Contacts of the helix formed by residues 301 - 319 (chain C) in PDB entry 2Y4T
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 ILE 301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TYR* 3.5 33.9 - - + -
234C GLN* 3.4 43.7 - - + +
298C GLU* 3.3 21.0 + - + +
299C PRO 3.7 0.2 - - - -
300C SER* 1.3 78.4 - - - +
302C ALA* 1.3 68.4 + - + +
303C GLU* 3.8 7.9 - - + +
304C TYR* 3.2 32.2 + - + +
305C THR* 3.7 10.5 + - - -
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C SER 3.6 5.2 + - - -
301C ILE* 1.3 72.0 - - + +
303C GLU* 1.3 62.8 + - - +
305C THR* 3.2 9.2 + - - -
306C VAL* 3.2 31.7 + - + +
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Residues in contact with GLU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLN 4.1 17.7 - - - +
235C LEU* 4.0 21.9 - - - +
236C GLY* 4.0 11.7 - - - +
301C ILE* 3.2 4.8 + - + +
302C ALA* 1.3 78.5 - - - +
304C TYR* 1.3 58.2 + - + +
306C VAL* 4.7 3.9 - - - +
307C ARG* 3.0 66.4 + - + +
336C GLU* 4.7 7.6 - - - +
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Residues in contact with TYR 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 2.6 47.4 + + - -
236C GLY* 3.4 26.8 - - - -
238C HIS* 4.0 11.7 - + + +
268C LEU* 3.7 38.4 - - + -
272C ILE* 4.4 13.9 - - + -
294C VAL* 4.3 6.4 - - + +
295C MET* 3.6 5.1 - - - +
298C GLU* 3.7 36.1 - - + +
301C ILE* 3.2 29.1 + - + +
303C GLU* 1.3 77.6 - - + +
305C THR* 1.3 55.8 + - - +
307C ARG* 5.4 1.1 - - - -
308C SER* 2.6 32.3 + - - +
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Residues in contact with THR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C MET* 3.8 25.3 - - + +
298C GLU 4.6 3.5 + - - -
299C PRO* 4.5 11.3 + - - +
301C ILE 3.7 11.6 + - - -
302C ALA* 3.2 7.5 + - - -
304C TYR* 1.3 76.4 - - - +
306C VAL* 1.3 56.9 + - - +
308C SER* 3.1 2.4 + - - -
309C LYS* 2.7 56.2 + - + +
335C MET* 5.9 4.5 - - + -
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Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ALA* 3.2 22.6 + - + +
303C GLU* 4.0 6.5 - - - +
305C THR* 1.3 77.1 - - - +
307C ARG* 1.3 67.0 + - - +
309C LYS* 3.3 3.1 + - - +
310C GLU* 2.8 25.1 + - - +
332C VAL* 4.3 7.7 - - + +
335C MET* 3.7 40.4 - - + -
336C GLU* 3.3 41.1 - - + +
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C TYR* 5.6 0.7 - - - -
303C GLU* 3.0 43.2 + - + +
304C TYR* 5.2 0.9 - - - +
306C VAL* 1.3 83.1 - - - +
308C SER* 1.3 61.0 + - - +
310C GLU* 2.2 45.7 + - - +
311C ARG* 3.0 35.6 + - + +
336C GLU* 3.4 20.0 + - - -
339C ASN* 3.0 21.2 + - - +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 5.7 0.2 - - - +
291C TYR* 3.5 24.9 - - - +
294C VAL* 3.3 23.0 - - - +
295C MET* 3.4 22.6 - - - +
304C TYR 2.6 25.6 + - - -
305C THR 3.1 1.2 + - - -
307C ARG* 1.3 77.7 - - - +
309C LYS* 1.3 56.4 + - - +
311C ARG* 3.2 2.9 + - - +
312C ILE* 3.0 35.4 + - - +
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Residues in contact with LYS 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C MET* 3.9 16.6 - - + -
305C THR* 2.7 42.2 + - + +
306C VAL 3.6 5.2 - - - +
308C SER* 1.3 73.1 - - - +
310C GLU* 1.3 57.0 + - - +
312C ILE* 4.4 7.0 - - + -
313C CYS* 2.9 29.3 + - - +
328C VAL* 3.5 10.8 - - + +
331C GLU* 2.9 43.1 + - - +
332C VAL* 3.5 16.5 - - + +
335C MET* 4.3 9.6 - - + -
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Residues in contact with GLU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL 2.8 15.2 + - - +
307C ARG* 2.2 58.0 + - - +
309C LYS* 1.3 76.9 - - - +
311C ARG* 1.3 73.2 + - - +
313C CYS* 3.2 6.4 - - - +
314C HIS* 2.7 31.1 + - + +
332C VAL* 3.7 10.3 - - + +
339C ASN* 3.0 21.2 + - - +
341C ASN* 3.7 24.5 + - + +
342C ALA* 4.8 10.3 - - + +
345C ASP* 5.3 2.2 - - - +
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 3.1 30.0 + - - -
279C ILE* 3.5 16.3 - - + +
291C TYR* 3.5 39.7 - - + +
307C ARG* 3.0 22.6 + - + +
308C SER 3.8 1.6 - - - +
310C GLU* 1.3 95.6 + - - +
312C ILE* 1.3 56.3 + - - +
314C HIS* 3.1 45.2 + - - +
315C CYS* 2.6 40.0 + - - -
341C ASN* 5.2 6.3 - - - +
345C ASP* 5.6 0.4 + - - -
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Residues in contact with ILE 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C THR* 3.8 29.8 - - + +
291C TYR* 3.9 15.7 - - + -
292C GLU* 3.8 22.2 - - - +
295C MET* 3.8 19.5 - - + -
308C SER 3.0 21.8 + - - +
309C LYS* 3.9 6.3 - - + +
311C ARG* 1.3 73.0 - - - +
313C CYS* 1.3 64.5 + - - +
315C CYS* 3.2 7.4 + - - +
316C PHE* 3.0 51.5 + - + -
328C VAL* 3.8 13.5 - - + -
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Residues in contact with CYS 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LYS 2.9 16.5 + - - +
310C GLU* 3.2 12.3 - - - +
312C ILE* 1.3 77.3 - - - +
314C HIS* 1.3 61.5 + - - +
316C PHE* 3.6 3.1 + - - +
317C SER* 3.2 22.0 + - - -
328C VAL* 3.8 8.7 - - + -
329C CYS* 2.0 62.4 - - - -
332C VAL* 4.3 1.6 - - + -
342C ALA* 4.2 14.8 - - - -
345C ASP* 3.8 15.0 - - - -
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Residues in contact with HIS 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 4.4 18.3 - - + +
284C TYR* 5.5 3.4 - + - -
310C GLU* 2.7 15.4 + - + +
311C ARG* 3.2 51.3 + - - +
313C CYS* 1.3 73.2 - - - +
315C CYS* 1.3 65.0 + - - +
317C SER* 3.3 3.1 + - - -
318C LYS* 3.1 55.3 + - + +
345C ASP* 3.0 36.8 + - - +
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Residues in contact with CYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.8 15.5 - - - -
284C TYR* 3.5 36.9 - - + +
287C ALA* 3.6 20.4 - - - -
288C THR* 3.3 22.4 - - - +
291C TYR* 5.5 1.6 - - - -
311C ARG* 2.6 26.2 + - - +
312C ILE* 3.2 7.8 + - - +
314C HIS* 1.3 75.0 - - - +
316C PHE* 1.3 63.9 + - + +
318C LYS* 3.5 0.3 + - - -
319C ASP* 3.0 26.0 + - - +
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Residues in contact with PHE 316 (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 THR* 4.9 8.3 - - + -
288C THR* 4.1 21.1 - - + -
312C ILE* 3.0 44.5 + - + +
313C CYS 4.1 0.7 - - - +
315C CYS* 1.3 76.9 - - + +
317C SER* 1.3 60.1 + - - +
319C ASP* 3.4 8.4 + - + -
321C LYS* 3.0 61.2 + - + +
324C GLU* 3.9 27.8 - - + -
325C ALA* 3.9 19.7 - - - +
327C ARG* 4.6 6.3 - - - -
328C VAL* 3.9 20.0 - - + -
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Residues in contact with SER 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C CYS 3.2 16.4 + - - -
314C HIS 3.3 4.7 + - - -
316C PHE* 1.3 78.8 - - - +
318C LYS* 1.3 61.7 + - - +
320C GLU* 3.3 14.2 + - - +
321C LYS 5.0 0.7 - - - +
325C ALA* 4.0 12.5 - - - +
345C ASP* 2.8 41.4 + - - -
348C GLU* 3.5 20.3 - - - +
349C ALA* 4.2 3.4 + - - -
352C ILE* 4.1 11.8 - - - +
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Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C TYR* 3.6 37.4 + - + +
314C HIS* 3.1 46.8 + - + +
315C CYS 4.2 0.2 - - - +
317C SER* 1.3 73.5 - - - +
319C ASP* 1.3 58.0 + - - +
320C GLU* 3.1 15.3 + - - +
345C ASP* 5.0 4.7 - - - +
348C GLU* 5.9 6.7 - - + -
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Residues in contact with ASP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLY 5.2 0.5 - - - +
284C TYR* 3.7 24.6 - - + +
285C THR* 3.8 14.2 + - - +
315C CYS 3.0 19.3 + - - +
316C PHE* 3.7 8.0 - - + +
317C SER 3.2 0.4 - - - -
318C LYS* 1.3 75.6 - - - +
320C GLU* 1.3 70.4 + - - +
321C LYS* 3.4 33.7 + - + +
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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