Contacts of the helix formed by residues 301 - 319 (chain A) in PDB entry 2Y4U
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A TYR* 3.6 36.3 - - + -
234A GLN* 3.6 44.0 - - + +
298A GLU* 2.8 20.0 + - - +
299A PRO 3.6 1.1 - - - -
300A SER* 1.3 75.1 - - - +
302A ALA* 1.3 67.6 + - - +
303A GLU* 3.7 11.4 - - + +
304A TYR* 3.1 37.6 + - + +
305A THR* 3.8 5.7 + - - +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER 3.5 5.9 + - - +
301A ILE* 1.3 70.8 - - - +
303A GLU* 1.3 67.1 + - - +
304A TYR 2.8 2.1 + - - -
305A THR* 2.9 26.8 + - - +
306A VAL* 3.1 16.0 + - + +
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN 4.5 4.7 - - - +
235A LEU* 3.9 23.1 - - - +
236A GLY* 4.2 14.8 - - - -
301A ILE* 3.3 13.0 + - + +
302A ALA* 1.3 78.0 - - - +
304A TYR* 1.3 58.8 + - + +
306A VAL* 3.9 5.3 - - - +
307A ARG* 3.1 68.0 + - + +
336A GLU* 5.0 0.3 - - - +
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Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 2.7 42.4 + + - -
236A GLY* 3.0 31.6 - - - -
238A HIS* 3.9 16.2 - + + +
268A LEU* 3.8 27.1 - - + -
272A ILE* 4.6 6.7 - - + -
294A VAL* 5.1 7.4 - - + +
295A MSE 4.1 2.8 - - - +
298A GLU* 3.6 36.6 - - + +
301A ILE* 3.1 31.2 + - + +
302A ALA 2.8 5.9 + - - -
303A GLU* 1.3 76.2 - - + +
305A THR* 1.3 58.3 + - - +
307A ARG* 4.7 2.6 - - + +
308A SER* 2.7 35.6 + - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MSE 3.5 38.6 - - + +
298A GLU 4.8 5.6 - - - +
299A PRO* 4.6 14.6 - - + +
301A ILE 3.8 7.6 + - - +
302A ALA* 2.9 18.3 + - - +
304A TYR* 1.3 75.4 - - - +
306A VAL* 1.3 63.6 + - - +
308A SER* 3.5 1.2 - - - -
309A LYS* 2.8 39.7 + - - +
335A MSE 5.5 2.7 - - - -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.1 25.5 + - + +
303A GLU* 3.9 5.6 - - - +
305A THR* 1.3 77.1 - - - +
307A ARG* 1.3 94.5 + - - +
309A LYS* 3.0 4.9 + - - +
310A GLU* 2.9 21.1 + - - +
332A VAL* 4.8 2.9 - - + +
335A MSE 3.6 42.0 - - + +
336A GLU* 3.3 20.0 - - + +
339A ASN* 5.5 0.4 - - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 5.3 1.8 - - + -
303A GLU* 3.1 47.6 + - - +
304A TYR* 4.7 2.7 - - + +
306A VAL* 1.3 116.6 + - - +
308A SER* 1.3 64.1 + - - +
310A GLU* 3.4 26.9 + - - +
311A ARG* 3.3 26.3 + - + +
336A GLU* 2.7 30.2 + - - -
339A ASN* 4.3 1.4 - - - +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 3.4 34.6 + - - -
294A VAL* 3.7 15.1 - - - +
295A MSE 3.7 20.2 - - - +
304A TYR* 2.7 24.5 + - - -
305A THR 3.5 3.6 - - - -
306A VAL 3.1 0.4 - - - -
307A ARG* 1.3 76.4 - - - +
309A LYS* 1.3 63.4 + - - +
311A ARG* 3.1 14.2 + - - +
312A ILE* 3.1 18.5 + - - +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MSE 3.7 30.3 - - + +
305A THR* 2.8 23.2 + - - +
306A VAL* 3.0 5.6 + - - +
308A SER* 1.3 73.0 - - - +
310A GLU* 1.3 66.7 + - - +
312A ILE* 2.9 12.8 + - + +
313A CYS* 2.7 23.9 + - - +
328A VAL* 3.8 9.0 - - + +
331A GLU* 2.9 49.0 + - + +
332A VAL* 3.8 14.8 - - + -
335A MSE 4.6 11.6 - - + -
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A VAL* 2.9 13.2 + - + +
307A ARG* 3.4 32.6 + - - +
308A SER 3.3 0.2 - - - -
309A LYS* 1.3 75.8 - - - +
311A ARG* 1.3 68.2 + - - +
313A CYS* 3.1 6.4 + - - +
314A HIS* 2.8 32.8 + - + +
332A VAL* 3.8 14.4 - - + +
339A ASN* 3.0 37.8 + - - +
341A ASN* 3.4 32.2 + - + +
342A ALA* 4.9 6.4 - - + +
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 2.9 33.5 + - - -
279A ILE* 3.1 26.7 - - + +
291A TYR* 3.6 35.4 - - + +
307A ARG* 3.3 14.8 + - + +
308A SER 3.1 8.8 + - - +
310A GLU* 1.3 89.2 + - - +
312A ILE* 1.3 54.9 + - - +
314A HIS* 3.1 43.5 + - - +
315A CYS* 2.6 38.7 + - - +
341A ASN* 5.5 4.2 + - - +
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 4.0 23.6 - - + +
291A TYR* 4.1 23.3 - - + -
292A GLU* 4.5 22.4 - - + +
295A MSE 4.5 9.9 - - - -
308A SER 3.1 22.1 + - - +
309A LYS* 2.9 14.1 + - + +
311A ARG* 1.3 73.8 - - - +
313A CYS* 1.3 59.4 + - - +
315A CYS* 2.7 28.0 + - - +
316A PHE* 3.0 38.7 + - + -
328A VAL* 4.2 11.9 - - + -
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Residues in contact with CYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS 2.7 12.4 + - - +
310A GLU* 3.3 12.3 - - - +
312A ILE* 1.3 73.9 - - - +
314A HIS* 1.3 62.1 + - - +
316A PHE* 3.7 4.7 + - - +
317A SER* 3.3 20.1 + - - -
325A ALA* 4.5 1.0 - - - +
328A VAL* 3.6 23.1 - - + +
329A CYS* 2.1 56.2 - - - +
332A VAL* 4.5 1.8 - - + -
342A ALA* 4.2 18.6 - - - -
345A ASP* 4.3 8.1 - - - -
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 5.0 11.2 - - + +
284A TYR* 4.8 7.6 - + - -
310A GLU* 2.8 15.4 + - + +
311A ARG* 3.1 47.8 + - - +
312A ILE 3.0 0.2 - - - -
313A CYS* 1.3 77.0 - - - +
315A CYS* 1.3 57.8 + - - +
317A SER* 3.4 1.4 + - - -
318A LYS* 3.0 64.7 + - + +
341A ASN* 5.8 4.0 + - + +
345A ASP* 2.7 28.8 + - - +
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Residues in contact with CYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 3.9 13.7 - - - -
284A TYR* 3.3 29.9 - - + +
287A ALA* 3.6 31.2 - - - -
288A THR* 3.5 20.6 - - - +
291A TYR* 5.6 2.0 - - - -
311A ARG* 2.6 20.5 + - - +
312A ILE* 2.7 15.8 + - - +
314A HIS* 1.3 70.6 - - - +
316A PHE* 1.3 64.9 + - + +
319A ASP* 3.2 23.4 + - - +
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A THR* 6.1 3.6 - - + -
288A THR* 4.3 23.1 - - + -
312A ILE* 3.0 37.1 + - + +
313A CYS 4.2 0.2 - - - +
315A CYS* 1.3 74.4 - - - +
317A SER* 1.3 67.1 + - - +
319A ASP* 2.9 14.5 + - + +
320A GLU 3.1 10.2 + - - -
321A LYS* 3.2 35.6 + - + +
324A GLU* 3.8 38.8 - - + -
325A ALA* 3.6 19.5 - - + +
327A ARG* 4.8 7.2 - - - -
328A VAL* 4.1 13.9 - - + -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A CYS 3.3 17.0 + - - -
314A HIS 3.5 4.7 - - - -
316A PHE* 1.3 77.9 - - - +
318A LYS* 1.3 62.4 + - - +
319A ASP 3.1 0.9 + - - -
320A GLU* 3.2 14.7 + - - +
321A LYS 5.2 0.7 - - - +
325A ALA* 3.7 12.7 - - - +
345A ASP* 2.6 46.7 + - - +
348A GLU* 4.1 18.0 + - - +
349A ALA* 4.4 5.4 + - - +
352A ILE* 4.7 7.0 - - - +
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 3.4 38.3 + - + +
314A HIS* 3.0 51.7 + - - +
317A SER* 1.3 73.6 - - - +
319A ASP* 1.3 58.1 + - - +
320A GLU* 3.3 9.2 + - - +
345A ASP* 3.9 9.9 - - - +
348A GLU* 4.0 24.4 + - - +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 3.6 27.9 + - + +
285A THR* 3.8 8.8 + - - +
315A CYS 3.2 18.7 + - - +
316A PHE* 2.9 9.0 + - + +
318A LYS* 1.3 77.7 - - - +
320A GLU* 1.3 73.0 + - - +
321A LYS* 3.3 36.2 + - + +
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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