Contacts of the helix formed by residues 305 - 328 (chain B) in PDB entry 5ZF6
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 ASP 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLU 3.5 4.0 + - - +
304B HIS* 1.3 75.6 - - - +
306B LYS* 1.3 66.4 + - - +
307B VAL* 2.9 18.7 + - - +
308B SER* 2.8 47.6 + - - -
309B ARG* 3.2 26.2 + - - +
390B GLN* 3.4 14.4 - - - +
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ASP* 1.3 72.9 - - - +
307B VAL* 1.3 71.5 + - + +
309B ARG* 3.9 13.5 + - - +
310B ASP* 3.4 36.7 + - - +
390B GLN* 2.9 29.7 + - - +
478B GLU* 5.1 5.0 - - - +
479B SER* 3.2 30.8 + - - +
480B ASN* 3.5 33.0 - - + +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ASP* 2.9 7.8 + - - +
306B LYS* 1.3 93.5 - - + +
308B SER* 1.3 61.1 + - - +
309B ARG 3.2 1.6 - - - -
310B ASP* 3.3 4.6 + - + +
311B GLU* 2.9 56.6 + - + +
390B GLN* 5.2 5.4 - - - +
478B GLU* 5.7 0.9 - - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU 4.8 0.2 + - - -
304B HIS* 3.1 20.7 + - - -
305B ASP* 2.8 52.2 + - - -
307B VAL* 1.3 73.1 - - - +
309B ARG* 1.3 56.7 + - - +
311B GLU* 4.0 9.6 - - - +
312B ALA* 3.0 26.9 + - - +
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B VAL* 3.7 21.4 + - + +
299B PHE* 4.0 13.9 - - + -
304B HIS* 3.5 36.3 + - + +
305B ASP 3.2 23.5 + - - +
306B LYS* 3.9 14.8 + - - +
308B SER* 1.3 79.5 + - - +
310B ASP* 1.3 66.9 + - - +
312B ALA* 3.4 1.3 + - - +
313B VAL* 3.2 31.1 + - + +
359B CYS* 3.6 25.8 + - - +
360B ASP* 4.3 10.9 - - - +
480B ASN* 5.7 1.4 + - - +
534B LEU* 3.7 21.2 - - - +
536B ILE* 3.9 37.8 - - + +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 3.4 31.4 + - - +
307B VAL* 3.3 7.9 + - + +
309B ARG* 1.3 82.5 + - - +
311B GLU* 1.3 62.7 + - + +
313B VAL* 3.3 12.9 - - - +
314B ASN* 3.3 20.6 + - - +
317B ARG* 4.9 1.6 + - - -
536B ILE* 4.5 20.3 - - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 2.9 40.5 + - + +
308B SER* 4.2 6.6 - - - +
310B ASP* 1.3 76.2 - - + +
312B ALA* 1.3 60.2 + - - +
314B ASN* 3.6 7.9 - - - +
315B LYS* 2.9 28.1 + - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B VAL* 3.9 16.2 - - + -
304B HIS* 3.6 20.6 - - + -
308B SER 3.0 20.4 + - - +
309B ARG 3.7 4.7 - - - +
310B ASP 3.3 0.4 - - - -
311B GLU* 1.3 77.3 - - - +
313B VAL* 1.3 62.1 + - - +
315B LYS* 3.3 9.0 + - - +
316B ILE* 3.2 27.4 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.1 14.6 - - + -
298B VAL* 3.9 12.8 - - + -
299B PHE* 3.8 30.3 - - + -
309B ARG* 3.2 14.8 - - + +
310B ASP* 3.3 17.0 - - - +
312B ALA* 1.3 76.8 - - - +
314B ASN* 1.3 55.4 + - - +
316B ILE* 3.4 9.6 + - - +
317B ARG* 2.7 51.8 + - - +
340B PHE* 3.4 11.2 - - + -
344B ALA* 5.8 2.7 - - + -
536B ILE* 5.8 1.8 - - + -
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Residues in contact with ASN 314 (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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310B ASP 3.3 13.9 + - - +
311B GLU* 3.2 8.9 + - + +
312B ALA 3.2 0.8 - - - -
313B VAL* 1.3 79.9 - - - +
315B LYS* 1.3 59.7 + - - +
317B ARG* 3.1 43.2 - - - +
318B LEU* 2.9 47.1 + - - +
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 4.3 10.5 - - - +
311B GLU 2.9 14.1 + - - +
312B ALA* 3.7 11.4 - - - +
314B ASN* 1.3 73.3 - - - +
316B ILE* 1.3 64.6 + - - +
318B LEU* 3.2 11.5 + - + +
319B ASP* 2.8 38.8 + - - +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 4.1 23.1 - - + -
294B ARG* 3.3 75.4 - - + +
295B LEU* 3.9 11.7 - - + +
298B VAL* 3.7 20.0 - - + -
312B ALA 3.2 11.8 + - - +
313B VAL* 3.6 7.0 - - - +
315B LYS* 1.3 77.9 - - + +
317B ARG* 1.3 52.2 + - - +
319B ASP* 3.6 0.5 + - - +
320B THR* 2.7 35.6 + - + +
340B PHE* 4.1 5.4 - - + -
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP 4.9 1.2 + - - -
313B VAL* 2.7 36.2 + - - +
314B ASN* 3.0 35.4 + - - +
316B ILE* 1.3 77.7 - - - +
318B LEU* 1.3 64.4 + - + +
320B THR* 3.2 4.0 + - - -
321B GLU* 2.9 51.2 - - - +
337B ILE* 4.8 14.8 - - + +
340B PHE* 3.5 28.6 - - + -
341B ASN* 3.2 25.9 + - - +
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Residues in contact with LEU 318 (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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314B ASN* 2.9 37.4 + - - +
315B LYS* 3.2 11.2 + - + +
317B ARG* 1.3 82.4 - - + +
319B ASP* 1.3 69.4 + - - +
320B THR 3.4 0.3 + - - -
321B GLU* 3.9 5.9 + - - +
322B GLU* 3.5 34.0 + - - +
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 3.4 33.9 + - - +
315B LYS* 2.8 26.4 + - - +
316B ILE 3.6 0.6 + - - +
317B ARG 3.4 0.2 - - - -
318B LEU* 1.3 82.5 - - - +
320B THR* 1.3 62.2 + - - +
322B GLU* 4.3 5.7 + - - +
323B GLN* 3.7 23.8 + - - +
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Residues in contact with THR 320 (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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287B THR* 5.4 1.8 - - - -
290B LEU* 3.7 27.9 - - + +
291B ALA* 3.9 24.5 - - + -
294B ARG* 4.6 6.1 - - - +
316B ILE* 2.7 29.1 + - + +
317B ARG 3.2 8.8 + - - -
319B ASP* 1.3 78.7 - - - +
321B GLU* 1.3 59.5 + - - +
323B GLN* 3.2 11.6 - - - +
324B LEU* 2.8 32.8 + - - +
340B PHE* 3.7 16.0 - - - -
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Residues in contact with GLU 321 (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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317B ARG* 2.9 48.6 + - - +
318B LEU* 3.9 3.7 + - - +
319B ASP 3.6 0.2 - - - -
320B THR* 1.3 76.3 - - - +
322B GLU* 1.3 57.1 + - + +
323B GLN 3.1 1.1 - - - -
324B LEU* 3.3 13.0 - - + +
325B LYS* 2.6 39.5 + - - +
336B ILE* 3.5 29.3 - - + +
337B ILE* 3.1 28.9 - - - +
340B PHE* 4.6 6.6 - - + +
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Residues in contact with GLU 322 (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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318B LEU* 3.5 28.4 + - - +
319B ASP* 4.6 4.7 - - - +
320B THR 3.5 0.2 - - - -
321B GLU* 1.3 76.8 - - + +
323B GLN* 1.3 59.9 + - - +
325B LYS* 3.7 7.2 + - - +
326B GLU* 3.3 25.3 + - - +
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Residues in contact with GLN 323 (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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286B TYR* 4.3 10.5 + - - +
290B LEU* 3.8 30.8 - - + +
319B ASP* 3.7 17.4 + - - +
320B THR* 3.2 15.0 + - - +
321B GLU 3.1 0.4 - - - -
322B GLU* 1.3 79.5 - - - +
324B LEU* 1.3 60.0 + - - +
326B GLU* 3.5 7.3 + - + +
327B LYS* 3.3 21.0 + - - +
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Residues in contact with LEU 324 (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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283B ILE* 4.2 6.1 - - + -
286B TYR* 3.5 27.8 - - + -
287B THR* 3.5 42.8 - - + +
290B LEU* 4.5 3.6 - - + -
320B THR* 2.8 20.5 + - - +
321B GLU* 2.8 15.6 + - + +
323B GLN* 1.3 74.6 - - - +
325B LYS* 1.3 60.1 + - - +
327B LYS* 3.1 3.8 + - - +
328B PHE* 2.8 49.0 + - + +
336B ILE* 3.7 36.6 - - + +
340B PHE* 5.4 0.4 - - + -
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Residues in contact with LYS 325 (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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321B GLU* 2.6 20.0 + - - +
322B GLU* 4.0 8.5 - - - +
324B LEU* 1.3 72.8 - - - +
326B GLU* 1.3 61.0 + - - +
328B PHE 4.3 7.6 - - - +
329B PRO* 3.4 27.0 - - + +
331B ALA 5.5 4.3 - - - -
333B PRO* 4.5 21.2 + - - +
336B ILE* 4.6 22.8 - - - +
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Residues in contact with GLU 326 (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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322B GLU 3.3 16.8 + - - +
323B GLN* 3.8 8.1 - - + +
324B LEU 3.2 0.8 - - - -
325B LYS* 1.3 80.0 - - + +
327B LYS* 1.3 59.9 + - - +
329B PRO* 4.1 9.4 - - - +
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Residues in contact with LYS 327 (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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286B TYR* 3.7 38.7 - - + +
323B GLN 3.3 14.8 + - - +
324B LEU 3.1 4.9 + - - +
326B GLU* 1.3 79.2 - - - +
328B PHE* 1.3 97.2 + - + +
329B PRO* 3.3 8.8 - - - +
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Residues in contact with PHE 328 (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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282B GLU* 3.9 29.2 - - + -
283B ILE* 3.8 36.6 - - + -
286B TYR* 3.8 24.2 - + + -
324B LEU* 2.8 26.5 + - + +
325B LYS* 3.6 9.9 - - - +
327B LYS* 1.3 105.8 - - + +
329B PRO* 1.3 64.8 - - - +
330B GLU* 3.2 3.8 - - + +
331B ALA* 3.2 30.6 + - + +
336B ILE* 4.6 1.1 - - + +
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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