLU* 3.6 7.2 - - - +
295C LEU* 1.3 76.1 - - - +
297C ALA* 1.3 64.0 + - - +
299C PHE* 3.2 1.7 + - - +
300C THR* 2.8 50.1 + - + +
347C VAL* 3.8 12.4 - - + +
351C ILE* 3.7 28.0 - - + -
355C GLU* 2.5 33.4 + - - -
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLU 2.9 13.4 + - - +
294C ARG* 3.4 11.9 - - - +
295C LEU 3.2 0.2 - - - -
296C TYR* 1.3 82.4 - - - +
298C VAL* 1.3 63.9 + - + +
300C THR* 3.3 6.6 + - - -
301C ASP* 3.1 24.0 + - - +
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG 3.0 18.1 + - - +
295C LEU* 3.1 8.7 + - - +
297C ALA* 1.3 75.3 - - + +
299C PHE* 1.3 65.8 + - + +
301C ASP* 3.1 26.2 + - - +
304C HIS* 3.6 16.2 - - + +
309C ARG* 3.7 33.0 - - + +
312C ALA* 3.7 22.0 - - + -
313C VAL* 4.0 12.3 - - + -
316C ILE* 3.9 15.9 - - + -
359C CYS 5.0 0.2 - - - +
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Residues in contact with PHE 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 2.9 33.4 + - + +
296C TYR 3.2 0.4 + - - -
298C VAL* 1.3 83.2 - - + +
300C THR* 1.3 60.5 + - - +
301C ASP 3.4 0.4 - - - -
302C TYR* 4.2 1.6 - - - -
309C ARG* 4.2 11.2 - - + -
313C VAL* 3.6 32.5 - - + -
344C ALA* 3.7 17.3 - - + -
347C VAL* 4.2 5.6 - - + -
348C PHE* 3.6 50.5 - + + -
351C ILE* 3.6 22.3 - - + +
358C ARG 4.4 0.5 - - - +
359C CYS* 3.2 31.5 - - + -
536C ILE* 3.7 21.5 - - + -
540C ASN* 5.0 1.6 - - - -
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Residues in contact with THR 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C TYR* 2.8 61.9 + - + +
297C ALA* 3.3 7.5 + - - -
299C PHE* 1.3 80.9 - - - +
301C ASP* 1.3 59.2 + - - +
302C TYR* 3.4 36.1 + - + +
351C ILE* 4.1 17.0 - - + -
355C GLU* 4.1 5.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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