Contacts of the helix formed by residues 287 - 306 (chain C) in PDB entry 3CMM
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 ASP 287 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ALA 4.1 5.0 - - - +
285C LYS* 3.5 15.2 - - - -
286C PHE* 1.3 97.1 + - + +
288C ARG* 1.3 73.6 + - - +
289C ALA 3.3 0.7 + - - -
290C ALA* 3.7 11.8 + - - +
291C GLN* 3.7 16.9 + - - +
344C ASN* 4.7 10.2 + - - -
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Residues in contact with ARG 288 (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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285C LYS* 2.8 48.0 + - + +
287C ASP* 1.3 82.5 + - - +
289C ALA* 1.3 56.7 + - - +
290C ALA 3.3 0.2 - - - -
291C GLN* 3.0 8.6 + - - +
292C LEU* 2.9 41.2 + - + +
344C ASN* 5.1 5.0 - - - +
347C LEU* 4.0 25.9 - - + +
392C ASP* 3.0 41.3 + - - +
394C LEU* 3.9 17.1 - - - +
395C GLU* 4.4 9.9 + - - -
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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
----------------------------------------------------------
278C PHE* 3.9 23.7 - - + -
279C VAL 6.0 0.9 - - - +
280C PHE* 3.7 33.9 - - + -
285C LYS 3.9 2.0 + - - +
286C PHE 3.5 2.5 + - - +
287C ASP 3.3 1.2 - - - -
288C ARG* 1.3 77.3 - - - +
290C ALA* 1.3 64.3 + - - +
292C LEU* 3.6 0.4 + - - -
293C HIS* 3.0 24.9 + - - +
390C TYR* 4.0 22.4 - - + +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE* 4.2 16.6 - - + -
286C PHE 4.6 1.2 + - - +
287C ASP 3.7 10.4 + - - +
289C ALA* 1.3 79.9 - - - +
291C GLN* 1.3 62.0 + - + +
293C HIS* 3.2 13.0 + - - +
294C LEU* 3.2 17.5 + - - +
336C VAL* 3.7 24.6 - - - +
337C LEU* 3.8 16.9 - - + +
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Residues in contact with GLN 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASP* 3.7 17.3 + - - +
288C ARG* 3.0 7.5 + - - +
290C ALA* 1.3 75.6 - - - +
292C LEU* 1.3 52.6 + - - +
294C LEU* 3.0 8.5 + - - +
295C GLY* 2.7 31.2 + - - -
326C VAL* 5.2 1.8 - - - +
337C LEU* 3.6 24.6 - - - +
341C VAL* 4.6 8.1 - - - +
342C ASP 3.2 22.4 + - - -
343C VAL* 3.6 8.7 - - - +
344C ASN* 2.7 41.6 + - + +
347C LEU* 3.6 18.6 - - + -
348C ILE* 3.9 11.3 - - + +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C PHE* 3.8 31.9 - - + -
288C ARG* 2.9 28.2 + - + +
289C ALA* 4.1 0.4 - - - +
291C GLN* 1.3 76.0 - - - +
293C HIS* 1.3 57.9 + - - +
295C GLY* 4.0 2.9 - - - +
296C PHE* 2.8 44.4 + - + -
347C LEU* 4.0 19.5 - - + -
348C ILE* 5.2 2.7 - - + -
351C LEU* 5.1 8.5 - - + -
390C TYR* 3.7 37.5 - - + -
391C PHE 4.2 20.4 - - - +
392C ASP* 4.6 6.7 - - - +
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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
----------------------------------------------------------
272C GLN 3.9 2.9 - - - -
273C LEU* 2.9 31.0 + - + -
276C PRO* 3.2 30.5 - - + +
278C PHE* 4.0 6.8 - + + -
289C ALA 3.0 15.9 + - - +
290C ALA* 3.3 10.8 - - - +
291C GLN 3.2 0.2 - - - -
292C LEU* 1.3 77.5 - - - +
294C LEU* 1.3 69.2 + - + +
296C PHE* 4.6 0.9 - - - +
297C GLN* 3.1 46.0 + - - +
336C VAL* 4.5 6.7 - - + -
388C PHE* 3.6 24.4 - + - -
390C TYR* 2.5 40.5 + - + +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ALA 3.2 10.3 + - - +
291C GLN* 3.0 7.4 + - - +
293C HIS* 1.3 78.1 - - + +
295C GLY* 1.3 68.0 + - - +
297C GLN* 3.1 17.4 + - - +
298C ALA* 2.8 24.6 + - - +
326C VAL* 4.0 27.6 - - + +
329C LEU* 4.0 18.4 - - + +
330C SER* 3.9 23.1 - - - +
333C GLN* 4.8 4.5 - - - +
336C VAL* 3.8 31.4 - - + -
337C LEU* 3.9 28.0 - - + -
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Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLN 2.7 18.7 + - - -
292C LEU 3.0 4.9 + - - -
294C LEU* 1.3 73.8 - - - +
296C PHE* 1.3 56.4 + - - +
298C ALA* 3.2 3.5 + - - +
299C LEU* 2.9 24.4 + - - +
322C LEU* 4.8 1.3 - - - +
326C VAL* 4.0 5.8 - - - +
348C ILE* 3.9 14.6 - - - -
351C LEU* 3.5 26.6 - - - +
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Residues in contact with PHE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LEU* 5.6 0.2 - - - -
155C GLU* 3.4 22.7 - - + +
157C ARG* 3.5 24.9 - - + -
160C PHE* 4.0 12.8 - - + -
161C GLY* 3.9 26.0 - - - -
162C ASN* 3.2 28.0 - - - +
292C LEU* 2.8 41.7 + - + +
293C HIS 4.6 1.8 - - - +
295C GLY* 1.3 71.3 - - - +
297C GLN* 1.3 61.7 + - + +
299C LEU* 3.3 14.2 + - + +
300C HIS* 2.6 32.6 + + + -
351C LEU* 4.1 15.5 - - + -
390C TYR* 3.7 26.2 - + + +
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LEU* 4.2 16.2 - - + +
273C LEU* 3.8 49.3 + - + +
293C HIS* 3.1 36.6 + - - +
294C LEU* 3.1 15.7 + - - +
296C PHE* 1.3 78.6 - - + +
298C ALA* 1.3 61.6 + - - +
300C HIS* 3.1 7.4 + - - +
301C GLN* 3.0 26.4 + - - +
329C LEU* 4.3 14.7 - - + +
333C GLN* 5.6 6.2 + - - +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU 2.8 15.7 + - - +
295C GLY 3.5 8.3 - - - +
297C GLN* 1.3 72.2 - - - +
299C LEU* 1.3 52.3 + - - +
301C GLN* 3.2 9.0 + - - -
302C PHE* 2.8 31.2 + - - +
322C LEU* 3.7 8.1 - - + -
325C LEU* 3.3 29.4 - - + +
326C VAL* 3.6 24.0 - - + +
329C LEU* 4.1 6.8 - - + +
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Residues in contact with LEU 299 (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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155C GLU* 5.4 0.2 - - - +
157C ARG* 3.8 34.3 - - + -
295C GLY 2.9 14.6 + - - +
296C PHE* 3.4 17.5 - - + +
297C GLN 3.2 0.4 - - - -
298C ALA* 1.3 76.1 - - - +
300C HIS* 1.3 63.1 + - + +
302C PHE* 3.3 6.2 + - - +
303C ALA* 3.1 24.6 + - - +
310C LEU* 5.2 10.0 - - + +
311C PRO* 3.7 37.7 - - + +
322C LEU* 3.8 16.5 - - + +
351C LEU* 4.1 23.8 - - + +
355C ALA* 4.1 14.4 - - + -
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Residues in contact with HIS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL 4.8 5.3 + - - -
133C SER* 4.5 7.4 - - - -
134C LEU* 3.6 52.5 + - + +
137C LYS* 5.6 2.6 + - + +
155C GLU* 3.1 39.4 + - - -
157C ARG* 4.7 6.2 + - - -
296C PHE* 2.6 27.6 + + + -
297C GLN 3.1 6.7 + - - +
299C LEU* 1.3 81.3 - - + +
301C GLN* 1.3 59.3 - - - +
303C ALA* 3.2 9.3 + - + +
304C VAL* 2.9 34.8 + - + +
310C LEU* 6.2 3.8 - - + +
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Residues in contact with GLN 301 (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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297C GLN* 3.0 15.7 + - - +
298C ALA* 3.2 8.9 + - - +
300C HIS* 1.3 74.1 - - - +
302C PHE* 1.3 63.2 + - - +
304C VAL* 3.3 10.7 + - + +
305C ARG* 3.1 26.7 + - - +
325C LEU* 3.5 36.7 + - + +
328C ASP* 5.5 2.4 - - - +
329C LEU* 3.4 39.7 - - - +
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Residues in contact with PHE 302 (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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298C ALA 2.8 15.7 + - - +
299C LEU* 3.3 10.3 - - - +
300C HIS 3.3 0.2 - - - -
301C GLN* 1.3 72.0 - - - +
303C ALA* 1.3 61.7 + - - +
305C ARG* 3.2 4.1 + - - +
306C HIS* 3.1 54.1 + + + -
309C GLU* 3.7 7.2 - - + -
310C LEU 3.8 4.9 - - - -
311C PRO* 3.4 38.6 - - + -
318C ASP* 3.4 39.9 - - + -
321C GLU* 3.3 43.7 - - + -
322C LEU* 4.1 9.0 - - + -
325C LEU* 3.5 12.9 - - + +
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU 3.1 12.9 + - - +
300C HIS* 3.2 13.9 + - + +
302C PHE* 1.3 74.2 - - - +
304C VAL* 1.3 67.1 + - + +
306C HIS 3.0 7.3 + - - -
308C GLY* 2.8 39.6 + - - +
309C GLU 3.3 21.5 - - - +
310C LEU* 5.1 7.0 - - + -
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Residues in contact with VAL 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 4.8 16.8 - - + +
300C HIS* 2.9 19.9 + - + +
301C GLN* 3.6 12.1 - - + +
303C ALA* 1.3 76.1 - - + +
305C ARG* 1.3 65.1 + - + +
306C HIS 3.3 0.2 + - - -
307C ASN* 4.1 5.2 + - - -
308C GLY* 5.6 0.2 - - - -
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Residues in contact with ARG 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C GLN* 3.1 15.9 + - - +
302C PHE* 3.4 10.8 - - - +
303C ALA 3.2 0.2 - - - -
304C VAL* 1.3 79.9 - - + +
306C HIS* 1.3 68.5 + - + +
307C ASN 3.7 1.4 + - - -
321C GLU* 2.8 40.3 + - - +
324C LYS* 5.9 5.5 - - - +
325C LEU* 3.5 30.2 - - - +
328C ASP* 5.2 5.5 + - - -
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Residues in contact with HIS 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PHE* 3.1 51.8 + + + +
303C ALA 3.0 4.7 + - - +
305C ARG* 1.3 85.0 + - + +
307C ASN* 1.3 71.0 + - - +
308C GLY 3.2 2.0 - - - -
309C GLU* 2.9 26.9 + - + +
318C ASP* 5.5 2.2 - - - -
321C GLU* 2.9 39.3 + - - -
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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