Contacts of the helix formed by residues 301 - 319 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B TYR* 3.5 38.1 - - + -
234B GLN* 3.5 42.0 - - + +
298B GLU* 2.9 26.4 + - + +
299B PRO 4.7 1.3 - - - -
300B SER* 1.3 75.7 - - - +
302B ALA* 1.3 66.9 + - - +
303B GLU* 3.4 9.9 + - + +
304B TYR* 3.6 28.7 + - + +
305B THR* 3.7 11.6 + - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B SER 3.6 4.8 + - - -
301B ILE* 1.3 73.2 - - - +
303B GLU* 1.3 64.9 + - - +
305B THR* 3.1 18.3 + - - -
306B VAL* 3.2 22.3 + - + +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLN 4.6 2.2 - - - +
235B LEU 3.8 24.2 - - - +
236B GLY* 4.0 14.1 - - - +
301B ILE* 3.4 12.7 - - + +
302B ALA* 1.3 78.0 - - - +
304B TYR* 1.3 53.4 + - + +
306B VAL* 3.4 5.9 + - - +
307B ARG* 2.8 81.6 + - + +
336B GLU* 4.6 4.3 - - - +
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Residues in contact with TYR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 2.6 46.6 + + - -
236B GLY* 3.4 30.4 - - - -
238B HIS* 4.0 8.8 - + - +
268B LEU* 3.5 24.9 - - + -
272B ILE* 4.2 19.1 - - + -
294B VAL* 4.8 8.7 - - + +
295B MET* 3.9 3.2 - - - +
298B GLU* 3.5 37.7 - - + +
301B ILE* 3.7 24.5 - - + +
302B ALA 3.3 1.0 - - - -
303B GLU* 1.3 74.3 - - + +
305B THR* 1.3 60.6 + - - +
307B ARG* 4.0 5.8 - - + +
308B SER* 2.6 35.4 + - - -
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 3.8 28.4 + - + +
298B GLU 4.0 9.9 + - - -
299B PRO* 4.3 8.8 + - - +
301B ILE 3.7 12.1 + - - -
302B ALA* 3.1 8.5 + - - -
304B TYR* 1.3 74.9 - - - +
306B VAL* 1.3 66.4 + - - +
309B LYS* 3.3 47.6 + - - +
335B MET* 5.3 3.1 - - - -
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA* 3.2 23.2 + - + +
303B GLU* 3.8 8.1 - - - +
305B THR* 1.3 79.3 - - - +
307B ARG* 1.3 65.9 + - - +
309B LYS* 3.3 2.8 + - - +
310B GLU* 3.0 26.3 + - - +
332B VAL* 4.6 7.8 - - + +
335B MET* 3.9 40.8 - - + -
336B GLU* 3.4 33.4 - - + +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 5.0 2.2 - - + -
303B GLU* 2.8 52.8 + - + +
304B TYR* 4.4 5.4 - - + +
306B VAL* 1.3 89.5 + - - +
308B SER* 1.3 64.7 + - - +
310B GLU* 3.3 29.4 + - - +
311B ARG* 3.0 34.7 + - + +
336B GLU* 2.8 43.7 + - - -
339B ASN* 4.0 2.0 - - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.2 36.8 - - - -
294B VAL* 3.6 15.2 - - - +
295B MET* 3.7 21.3 - - - +
304B TYR* 2.6 24.4 + - - -
307B ARG* 1.3 75.9 - - - +
309B LYS* 1.3 52.5 + - - +
311B ARG* 3.0 4.7 + - - +
312B ILE* 2.7 39.4 + - - +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 4.0 16.8 - - + -
305B THR* 3.3 39.1 + - + +
306B VAL* 3.7 4.3 - - - +
308B SER* 1.3 75.9 - - - +
310B GLU* 1.3 54.1 + - - +
312B ILE* 4.0 9.0 - - + -
313B CYS* 2.6 37.4 + - - +
328B VAL* 3.4 13.8 - - + +
331B GLU* 2.6 32.0 + - + +
332B VAL* 3.6 14.1 - - + -
335B MET* 4.3 14.7 - - + +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL 3.0 13.6 + - - +
307B ARG* 3.3 35.1 + - - +
308B SER 3.2 0.2 - - - -
309B LYS* 1.3 76.0 - - - +
311B ARG* 1.3 70.7 + - - +
313B CYS* 3.5 4.6 - - - +
314B HIS* 2.9 26.0 + - - +
332B VAL* 3.6 18.0 - - + +
339B ASN* 3.1 36.4 + - - +
341B ASN* 3.3 28.5 + - + +
342B ALA* 4.7 4.5 - - + +
345B ASP* 4.5 1.4 - - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 2.7 32.6 + - - -
279B ILE* 3.5 23.6 - - + +
291B TYR* 3.4 38.8 - - + +
307B ARG* 3.0 21.3 - - + +
308B SER 3.0 4.0 + - - +
310B GLU* 1.3 84.5 + - - +
312B ILE* 1.3 54.1 + - - +
314B HIS* 3.2 45.6 + - - +
315B CYS* 2.8 39.4 + - - -
341B ASN* 3.7 18.2 - - - +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR* 3.7 31.0 - - + +
291B TYR* 3.9 20.9 - - + -
292B GLU* 4.1 7.6 - - - +
295B MET* 3.6 31.0 - - + -
308B SER 2.7 21.9 + - - +
309B LYS* 3.6 8.3 - - + +
311B ARG* 1.3 69.5 - - - +
313B CYS* 1.3 65.1 + - - +
315B CYS* 3.1 9.2 + - - +
316B PHE* 3.0 49.4 + - + -
328B VAL* 4.1 11.0 - - + -
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Residues in contact with CYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS 2.6 22.0 + - - +
310B GLU* 3.5 9.2 - - - +
312B ILE* 1.3 73.8 - - - +
314B HIS* 1.3 64.8 + - - +
316B PHE* 3.4 4.4 + - - +
317B SER* 3.2 18.7 + - - -
328B VAL* 3.7 10.0 - - + +
329B CYS* 2.0 66.2 - - - +
332B VAL* 4.2 0.9 - - + -
342B ALA* 4.2 14.1 - - - -
345B ASP* 3.8 13.2 - - - -
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 4.8 15.5 - - + +
284B TYR* 5.1 4.1 - + - -
310B GLU 2.9 9.4 + - - +
311B ARG* 3.2 47.7 + - - +
313B CYS* 1.3 75.6 - - - +
315B CYS* 1.3 66.2 + - - +
317B SER* 3.3 4.0 + - - -
318B LYS* 3.1 51.5 + - + +
341B ASN* 4.4 6.1 + - - -
345B ASP* 3.0 40.5 + - - +
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Residues in contact with CYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.7 29.2 - - - -
284B TYR* 3.5 39.7 - - + +
287B ALA* 3.9 5.6 - - - -
288B THR* 3.5 19.7 - - - +
291B TYR* 5.6 1.3 - - - -
311B ARG* 2.8 26.6 + - - -
312B ILE* 3.1 10.5 + - - +
314B HIS* 1.3 74.2 - - - +
316B PHE* 1.3 58.4 + - + +
318B LYS* 3.4 0.5 + - - -
319B ASP* 3.0 31.1 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B THR* 5.6 11.2 - - + -
288B THR* 4.4 17.9 - - + -
312B ILE* 3.0 45.9 + - + +
313B CYS 3.9 1.6 - - - +
314B HIS 3.3 0.2 - - - -
315B CYS* 1.3 78.0 - - + +
317B SER* 1.3 61.5 + - - +
319B ASP* 3.3 7.9 + - + -
321B LYS* 2.8 45.6 + - + +
324B GLU* 3.4 34.1 - - + -
325B ALA* 3.6 21.3 - - - +
327B ARG* 4.4 6.3 - - - -
328B VAL* 3.7 24.2 - - + -
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B CYS 3.2 11.2 + - - -
314B HIS 3.3 7.6 + - - -
316B PHE* 1.3 78.9 - - - +
318B LYS* 1.3 60.6 + - - +
320B GLU* 3.3 15.9 + - - +
321B LYS 5.0 0.9 - - - +
325B ALA* 3.7 12.0 - - - +
345B ASP* 2.8 41.8 + - - -
348B GLU* 3.3 24.2 - - - +
349B ALA* 4.0 3.7 + - - +
352B ILE* 4.3 9.6 - - - +
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 3.6 42.3 + - + +
314B HIS* 3.1 42.6 + - + +
315B CYS 4.0 0.4 - - - +
317B SER* 1.3 74.1 - - - +
319B ASP* 1.3 57.0 + - - +
320B GLU* 3.2 21.9 + - - +
345B ASP* 5.4 1.3 - - - +
348B GLU* 6.1 0.4 - - + -
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TYR* 3.8 23.9 - - + +
285B THR* 3.7 26.0 + - - +
315B CYS 3.0 18.5 + - - +
316B PHE* 4.0 4.7 - - + +
317B SER 3.3 0.6 - - - -
318B LYS* 1.3 74.7 - - - +
320B GLU* 1.3 70.4 + - - +
321B LYS* 3.2 31.3 + - + +
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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) + - + + + + + -
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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