Contacts of the helix formed by residues 276 - 296 (chain C) in PDB entry 3Q41
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 ASN 276 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ASN* 3.7 30.0 + - - +
274C GLY 3.7 0.6 + - - -
275C LYS* 1.3 75.4 - - - +
277C GLU* 1.3 52.3 + - - +
278C SER* 3.1 7.8 + - - -
279C ALA* 2.5 44.1 + - + +
280C HIS* 3.6 5.5 + - - -
408C NAG 1.4 66.8 + - - +
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Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.8 4.9 - - - +
34C SER* 2.7 40.3 + - - -
38C HIS* 3.5 30.4 + - + +
93C SER* 2.9 32.6 + - - +
94C HIS 3.7 8.3 - - - +
95C PRO* 5.3 0.5 - - - +
96C PRO* 5.5 2.4 - - - +
121C LEU* 4.9 2.4 - - + +
122C THR* 4.4 7.6 + - - +
275C LYS 3.4 5.4 + - - +
276C ASN* 1.3 72.9 - - - +
278C SER* 1.3 55.0 + - - +
279C ALA 2.9 1.0 + - - -
280C HIS* 2.9 11.6 + - - +
281C ILE* 2.7 46.3 + - + +
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C HIS* 4.0 5.7 + - - -
41C MET* 3.7 35.2 - - - +
276C ASN* 2.6 13.1 + - - -
277C GLU* 1.3 76.1 - - - +
279C ALA* 1.3 58.3 + - - -
281C ILE* 3.7 14.0 - - - +
282C SER* 3.2 21.7 + - - -
408C NAG 5.0 17.4 - - - -
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ASN* 5.1 3.4 - - - +
276C ASN* 2.5 36.2 + - + +
277C GLU 2.9 0.2 + - - -
278C SER* 1.3 68.6 + - - +
280C HIS* 1.3 59.6 + - + +
281C ILE 2.9 9.2 + - - -
282C SER* 3.0 22.4 + - - -
283C ASP* 3.1 12.8 + - - +
334C VAL* 4.2 23.6 - - + -
335C THR* 3.9 16.8 - - - +
408C NAG 4.4 2.9 - - - +
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Residues in contact with HIS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.4 33.3 - - + +
140C THR* 2.6 45.9 + - - +
141C VAL* 3.6 16.5 - - + +
271C LEU* 5.4 1.3 - - + +
273C ASN 2.7 30.5 + - - -
274C GLY 4.8 2.0 - - - -
276C ASN 3.6 12.9 + - - -
277C GLU* 2.9 8.8 + - - +
279C ALA* 1.3 78.9 - - + +
281C ILE* 1.3 55.6 + - - +
283C ASP* 4.7 4.0 - - - +
284C ALA* 3.1 28.3 + - - +
335C THR* 3.3 32.5 + - + +
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.8 22.9 - - + -
38C HIS* 3.8 39.5 - - + +
41C MET* 4.3 9.9 - - + +
42C PHE* 3.8 31.4 - - + +
45C ALA* 4.5 2.2 - - + -
91C LEU* 5.0 1.3 - - + -
121C LEU* 3.9 19.3 - - + -
277C GLU* 2.7 24.5 + - + +
278C SER* 3.7 10.1 - - - +
279C ALA 2.9 1.2 + - - -
280C HIS* 1.3 72.8 - - - +
282C SER* 1.3 59.4 + - - +
284C ALA* 3.0 5.8 + - - +
285C VAL* 2.8 39.2 + - + +
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 4.4 16.2 - - - -
278C SER 3.2 11.5 + - - -
279C ALA* 3.0 15.6 + - - -
281C ILE* 1.3 80.6 - - - +
283C ASP* 1.3 64.5 + - - +
285C VAL* 3.4 7.4 + - - +
286C GLY* 3.0 19.8 + - - -
330C TYR* 4.4 6.0 + - - -
334C VAL* 4.6 5.4 - - - +
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Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C THR* 5.2 7.6 - - + -
279C ALA 3.1 12.1 + - - +
280C HIS* 4.6 5.2 - - - +
282C SER* 1.3 76.0 + - - +
284C ALA* 1.3 58.4 + - - +
286C GLY* 3.3 2.1 + - - -
287C VAL* 2.9 30.8 + - - +
330C TYR* 3.9 15.8 - - + -
333C GLY* 2.2 44.6 - - - +
334C VAL* 3.5 3.6 - - - +
335C THR* 3.0 29.2 + - - +
336C GLY 4.6 0.2 - - - +
338C VAL* 4.6 16.6 - - + +
347C LYS* 4.9 0.4 + - - +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.9 10.1 - - + -
119C LEU* 3.5 21.5 - - + -
121C LEU* 3.6 13.0 - - + -
140C THR* 4.1 6.3 - - + +
280C HIS 3.1 21.2 + - - +
281C ILE 3.0 3.2 + - - +
283C ASP* 1.3 77.7 - - - +
285C VAL* 1.3 64.6 + - - +
287C VAL* 3.3 11.6 - - - +
288C VAL* 3.1 27.7 + - - +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 4.6 8.8 - - + +
42C PHE* 3.8 31.9 - - + +
45C ALA* 3.3 29.4 - - + +
46C VAL* 3.9 22.0 - - + -
49C ALA* 4.2 9.4 - - + -
60C LEU* 5.6 1.1 - - + -
91C LEU* 4.4 2.7 - - + -
281C ILE* 2.8 28.8 + - + +
282C SER* 3.7 6.7 - - - +
284C ALA* 1.3 77.0 - - - +
286C GLY* 1.3 55.9 + - - +
288C VAL* 3.2 6.6 + - - +
289C ALA* 2.8 29.1 + - + +
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Residues in contact with GLY 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 5.2 4.3 - - - -
282C SER 3.0 13.2 + - - -
283C ASP 3.3 2.2 + - - -
285C VAL* 1.3 78.5 - - - +
287C VAL* 1.3 54.8 + - - +
289C ALA* 3.8 7.0 - - - +
290C GLN* 3.1 25.1 + - - +
330C TYR* 3.4 35.7 - - - -
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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
----------------------------------------------------------
119C LEU* 4.1 13.7 - - + -
140C THR* 5.3 1.6 - - + -
283C ASP 2.9 15.3 + - - +
284C ALA* 3.3 21.3 - - - +
286C GLY* 1.3 73.7 - - - +
288C VAL* 1.3 59.9 + - + +
290C GLN* 4.1 3.6 - - - +
291C ALA* 3.4 13.2 + - - +
325C LEU* 3.4 17.5 - - + +
328C SER* 3.7 26.7 + - - +
330C TYR* 4.0 22.9 - - + +
338C VAL* 4.3 12.1 - - + +
340C PHE* 4.3 22.7 - - + -
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 3.8 39.5 - - + -
60C LEU* 5.8 1.3 - - + -
89C ALA* 4.7 12.1 - - + -
91C LEU* 4.3 10.3 - - + -
119C LEU* 3.9 19.3 - - + -
284C ALA 3.1 19.2 + - - +
285C VAL 3.8 2.7 - - - +
287C VAL* 1.3 79.4 - - - +
289C ALA* 1.3 58.5 + - - +
290C GLN 3.4 0.2 - - - -
291C ALA* 3.1 5.5 + - - +
292C VAL* 3.0 32.7 + - + +
321C PHE* 4.8 11.9 - - + -
325C LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 5.8 0.2 - - - +
49C ALA* 4.1 21.8 - - + -
53C HIS* 3.2 29.7 - - + +
60C LEU* 4.3 11.9 - - + +
285C VAL 2.8 17.4 + - - +
286C GLY* 3.8 7.0 - - - +
288C VAL* 1.3 77.2 - - - +
290C GLN* 1.3 61.3 + - - +
292C VAL* 3.3 12.2 - - - +
293C HIS 3.2 18.4 + - - -
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS* 4.2 12.3 - - + +
286C GLY 3.1 14.6 + - - +
287C VAL* 4.2 5.8 - - - +
289C ALA* 1.3 78.9 - - - +
291C ALA* 1.3 61.1 + - - +
293C HIS* 3.6 3.5 - - - +
294C GLU* 3.3 22.9 + - - +
328C SER* 4.7 7.7 - - - +
329C LYS 3.8 25.0 + - - +
330C TYR* 3.5 33.4 + - + +
331C ALA 5.2 1.2 - - - +
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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 VAL 3.4 15.8 + - - +
288C VAL 3.1 10.4 + - - +
290C GLN* 1.3 77.8 - - - +
292C VAL* 1.3 59.8 + - - +
294C GLU 3.4 0.5 + - - -
295C LEU* 2.9 28.4 + - - +
321C PHE* 3.4 22.7 - - + -
324C VAL* 3.4 21.4 - - + +
325C LEU* 3.5 16.8 - - + -
328C SER* 4.3 4.5 - - - +
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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
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27C VAL* 4.3 21.1 - - + -
29C ILE* 5.6 1.6 - - + -
58C ILE* 3.8 21.5 - - + -
60C LEU* 4.4 12.8 - - + -
88C TYR* 4.6 11.0 - - + -
288C VAL* 3.0 20.0 + - + +
289C ALA* 3.3 21.3 - - - +
291C ALA* 1.3 73.0 - - - +
293C HIS* 1.3 65.9 + - - +
295C LEU* 4.0 8.1 - - + -
296C LEU* 3.0 37.5 + - + +
321C PHE* 3.8 23.1 - - + -
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Residues in contact with HIS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C HIS* 3.3 41.5 - + + -
54C GLY 5.3 0.6 + - - -
58C ILE* 3.6 20.2 - - + +
289C ALA 3.2 8.4 + - - +
290C GLN* 3.6 7.2 - - - +
292C VAL* 1.3 80.0 - - - +
294C GLU* 1.3 63.4 + - - +
296C LEU* 3.5 3.1 + - - +
297C GLU* 3.2 52.1 + - - +
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Residues in contact with GLU 294 (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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290C GLN 3.3 14.0 + - - +
291C ALA 4.0 2.9 - - - +
293C HIS* 1.3 80.6 - - - +
295C LEU* 1.3 62.3 + - - +
296C LEU 3.3 0.4 + - - -
297C GLU* 3.7 11.4 + - + +
298C LYS* 3.1 54.8 + - - +
324C VAL* 4.0 21.5 - - + +
327C SER* 5.6 4.3 - - - -
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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
----------------------------------------------------------
88C TYR* 5.5 7.4 - - + -
291C ALA 2.9 18.9 + - - +
292C VAL* 3.3 11.4 + - + +
294C GLU* 1.3 77.6 - - - +
296C LEU* 1.3 66.7 + - + +
297C GLU 3.3 0.7 - - - -
298C LYS* 3.3 26.6 + - + +
301C ILE* 3.8 25.9 - - + +
315C TRP* 5.4 6.5 - - + -
317C THR* 3.8 25.4 - - + -
320C LEU* 3.8 29.6 - - + -
321C PHE* 4.0 23.1 - - + -
324C VAL* 4.2 9.2 - - + +
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LYS* 6.0 8.3 - - + -
27C VAL* 5.5 7.9 - - + -
57C LYS* 5.1 9.6 - - + +
58C ILE* 3.8 26.5 - - + +
88C TYR* 5.4 11.9 - - + +
292C VAL* 3.0 27.4 + - + +
293C HIS* 4.0 3.1 - - - +
295C LEU* 1.3 83.9 - - + +
297C GLU* 1.3 58.1 + - - +
298C LYS 3.2 11.8 - - - +
299C GLU* 5.4 1.0 - - - +
301C ILE* 3.6 24.4 - - + +
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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) + - + + + + + -
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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