Contacts of the helix formed by residues 315 - 336 (chain Q) in PDB entry 5KZ5
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 MET 315 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169N GLU* 3.8 20.1 - - + +
241Q PRO* 4.0 20.9 - - + -
311Q ALA 3.2 20.2 + - - +
312Q GLN* 3.5 35.7 - - - +
313Q GLN 3.4 2.2 + - - -
314Q GLU* 1.4 73.4 - - - +
316Q GLU* 1.4 65.1 + - - +
318Q ASP* 3.9 4.5 - - - -
319Q HIS* 2.9 40.5 + - + +
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Residues in contact with GLU 316 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N LYS* 3.6 23.2 + - - -
169N GLU 3.3 24.2 + - - +
170N GLY* 3.4 27.5 - - - +
314Q GLU 3.1 1.4 + - - -
315Q MET* 1.4 75.7 - - - +
317Q TYR* 1.4 62.9 + - - +
319Q HIS* 3.1 25.5 + - + -
320Q LYS* 3.4 39.9 + - + +
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Residues in contact with TYR 317 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J LEU* 3.6 40.3 + - + +
168N ALA* 3.9 16.6 + - + +
314Q GLU* 3.2 16.7 + - + +
316Q GLU* 1.4 77.1 - - - +
318Q ASP* 1.4 60.4 + - - +
320Q LYS* 3.8 5.7 + - + +
321Q ARG* 3.5 22.4 + - - +
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Residues in contact with ASP 318 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J LEU* 3.5 18.2 - - + +
44J THR 4.3 4.5 - - - +
46J ILE* 3.4 29.0 - - - +
310Q VAL 5.6 0.4 - - - -
311Q ALA* 4.7 7.3 - - - +
314Q GLU* 3.2 33.1 + - + +
315Q MET* 3.9 5.6 - - - +
317Q TYR* 1.4 77.6 - - - +
319Q HIS* 1.3 62.6 + - - +
321Q ARG* 3.4 4.3 + - - +
322Q ILE* 3.3 45.3 + - - +
412Q ARG* 3.8 14.2 + - - -
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Residues in contact with HIS 319 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239Q LYS 6.0 2.0 - - - +
315Q MET* 2.9 45.2 + - + +
316Q GLU* 3.1 28.8 + - + -
318Q ASP* 1.3 72.5 + - - +
320Q LYS* 1.3 86.8 + - + +
322Q ILE* 3.5 8.7 + - - +
323Q SER* 3.1 30.0 + - - -
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Residues in contact with LYS 320 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316Q GLU* 3.4 43.6 + - + +
317Q TYR* 4.1 6.3 - - + +
318Q ASP 3.4 0.6 - - - -
319Q HIS* 1.3 93.1 + - - +
321Q ARG* 1.4 62.2 + - - +
323Q SER* 3.0 19.6 + - - -
324Q LYS* 3.4 14.0 + - - +
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Residues in contact with ARG 321 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J LEU* 4.0 34.0 - - + +
43J ARG* 5.9 9.5 - - + +
317Q TYR* 3.5 13.4 + - - +
318Q ASP 3.4 8.9 + - - +
319Q HIS 3.3 0.4 - - - -
320Q LYS* 1.4 79.6 - - - +
322Q ILE* 1.4 61.8 + - + +
324Q LYS* 3.7 19.4 + - - +
325Q LEU* 3.3 53.4 + - + +
412Q ARG* 5.6 3.1 - - - +
415Q THR* 5.8 2.6 - - - +
416Q GLU* 3.2 42.1 + - - +
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Residues in contact with ILE 322 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE* 3.6 21.8 - - + -
239Q LYS* 4.9 13.2 - - + +
318Q ASP* 3.3 41.7 + - - +
319Q HIS* 4.0 7.0 - - - +
320Q LYS 3.4 0.2 - - - -
321Q ARG* 1.4 75.2 - - + +
323Q SER* 1.3 57.5 + - - +
325Q LEU* 3.5 9.5 + - - +
326Q SER* 3.1 27.0 + - - -
351Q PRO* 4.2 22.9 - - + -
412Q ARG* 3.8 32.5 - - + +
414Q THR* 5.6 3.2 - - - +
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Residues in contact with SER 323 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319Q HIS* 3.1 18.7 + - - -
320Q LYS* 3.0 20.8 + - - -
322Q ILE* 1.3 75.4 - - - +
324Q LYS* 1.4 59.7 + - - +
326Q SER* 3.1 18.2 + - - -
327Q GLU* 3.3 18.3 + - - +
349Q HIS* 5.0 0.9 - - - -
351Q PRO* 5.4 5.4 - - - -
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Residues in contact with LYS 324 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320Q LYS 3.4 13.6 + - - +
321Q ARG* 3.8 18.8 - - - +
322Q ILE 3.4 0.2 - - - -
323Q SER* 1.4 76.9 + - - +
325Q LEU* 1.3 65.9 + - + +
327Q GLU* 3.0 31.1 - - - +
328Q ARG* 3.6 12.9 - - - +
416Q GLU* 3.3 28.7 + - - -
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Residues in contact with LEU 325 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Q ARG* 3.3 39.0 + - + +
322Q ILE* 3.7 9.9 - - - +
323Q SER 3.4 0.4 - - - -
324Q LYS* 1.3 77.5 - - - +
326Q SER* 1.3 64.2 + - - +
328Q ARG* 3.6 6.3 + - - +
329Q LEU* 3.2 22.5 + - - +
412Q ARG* 4.5 6.1 - - - +
414Q THR* 3.6 34.3 - - + +
415Q THR* 3.8 10.8 - - + +
416Q GLU* 3.5 48.5 - - - +
419Q VAL* 3.6 12.4 - - + +
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Residues in contact with SER 326 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322Q ILE* 3.1 12.5 + - - -
323Q SER* 3.1 18.2 + - - -
325Q LEU* 1.3 79.7 - - - +
327Q GLU* 1.4 59.4 + - - +
329Q LEU* 3.4 10.0 + - - +
330Q ILE* 3.4 27.5 + - - +
349Q HIS* 3.4 19.8 - - - -
351Q PRO* 3.9 30.3 - - - +
414Q THR* 4.7 7.9 - - - -
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Residues in contact with GLU 327 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323Q SER 3.3 15.9 - - - +
324Q LYS* 3.0 24.0 - - - +
326Q SER* 1.4 77.6 + - - +
328Q ARG* 1.3 79.0 + - - +
330Q ILE* 3.7 2.5 + - - +
331Q GLN* 3.2 47.2 + - - +
346Q PRO 5.0 6.8 - - - +
347Q LYS* 6.2 0.9 - - - -
349Q HIS* 3.6 21.1 - - - +
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Residues in contact with ARG 328 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324Q LYS* 3.6 16.1 + - - +
325Q LEU* 3.7 7.6 - - - +
326Q SER 3.3 0.2 - - - -
327Q GLU* 1.3 95.0 + - - +
329Q LEU* 1.3 54.6 + - - +
331Q GLN* 3.4 11.2 + - - +
332Q ASN* 3.0 45.5 + - - +
416Q GLU* 3.1 29.2 + - - -
419Q VAL* 3.6 29.9 - - + +
420Q ASP* 3.7 31.5 + - - +
423Q VAL* 4.4 11.5 - - - +
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Residues in contact with LEU 329 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325Q LEU 3.2 11.2 + - - +
326Q SER* 3.5 13.5 - - - +
328Q ARG* 1.3 77.6 - - - +
330Q ILE* 1.4 60.6 + - + +
332Q ASN* 3.3 4.7 + - - +
333Q ILE* 3.3 37.8 + - + +
354Q ILE* 4.7 14.6 - - + -
408Q PHE* 5.0 2.0 - - + -
410Q ILE* 4.0 27.6 - - + -
414Q THR* 4.2 14.8 - - + +
418Q GLU* 4.7 4.9 - - + +
419Q VAL* 3.8 26.4 - - + +
422Q THR* 3.6 36.1 - - + +
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Residues in contact with ILE 330 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326Q SER* 3.4 10.4 + - - +
327Q GLU* 4.2 4.0 - - - +
328Q ARG 3.4 0.4 - - - -
329Q LEU* 1.4 73.7 - - + +
331Q GLN* 1.3 67.4 + - + +
333Q ILE* 3.6 7.9 + - - +
334Q MET* 3.3 24.3 + - + +
342Q MET* 3.6 38.6 - - + -
346Q PRO* 5.2 6.5 - - + +
349Q HIS* 3.6 46.7 - - + +
350Q TYR 5.2 0.7 - - - +
351Q PRO* 6.2 0.2 - - + -
353Q CYS 5.2 2.2 - - - +
354Q ILE* 4.1 36.6 - - + -
356Q LEU* 5.6 3.8 - - + +
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Residues in contact with GLN 331 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327Q GLU* 3.2 42.8 + - - +
328Q ARG* 3.6 11.6 - - - +
330Q ILE* 1.3 80.7 - - + +
332Q ASN* 1.4 64.5 + - - +
334Q MET* 3.4 4.1 + - - +
335Q LYS* 3.2 59.1 + - + +
346Q PRO* 5.5 11.9 - - + +
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Residues in contact with ASN 332 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328Q ARG* 3.0 34.8 + - - +
329Q LEU* 3.3 6.7 + - - +
331Q GLN* 1.4 77.6 - - - +
333Q ILE* 1.4 64.2 + - + +
335Q LYS* 4.1 3.2 - - - +
336Q SER* 3.2 27.4 + - - -
419Q VAL* 3.5 24.9 + - - +
422Q THR* 5.1 1.8 - - + -
423Q VAL* 3.3 42.3 - - + +
426Q CYS* 5.1 1.3 - - - -
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Residues in contact with ILE 333 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329Q LEU* 3.3 29.1 + - + +
330Q ILE* 3.9 7.9 - - - +
332Q ASN* 1.4 74.5 - - - +
334Q MET* 1.4 64.6 + - - +
336Q SER* 3.4 1.2 + - - -
337Q LEU* 3.3 43.0 + - + +
340Q VAL* 5.0 0.6 - - + +
354Q ILE* 5.4 3.1 - - + -
356Q LEU* 4.0 23.8 - - + -
408Q PHE* 4.0 26.7 - - + -
422Q THR* 3.5 28.5 - - + -
425Q LYS* 5.0 8.1 - - - +
426Q CYS* 3.8 12.8 - - - -
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Residues in contact with MET 334 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330Q ILE* 3.3 16.6 + - + +
331Q GLN* 3.7 6.3 - - - +
332Q ASN 3.3 0.2 - - - -
333Q ILE* 1.4 78.7 - - - +
335Q LYS* 1.3 60.4 + - + +
337Q LEU 3.0 25.5 - - - +
340Q VAL* 3.5 39.0 - - + +
341Q VAL* 4.4 0.7 - - - -
342Q MET* 3.5 35.0 - - + +
356Q LEU* 3.6 27.8 - - + -
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Residues in contact with LYS 335 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331Q GLN* 3.2 45.2 + - + +
332Q ASN* 4.3 4.0 - - - +
334Q MET* 1.3 78.6 - - + +
336Q SER* 1.3 59.8 + - - +
337Q LEU 3.4 1.4 - - - +
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Residues in contact with SER 336 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332Q ASN 3.2 20.6 + - - -
333Q ILE 3.9 0.9 - - - -
334Q MET 3.3 0.2 - - - -
335Q LYS* 1.3 78.5 - - - +
337Q LEU* 1.3 60.3 + - - +
338Q PRO* 4.2 2.3 - - - +
423Q VAL* 4.1 7.9 + - - +
426Q CYS* 3.4 23.2 - - - +
427Q ILE* 3.3 28.6 - - - +
430Q VAL* 4.1 14.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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