Contacts of the helix formed by residues 294 - 311 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A TYR 5.7 0.9 - - - +
158B TYR* 3.7 24.0 - - + +
186B LEU* 5.2 5.6 - - + -
276B GLY* 5.9 0.7 - - - -
277B ASP* 4.4 1.2 - - - +
292B VAL* 2.9 29.5 + - + +
293B PRO* 1.3 83.3 - - + +
295B ALA* 1.3 66.1 + - - +
296B TRP* 3.4 6.0 + - + +
297B GLY* 3.5 5.8 + - - +
298B ALA* 3.4 16.6 + - - +
323B ASN 3.6 23.8 - - - +
324B ASN* 3.7 20.9 - - + -
440B FAD 3.1 38.4 + - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A TYR* 4.0 2.7 - - + -
426A PRO* 4.0 9.4 - - + -
11B ALA* 5.5 0.2 - - - -
294B LEU* 1.3 71.3 - - - +
296B TRP* 1.3 65.7 + - - +
298B ALA* 3.1 7.0 + - - +
299B HIS* 3.0 28.3 + - - -
440B FAD 2.9 29.4 + - + +
442B COA 3.5 42.6 - - + -
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Residues in contact with TRP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR 4.5 1.0 + - - -
414A GLU* 3.7 18.2 - - - -
415A PHE 3.0 26.6 + - - -
416A GLU* 3.6 42.2 - - + -
417A VAL* 3.9 29.4 - - + +
419A TYR* 5.3 4.5 - - + +
426A PRO* 3.2 33.5 - - + +
431A ASN* 3.7 8.4 + - - +
294B LEU* 3.4 4.1 - - + +
295B ALA* 1.3 77.9 - - - +
297B GLY* 1.3 64.0 + - - +
299B HIS* 3.4 2.3 + - - +
300B ARG* 2.8 57.3 + - + +
317B PHE* 4.1 22.0 - + - -
319B GLY 5.0 2.5 - - - -
320B PHE* 4.1 10.1 - + - -
323B ASN 6.0 2.0 - - - +
440B FAD 4.4 2.4 + - - -
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B PHE* 5.2 0.7 - - - -
276B GLY* 4.9 3.3 + - - -
292B VAL* 5.0 2.4 + - - +
294B LEU* 3.5 7.8 + - - +
295B ALA 3.2 0.4 - - - -
296B TRP* 1.3 92.7 - - - +
298B ALA* 1.3 65.3 + - - +
300B ARG* 4.1 1.3 - - - +
301B ALA* 2.9 28.1 + - - +
317B PHE* 6.0 0.6 - - - -
320B PHE* 3.8 24.0 - - - -
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 4.2 8.7 - - + -
12B GLY* 4.0 20.1 - - - +
275B ILE* 4.7 0.9 - - - +
276B GLY* 4.2 18.5 - - - +
294B LEU 3.4 12.4 + - - +
295B ALA* 3.1 9.0 + - - +
297B GLY* 1.3 76.9 - - - +
299B HIS* 1.3 60.2 + - + +
301B ALA* 3.9 1.2 - - - +
302B ALA* 2.9 29.6 + - - +
440B FAD 3.8 24.5 - - - +
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PRO* 3.7 26.1 - - + +
427A LYS* 3.0 43.0 + - + +
435A TYR* 4.8 0.3 + - - -
11B ALA* 3.9 9.2 - - + -
15B THR* 3.8 8.5 + - + +
295B ALA* 3.0 21.3 + - + +
296B TRP 3.8 2.7 - - - +
298B ALA* 1.3 79.3 - - + +
300B ARG* 1.3 63.9 + - - +
302B ALA* 3.3 7.7 + - - +
303B SER* 3.1 23.9 + - - -
442B COA 2.7 55.3 + - - -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 3.7 34.8 + - - -
414A GLU* 4.2 15.4 - - - +
427A LYS* 6.1 0.2 - - - -
435A TYR* 3.0 41.1 + - - -
296B TRP* 2.8 53.9 + - + +
297B GLY 4.1 2.7 - - - +
299B HIS* 1.3 73.3 - - - +
301B ALA* 1.3 64.2 + - - +
303B SER* 3.2 8.0 + - - -
304B ILE* 3.0 58.7 + - + +
315B ILE* 3.9 17.2 - - - +
316B GLU 4.8 4.8 + - - -
317B PHE* 4.3 8.6 - - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B PHE* 3.4 43.0 - - + -
275B ILE* 3.6 23.3 - - + -
276B GLY 4.6 1.8 - - - +
297B GLY 2.9 19.7 + - - +
298B ALA 4.0 0.9 - - - +
300B ARG* 1.3 74.1 - - - +
302B ALA* 1.3 67.1 + - - +
304B ILE* 3.8 0.6 - - - +
305B VAL* 2.9 29.5 + - - +
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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
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12B GLY 3.7 5.2 - - - +
15B THR* 3.7 15.0 - - + -
16B CYS* 3.5 47.0 - - + +
19B GLN* 4.7 1.8 - - + -
275B ILE* 4.2 4.4 - - + +
298B ALA 2.9 19.6 + - - +
299B HIS 3.5 6.3 - - - +
300B ARG 3.2 0.2 - - - -
301B ALA* 1.3 76.6 - - - +
303B SER* 1.3 61.3 + - - +
306B ALA* 3.0 23.2 + - - +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 4.6 5.9 + - - +
435A TYR* 3.6 35.3 + - - -
19B GLN* 3.6 24.6 + - - +
299B HIS 3.1 11.5 + - - -
300B ARG* 3.2 11.6 + - - -
302B ALA* 1.3 74.6 - - - +
304B ILE* 1.3 64.7 + - - +
306B ALA* 3.2 7.8 + - - +
307B GLU* 3.0 28.2 + - - +
442B COA 5.0 0.3 + - - -
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASP 4.2 9.9 - - - +
264B LYS* 4.6 1.6 - - - -
265B PHE* 3.9 19.5 - - + -
300B ARG* 3.0 55.0 + - + +
301B ALA 3.3 3.8 + - - +
303B SER* 1.3 74.6 - - - +
305B VAL* 1.3 58.5 + - - +
307B GLU* 3.1 10.3 + - - +
308B GLN* 2.9 33.0 + - + +
315B ILE* 3.8 24.9 - - + +
317B PHE* 3.6 41.1 - - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B CYS* 3.8 22.2 - - - -
110B ILE* 3.9 8.3 - - + -
264B LYS 4.1 0.7 - - - +
265B PHE* 3.5 21.3 - - + -
273B TYR* 3.9 23.3 - - + -
275B ILE* 3.5 22.0 - - + -
301B ALA 2.9 19.7 + - - +
304B ILE* 1.3 76.1 - - - +
306B ALA* 1.3 63.1 + - - +
308B GLN* 3.1 6.9 + - - +
309B ILE* 2.9 42.8 + - + +
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Residues in contact with ALA 306 (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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16B CYS* 4.3 0.6 - - - +
19B GLN* 3.5 29.6 - - + +
20B ILE* 3.7 27.8 - - + +
23B LEU* 3.4 11.2 - - + +
302B ALA 3.0 15.3 + - - +
303B SER* 3.2 8.5 + - - +
305B VAL* 1.3 76.6 - - - +
307B GLU* 1.3 58.2 + - + +
310B ALA* 2.9 27.5 + - - +
311B GLY 3.4 2.8 + - - -
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Residues in contact with GLU 307 (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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435A TYR* 6.2 0.2 - - - -
438A LYS* 6.0 1.7 - - - +
23B LEU* 4.3 17.1 - - + +
303B SER* 3.0 21.5 + - - +
304B ILE 3.5 6.7 - - - +
306B ALA* 1.3 77.1 - - - +
308B GLN* 1.3 60.0 + - - +
311B GLY* 2.7 37.3 + - - +
312B ASN* 2.9 42.4 + - - +
313B ASP 3.8 0.2 + - - -
315B ILE* 3.7 31.0 - - + +
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Residues in contact with GLN 308 (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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264B LYS* 3.3 54.8 + - + +
266B GLU* 4.6 3.1 - - - +
273B TYR* 3.9 21.0 + - + +
304B ILE* 2.9 19.1 + - + +
305B VAL* 3.1 7.8 + - - +
307B GLU* 1.3 77.6 - - - +
309B ILE* 1.3 62.4 + - - +
311B GLY 4.8 0.9 + - - +
313B ASP* 3.0 46.6 + - - +
315B ILE 2.8 26.9 + - - -
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Residues in contact with ILE 309 (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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2B PRO* 4.4 19.1 - - + +
4B ILE* 4.0 24.0 - - + -
20B ILE* 4.2 9.0 - - + -
24B ASP* 5.6 0.2 - - - +
108B LYS* 4.2 20.9 - - + +
110B ILE* 3.6 31.6 - - + -
273B TYR* 3.7 35.7 - - + +
305B VAL* 2.9 20.9 + - + +
306B ALA 4.2 1.3 - - - +
308B GLN* 1.3 79.7 - - - +
310B ALA* 1.3 64.2 + - + +
311B GLY 3.9 0.2 - - - -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.5 7.2 - - + -
23B LEU* 3.7 25.3 - - + +
24B ASP* 3.7 34.1 - - + +
306B ALA 2.9 14.1 + - - +
309B ILE* 1.3 80.6 - - + +
311B GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.1 9.6 - - - -
306B ALA 3.4 2.6 + - - -
307B GLU* 2.7 31.6 + - - +
308B GLN 5.0 0.7 - - - +
309B ILE 3.9 0.2 - - - -
310B ALA* 1.3 75.3 - - - +
312B ASN* 1.3 57.1 + - - -
313B ASP* 3.2 9.7 + - - +
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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
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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