Contacts of the helix formed by residues 313 - 333 (chain F) in PDB entry 3HYW
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 THR 313 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F PRO* 4.2 19.3 - - + -
312F LYS* 1.3 76.1 - - - +
314F GLY* 1.3 65.9 + - - +
315F MET* 3.8 2.6 + - - +
316F MET* 3.2 24.9 + - - +
317F ILE* 3.0 21.8 + - - +
345F ALA* 3.3 22.6 - - + +
346F ILE 5.1 0.3 + - - -
347F CSS 3.7 25.1 - - - -
363F VAL* 5.7 1.3 - - + -
441F FAD 3.5 18.4 - - - -
800F PS9 4.5 12.8 - - - -
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Residues in contact with GLY 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.6 8.7 - - - +
313F THR* 1.3 69.7 - - - +
315F MET* 1.3 56.0 + - - +
317F ILE* 3.2 8.1 + - - +
318F GLU* 2.8 35.3 + - - +
441F FAD 2.7 35.1 + - - -
500F DCQ 3.2 12.6 - - - -
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Residues in contact with MET 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F THR* 3.4 2.3 + - - +
314F GLY* 1.3 74.0 - - - +
316F MET* 1.3 62.3 + - - +
318F GLU* 3.3 3.8 + - + +
319F GLN* 3.0 35.8 + - + +
344F SER* 3.4 23.3 - - - +
345F ALA* 3.6 16.6 - - - -
346F ILE* 3.4 49.6 - - + +
359F PHE* 4.7 3.1 - - - -
407F LEU* 3.8 20.0 - - + -
413F VAL* 4.9 7.6 - - + -
441F FAD 4.3 0.8 + - - -
500F DCQ 2.7 44.3 + - + +
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Residues in contact with MET 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F ILE* 4.9 7.4 - - + -
310F VAL* 4.9 4.9 - - + -
311F PRO 3.4 21.5 - - - +
312F LYS* 4.1 10.5 - - + -
313F THR* 3.2 38.0 + - - +
315F MET* 1.3 76.3 - - - +
317F ILE* 1.3 58.5 + - - +
319F GLN* 3.3 7.5 + - - +
320F MET* 2.9 37.3 + - + +
343F LEU* 3.6 33.1 - - + +
344F SER 3.4 19.0 + - - +
363F VAL* 3.9 28.9 - - + -
364F ILE* 5.6 4.7 - - + -
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Residues in contact with ILE 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.0 8.3 - - + +
13F GLY* 3.5 35.7 - - - +
292F VAL* 3.8 1.7 - - + +
293F GLY* 3.6 27.1 - - - -
294F VAL 4.1 0.2 - - - +
312F LYS* 3.3 34.1 - - + +
313F THR 3.0 17.3 + - - +
314F GLY* 3.6 5.4 - - - +
316F MET* 1.3 74.6 - - - +
318F GLU* 1.3 59.7 + - - +
320F MET* 3.2 9.9 + - + +
321F ALA* 2.8 27.7 + - - +
441F FAD 3.5 31.0 - - - +
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Residues in contact with GLU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.7 8.3 - - + -
16F ALA* 4.9 3.1 - - + -
20F ASN* 4.6 0.9 + - - -
314F GLY* 2.8 17.4 + - - +
315F MET* 3.7 5.4 - - - +
317F ILE* 1.3 76.0 - - - +
319F GLN* 1.3 57.2 + - - +
321F ALA* 3.3 8.2 + - - +
322F MET* 3.0 45.9 + - + +
385F PHE* 4.2 1.2 - - - -
389F PHE* 3.5 27.3 - - + -
392F LYS* 3.5 18.5 + - - -
398F ILE* 3.8 19.6 - - + +
403F GLU* 3.8 8.5 - - - +
500F DCQ 3.3 33.3 + - + +
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Residues in contact with GLN 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F MET* 3.0 29.8 + - + +
316F MET 3.5 6.3 - - - +
317F ILE 3.2 0.2 - - - -
318F GLU* 1.3 74.0 - - + +
320F MET* 1.3 62.9 + - - +
322F MET* 3.4 10.7 + - + -
323F ALA* 3.0 23.6 + - - +
341F PRO* 3.5 10.7 - - + +
342F ARG* 4.3 1.5 - - - +
343F LEU* 2.7 31.2 + - - -
344F SER* 3.0 32.5 + - - +
413F VAL* 3.8 9.9 - - - +
415F PRO* 3.6 43.9 - - + +
416F ILE* 3.6 4.7 - - - +
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Residues in contact with MET 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F PHE* 3.5 43.1 - - + -
291F GLY 5.1 0.4 - - - +
292F VAL* 3.8 9.2 - - + -
293F GLY* 3.3 27.6 - - - +
296F THR* 4.2 1.3 - - - +
298F ILE* 4.0 4.7 - - + -
312F LYS* 3.8 32.3 - - + -
316F MET* 2.9 23.5 + - + +
317F ILE* 3.3 10.5 - - + +
319F GLN* 1.3 76.0 - - - +
321F ALA* 1.3 58.0 + - - +
323F ALA* 3.2 2.3 + - - +
324F VAL* 2.9 35.6 + - - +
341F PRO* 3.7 9.6 - - + +
343F LEU* 3.8 22.7 - - + -
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Residues in contact with ALA 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ALA* 3.6 27.1 - - + -
17F THR* 3.4 28.4 - - - +
20F ASN* 3.7 6.9 + - - +
292F VAL* 3.8 5.7 - - + +
317F ILE 2.8 16.1 + - - +
318F GLU 3.4 9.6 - - - +
319F GLN 3.3 0.2 - - - -
320F MET* 1.3 72.5 - - - +
322F MET* 1.3 56.4 + - - +
324F VAL* 3.9 2.0 - - - +
325F ALA* 2.9 32.7 + - - +
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Residues in contact with MET 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ASN* 3.6 19.3 - - - +
318F GLU* 3.0 38.3 + - + +
319F GLN* 3.7 9.2 - - + +
320F MET 3.3 0.2 - - - -
321F ALA* 1.3 73.0 - - - +
323F ALA* 1.3 65.1 + - - +
325F ALA* 3.5 1.1 + - - +
326F HIS* 3.1 36.0 + - + +
399F ALA* 4.5 22.9 - - + -
403F GLU* 6.1 0.4 - - - +
404F GLU* 5.0 7.0 - - + +
415F PRO* 3.7 38.4 - - + -
416F ILE* 3.9 13.0 - - + -
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Residues in contact with ALA 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F CYS 5.1 1.3 - - - +
281F PHE* 5.9 0.2 - - + -
319F GLN 3.0 17.5 + - - +
320F MET 3.2 4.2 + - - +
322F MET* 1.3 79.4 - - - +
324F VAL* 1.3 58.3 + - + +
326F HIS* 3.3 1.7 + - - +
327F ASN* 2.8 36.6 + - - +
339F TYR* 3.8 20.2 - - - +
340F ALA 4.2 0.4 - - - -
341F PRO* 3.7 29.2 - - + -
416F ILE* 3.8 10.3 - - + +
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Residues in contact with VAL 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F THR* 3.9 16.2 - - + +
102F VAL* 4.1 5.4 - - + -
280F CYS 4.1 1.8 - - - +
281F PHE* 3.8 28.9 - - + +
290F PHE* 3.6 35.2 - - + -
291F GLY 4.1 8.5 - - - +
292F VAL* 5.1 2.0 - - + -
320F MET 2.9 21.3 + - - +
321F ALA* 4.0 3.1 - - - +
323F ALA* 1.3 72.0 - - - +
325F ALA* 1.3 61.3 + - - +
327F ASN* 3.1 7.7 + - - +
328F ILE* 2.9 44.5 + - + +
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Residues in contact with ALA 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F THR* 4.2 2.4 - - + +
20F ASN* 3.5 29.2 - - + -
21F LEU* 3.7 28.5 - - + +
24F LEU* 3.9 6.7 - - + -
321F ALA 2.9 19.9 + - - +
322F MET 3.9 2.9 - - - +
324F VAL* 1.3 77.1 - - - +
326F HIS* 1.3 58.1 + - + +
329F VAL* 3.0 33.8 + - - +
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Residues in contact with HIS 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F LEU* 3.9 35.5 - - + +
322F MET* 3.1 32.6 + - + +
323F ALA 3.6 3.8 - - - +
325F ALA* 1.3 73.7 - - + +
327F ASN* 1.3 60.7 + - - +
329F VAL* 4.6 2.2 - - - +
330F ASN* 2.8 42.8 + - - +
339F TYR* 3.7 27.0 + + + -
416F ILE* 3.8 20.5 - - + +
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Residues in contact with ASN 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F CYS* 3.2 21.7 - - - +
290F PHE* 3.7 20.0 - - + -
323F ALA 2.8 22.0 + - - +
324F VAL 3.1 4.5 + - - +
326F HIS* 1.3 76.1 - - - +
328F ILE* 1.3 57.6 + - - +
330F ASN* 3.9 4.0 - - - +
331F ASP* 3.0 28.4 + - - +
338F LYS* 3.4 27.5 - - - +
339F TYR* 2.8 51.2 - - - +
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Residues in contact with ILE 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 4.6 7.4 - - + -
21F LEU* 3.8 25.1 - - + -
100F TYR* 3.8 32.5 - - + -
102F VAL* 3.6 30.7 - - + -
290F PHE* 3.4 28.0 - - + -
324F VAL* 2.9 28.2 + - + +
327F ASN* 1.3 73.9 - - - +
329F VAL* 1.3 66.2 + - - +
331F ASP* 3.2 7.3 + - - +
332F ILE* 3.0 37.6 + - + +
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Residues in contact with VAL 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 4.2 14.1 - - + +
24F LEU* 3.9 37.5 - - + +
25F MET* 3.9 33.7 - - + -
28F LEU* 4.8 2.2 - - + -
325F ALA 3.0 21.0 + - - +
326F HIS* 4.1 2.7 - - - +
328F ILE* 1.3 74.8 - - - +
330F ASN* 1.3 65.9 + - - +
332F ILE* 3.2 9.6 + - - +
333F ARG* 3.0 41.3 + - - +
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Residues in contact with ASN 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F HIS* 2.8 28.8 + - - +
327F ASN* 4.0 3.6 - - - +
329F VAL* 1.3 80.2 - - - +
331F ASP* 1.3 57.8 + - - +
333F ARG* 3.4 2.3 + - - +
334F ASN 3.1 6.8 + - - -
335F ASN* 2.7 65.1 + - - +
337F ASP* 2.7 39.4 + - - +
338F LYS* 5.7 0.4 - - + -
339F TYR* 3.7 15.9 + - - -
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Residues in contact with ASP 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F TYR* 2.5 36.3 + - + +
282F GLN* 6.2 1.8 - - - -
287F LYS 5.7 2.2 - - - +
290F PHE* 6.0 2.2 - - + -
327F ASN 3.0 18.5 + - - +
328F ILE* 3.2 4.7 + - - +
330F ASN* 1.3 72.7 - - - +
332F ILE* 1.3 65.7 + - - +
334F ASN* 3.3 18.3 + - - +
335F ASN 4.9 1.6 - - - -
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Residues in contact with ILE 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LYS* 4.1 22.2 - - + +
25F MET* 4.0 25.6 - - + -
28F LEU* 3.6 30.5 - - + -
100F TYR* 3.4 26.2 - - + +
328F ILE* 3.0 36.0 + - + +
329F VAL* 3.5 7.6 - - - +
331F ASP* 1.3 78.1 - - - +
333F ARG* 1.3 59.0 + - + +
334F ASN* 3.4 6.1 + - - -
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Residues in contact with ARG 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F LEU 5.3 5.9 + - - -
25F MET* 3.5 33.2 - - + +
329F VAL* 3.0 25.7 + - - +
330F ASN* 4.3 4.7 - - - +
332F ILE* 1.3 76.7 - - + +
334F ASN* 1.3 70.0 + - - +
335F ASN* 3.2 7.5 + - + +
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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