Contacts of the helix formed by residues 294 - 311 (chain A) in PDB entry 1YQZ
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 LEU 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TYR* 3.4 36.1 - - + +
186A LEU* 5.0 7.6 - - + -
276A GLY* 5.9 0.7 - - - -
277A ASP* 4.4 1.4 - - - +
292A VAL* 2.9 29.3 + - + +
293A PRO* 1.3 83.6 - - + +
295A ALA* 1.3 66.7 + - - +
296A TRP* 3.4 5.6 - - + +
297A GLY* 3.5 5.9 + - - +
298A ALA* 3.4 16.5 + - - +
323A ASN 3.6 23.3 - - - +
324A ASN* 3.8 19.7 - - + -
439A FAD 3.1 27.2 + - + +
419B TYR 6.0 1.1 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 1.3 71.2 - - - +
296A TRP* 1.3 66.5 + - - +
298A ALA* 3.1 6.6 + - - +
299A HIS* 3.0 26.9 + - - -
439A FAD 2.8 29.8 + - + +
441A COA 3.5 40.6 - - + -
419B TYR* 3.9 4.5 - - + -
426B PRO* 3.9 11.7 - - + -
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Residues in contact with TRP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.4 4.3 - - + +
295A ALA* 1.3 78.9 - - - +
297A GLY* 1.3 72.5 + - - +
299A HIS* 3.3 2.3 + - - +
300A ARG* 2.8 58.8 + - + +
317A PHE* 4.2 11.4 - + - -
319A GLY 5.2 2.2 - - - -
320A PHE* 4.1 17.9 - + - -
323A ASN 6.1 1.1 - - - +
439A FAD 4.4 2.0 + - - -
413B THR 4.3 1.1 + - - -
414B GLU* 3.6 20.6 - - - -
415B PHE 2.9 26.1 + - - -
416B GLU* 3.6 38.6 - - + -
417B VAL* 3.9 26.2 - - + +
419B TYR* 5.2 5.0 - - + +
426B PRO* 3.2 33.0 - - + +
431B ASN* 3.5 14.1 + - - +
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Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 5.1 0.7 - - - -
276A GLY* 4.9 3.0 + - - -
292A VAL* 5.1 2.0 + - - +
294A LEU* 3.5 7.7 + - - +
295A ALA 3.2 0.8 - - - -
296A TRP* 1.3 91.9 - - - +
298A ALA* 1.3 65.4 + - - +
300A ARG* 4.1 1.3 - - - +
301A ALA* 3.0 27.9 + - - +
317A PHE* 6.0 1.0 - - - -
320A PHE* 3.8 24.8 - - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 4.1 9.2 - - + -
12A GLY* 3.9 19.2 - - - +
275A ILE* 4.7 1.2 - - - +
276A GLY* 4.1 20.5 - - - +
294A LEU 3.4 11.3 + - - +
295A ALA 3.1 9.0 + - - +
297A GLY* 1.3 76.1 - - - +
299A HIS* 1.3 59.7 + - - +
301A ALA* 4.0 1.4 - - - +
302A ALA* 3.0 28.6 + - - +
439A FAD 3.7 24.2 - - - +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 3.7 11.8 + - + -
15A THR* 3.7 7.1 + - + +
295A ALA 3.0 21.1 + - - +
296A TRP 3.8 2.7 - - - +
298A ALA* 1.3 76.5 - - - +
300A ARG* 1.3 64.3 + - - +
302A ALA* 3.3 8.9 + - - +
303A SER* 3.1 23.4 + - - -
441A COA 2.8 53.5 + - - -
426B PRO* 3.5 28.2 - - + +
427B LYS* 3.0 44.4 + - + +
435B TYR* 4.6 0.5 + - - -
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TRP* 2.8 53.3 + - + +
297A GLY 4.1 2.2 - - - +
298A ALA 3.4 0.2 - - - -
299A HIS* 1.3 72.4 - - - +
301A ALA* 1.3 64.1 + - - +
303A SER* 3.1 9.7 + - - -
304A ILE* 3.0 57.4 + - + +
315A ILE* 4.0 17.8 - - - +
316A GLU 4.8 4.2 + - - -
317A PHE* 4.3 9.5 - - + +
413B THR* 3.5 38.8 + - - -
414B GLU* 4.1 18.4 + - - +
427B LYS* 6.1 0.4 - - - -
435B TYR* 3.0 36.9 + - - -
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 3.5 42.7 - - + -
275A ILE* 3.7 23.6 - - + -
276A GLY 4.6 1.1 - - - +
297A GLY 3.0 20.0 + - - +
298A ALA 4.0 1.1 - - - +
300A ARG* 1.3 75.6 - - - +
302A ALA* 1.3 63.6 + - - +
304A ILE* 3.2 1.5 + - - +
305A VAL* 2.9 29.3 + - - +
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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
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12A GLY 3.8 4.5 - - - +
15A THR* 3.7 14.4 - - + -
16A CYS* 3.5 45.7 - - + +
19A GLN* 4.2 2.0 - - + +
275A ILE* 4.1 4.9 - - + +
298A ALA 3.0 19.8 + - - +
299A HIS 3.5 6.7 - - - +
300A ARG 3.2 0.2 - - - -
301A ALA* 1.3 76.6 - - - +
303A SER* 1.3 56.9 + - - +
305A VAL 3.6 0.2 + - - -
306A ALA* 3.1 27.4 + - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.4 27.0 + - - +
299A HIS 3.1 8.5 + - - -
300A ARG* 3.1 12.3 + - - -
302A ALA* 1.3 75.5 - - - +
304A ILE* 1.3 64.4 + - - +
306A ALA* 3.3 7.3 + - - +
307A GLU* 3.0 29.2 + - - +
427B LYS* 4.6 3.8 - - - +
435B TYR* 3.6 37.4 + - - -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP 4.1 10.3 - - - +
264A LYS* 4.6 1.8 - - - -
265A PHE* 3.9 18.6 - - + -
300A ARG* 3.0 47.8 + - + +
301A ALA 3.7 5.2 - - - +
303A SER* 1.3 75.8 - - - +
305A VAL* 1.3 60.1 + - - +
307A GLU* 3.2 8.3 + - - +
308A GLN* 2.9 34.2 + - + +
315A ILE* 3.8 25.5 - - + +
316A GLU 4.1 0.2 - - - -
317A PHE* 3.6 42.6 - - + +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 3.8 23.3 - - - -
110A ILE* 3.9 8.1 - - + -
264A LYS 4.0 2.2 - - - +
265A PHE* 3.6 29.8 - - + -
273A TYR* 3.8 24.7 - - + -
275A ILE* 3.6 12.3 - - + -
301A ALA 2.9 19.4 + - - +
304A ILE* 1.3 75.1 - - - +
306A ALA* 1.3 63.0 + - - +
308A GLN* 3.2 7.4 + - - +
309A ILE* 2.9 42.8 + - + +
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Residues in contact with ALA 306 (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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16A CYS* 4.4 0.2 - - - -
19A GLN* 3.5 40.4 - - + +
20A ILE* 3.7 17.5 - - + +
23A LEU* 3.6 10.9 - - + +
302A ALA 3.1 18.3 + - - +
303A SER* 3.6 5.2 - - - +
304A ILE 3.2 0.2 - - - -
305A VAL* 1.3 78.2 - - - +
307A GLU* 1.3 56.2 + - + +
309A ILE* 4.1 0.2 - - - +
310A ALA* 2.8 28.1 + - - +
311A GLY 3.4 2.9 + - - -
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.1 18.0 - - + +
303A SER* 3.0 21.1 + - - +
304A ILE 3.2 6.5 + - - +
306A ALA* 1.3 75.7 - - + +
308A GLN* 1.3 62.1 + - - +
311A GLY* 2.8 36.8 + - - +
312A ASN* 2.9 42.4 + - - +
313A ASP 3.8 0.2 + - - -
315A ILE* 3.8 31.5 - - + +
435B TYR* 6.1 1.6 - - - -
438B LYS* 5.6 4.0 + - - -
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Residues in contact with GLN 308 (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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264A LYS* 3.5 49.6 - - + +
266A GLU* 4.4 4.9 - - - +
273A TYR* 4.0 18.7 + - + +
304A ILE* 2.9 19.2 + - + +
305A VAL* 3.4 10.5 - - - +
307A GLU* 1.3 79.3 - - - +
309A ILE* 1.3 61.5 + - - +
311A GLY 5.2 0.3 - - - +
312A ASN 4.5 0.2 + - - -
313A ASP* 3.0 48.6 + - - +
315A ILE 2.9 25.7 + - - +
316A GLU* 4.2 0.2 - - - +
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Residues in contact with ILE 309 (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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2A PRO* 4.1 28.5 - - + +
4A ILE* 4.1 15.5 - - + -
20A ILE* 4.1 8.3 - - + -
24A ASP* 5.8 0.4 - - - +
108A LYS* 4.1 21.7 - - + +
110A ILE* 3.6 30.7 - - + -
273A TYR* 3.7 35.9 - - + +
305A VAL* 2.9 20.5 + - + +
306A ALA 4.1 1.8 - - - +
308A GLN* 1.3 79.3 - - - +
310A ALA* 1.3 64.3 + - + +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 6.3 0.4 - - + -
20A ILE* 4.4 9.4 - - + -
23A LEU* 3.7 24.4 - - + +
24A ASP* 3.8 31.4 - - + +
306A ALA 2.8 14.1 + - - +
309A ILE* 1.3 81.1 - - + +
311A GLY* 1.3 60.6 + - - +
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Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.9 9.2 - - - -
306A ALA 3.4 2.6 + - - -
307A GLU* 2.8 30.4 + - - +
308A GLN 5.2 0.7 - - - +
309A ILE 3.8 0.4 - - - -
310A ALA* 1.3 76.1 - - - +
312A ASN* 1.3 59.0 + - - -
313A ASP* 3.4 6.4 + - - +
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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