Contacts of the helix formed by residues 305 - 328 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLU 3.5 4.2 + - - +
304A HIS* 1.3 73.4 - - - +
306A LYS* 1.3 69.0 + - - +
307A VAL* 3.1 23.1 + - - +
308A SER* 3.2 27.8 + - - -
309A ARG* 3.1 28.2 + - - +
390A GLN* 3.3 21.5 + - - +
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Residues in contact with LYS 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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305A ASP* 1.3 73.3 - - - +
307A VAL* 1.3 73.1 + - + +
309A ARG* 4.0 11.9 + - - +
310A ASP* 3.2 37.3 + - - +
390A GLN* 2.9 31.7 + - - +
478A GLU* 5.9 3.2 - - + +
479A SER* 2.8 25.0 + - - +
480A ASN* 3.7 36.1 - - + +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 3.1 21.1 - - - +
306A LYS* 1.3 90.6 - - + +
308A SER* 1.3 62.5 + - - +
310A ASP* 3.3 6.4 + - + +
311A GLU* 2.8 29.3 + - - +
390A GLN* 5.6 1.6 - - - +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A HIS* 2.8 30.4 + - - -
305A ASP* 3.2 29.9 + - - -
307A VAL* 1.3 77.8 - - - +
309A ARG* 1.3 59.0 + - - +
311A GLU* 3.5 7.6 + - - +
312A ALA* 3.0 22.0 + - - +
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.3 17.5 + - + +
299A PHE* 4.5 11.9 - - + -
304A HIS* 3.1 43.0 + - + +
305A ASP* 3.1 32.3 + - - +
306A LYS* 4.0 8.8 + - - +
308A SER* 1.3 78.9 + - - +
310A ASP* 1.3 68.3 + - - +
312A ALA* 3.3 1.8 + - - +
313A VAL* 3.0 24.7 + - + +
359A CYS* 3.6 42.8 + - - +
360A ASP* 4.1 11.5 - - - +
480A ASN* 5.5 2.8 - - - +
534A LEU* 4.3 13.5 - - - +
536A ILE* 3.9 30.7 - - + +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS* 3.2 30.5 + - - +
307A VAL* 3.7 6.9 - - - +
309A ARG* 1.3 81.0 + - - +
311A GLU* 1.3 57.5 + - - +
313A VAL* 3.5 6.2 + - - +
314A ASN* 3.0 28.8 + - - +
536A ILE* 4.8 17.7 - - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL 2.8 17.2 + - - +
308A SER* 3.7 7.6 - - - +
310A ASP* 1.3 75.2 - - - +
312A ALA* 1.3 63.2 + - - +
314A ASN* 3.2 6.2 + - + +
315A LYS* 2.9 36.7 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.0 18.8 - - + -
304A HIS* 3.7 19.5 - - + +
308A SER 3.0 17.6 + - - +
309A ARG 3.3 4.0 + - - +
311A GLU* 1.3 78.7 + - - +
313A VAL* 1.3 61.2 + - - +
315A LYS* 3.4 9.1 + - - +
316A ILE* 3.3 29.3 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.0 13.0 - - + -
298A VAL* 4.0 11.4 - - + -
299A PHE* 3.8 33.0 - - + -
309A ARG* 3.0 22.2 + - + +
310A ASP* 3.9 6.7 - - - +
312A ALA* 1.3 75.3 - - - +
314A ASN* 1.3 58.9 + - - +
316A ILE* 3.3 4.1 + - - +
317A ARG* 3.0 27.8 + - - +
340A PHE* 3.6 27.3 - - + -
344A ALA* 5.1 4.0 - - + -
536A ILE* 5.3 2.9 - - + -
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Residues in contact with ASN 314 (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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310A ASP 3.0 18.3 + - - +
311A GLU* 3.2 7.2 + - + +
313A VAL* 1.3 75.5 - - - +
315A LYS* 1.3 65.2 + - - +
317A ARG* 3.0 39.7 + - - +
318A LEU* 3.0 43.1 + - + +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 4.0 18.8 + - - +
311A GLU* 2.9 27.2 + - - +
312A ALA* 3.6 9.6 - - - +
313A VAL 3.3 0.2 - - - -
314A ASN* 1.3 77.3 - - - +
316A ILE* 1.3 63.8 + - - +
318A LEU* 3.9 8.7 + - + +
319A ASP* 3.7 26.9 + - - +
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Residues in contact with ILE 316 (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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291A ALA* 4.1 16.6 - - + -
294A ARG* 3.6 73.1 - - + +
295A LEU* 4.0 11.7 - - + +
298A VAL* 3.7 14.8 - - + -
312A ALA 3.3 16.4 - - - +
313A VAL 3.3 6.1 + - - +
314A ASN 3.1 0.4 - - - -
315A LYS* 1.3 80.2 - - + +
317A ARG* 1.3 63.6 + - - +
319A ASP* 3.7 1.3 + - - +
320A THR* 2.8 40.3 + - - +
340A PHE* 4.0 6.1 - - + -
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Residues in contact with ARG 317 (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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313A VAL* 3.0 13.2 + - - +
314A ASN* 3.0 35.1 + - - +
316A ILE* 1.3 79.2 - - - +
318A LEU* 1.3 60.7 + - - +
321A GLU* 2.7 77.6 + - + +
337A ILE* 3.7 18.8 + - - +
340A PHE* 3.5 40.4 - - + -
341A ASN* 3.2 29.3 + - - +
539A TYR* 5.6 0.8 + - - -
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Residues in contact with LEU 318 (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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314A ASN* 3.0 38.2 + - + +
315A LYS* 4.4 8.5 - - + +
317A ARG* 1.3 84.0 - - - +
319A ASP* 1.3 66.9 + - - +
321A GLU* 4.1 6.5 - - - +
322A GLU* 3.2 23.4 + - - +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 3.5 33.5 + - - +
315A LYS* 3.7 18.4 + - - +
316A ILE 4.1 0.9 - - - +
317A ARG 3.3 0.2 - - - -
318A LEU* 1.3 81.7 - - - +
320A THR* 1.3 60.9 + - - +
322A GLU* 3.4 4.7 + - - +
323A GLN* 3.2 35.6 + - - +
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 4.1 16.6 - - + +
290A LEU* 3.8 35.7 + - + +
291A ALA* 3.9 13.5 - - + +
294A ARG* 5.0 2.4 + - - -
316A ILE* 2.8 27.0 + - - +
317A ARG 3.8 1.8 - - - -
319A ASP* 1.3 75.7 - - - +
321A GLU* 1.3 60.6 + - - +
323A GLN* 3.0 4.8 + - - +
324A LEU* 2.8 43.6 + - + +
340A PHE* 4.3 11.0 - - + -
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Residues in contact with GLU 321 (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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317A ARG* 2.7 57.2 + - + +
318A LEU* 4.4 6.5 - - - +
320A THR* 1.3 71.7 - - - +
322A GLU* 1.3 60.7 + - - +
324A LEU* 3.9 2.5 - - + -
325A LYS* 3.3 31.2 + - + +
336A ILE* 3.8 26.3 - - + +
337A ILE* 3.3 39.8 - - - +
340A PHE* 4.3 7.6 - - + +
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Residues in contact with GLU 322 (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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318A LEU 3.2 18.3 + - - +
319A ASP* 3.7 6.5 - - - +
320A THR 3.1 0.8 - - - -
321A GLU* 1.3 76.9 - - - +
323A GLN* 1.3 65.7 + - + +
325A LYS* 3.3 29.5 + - - +
326A GLU* 3.3 44.5 + - + +
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Residues in contact with GLN 323 (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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286A TYR* 4.4 9.4 + - + +
290A LEU* 3.6 36.1 - - + +
294A ARG* 5.3 5.3 - - - +
319A ASP* 3.2 27.2 + - - +
320A THR* 3.0 2.6 + - - +
322A GLU* 1.3 76.9 - - + +
324A LEU* 1.3 58.4 + - - +
326A GLU* 3.3 9.1 + - - +
327A LYS* 2.9 29.0 + - - +
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Residues in contact with LEU 324 (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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283A ILE* 4.1 4.9 - - + -
286A TYR* 3.6 28.5 - - + -
287A THR* 3.4 35.4 - - + +
290A LEU* 4.5 1.6 - - + -
320A THR* 2.8 30.3 + - + +
321A GLU* 4.0 2.9 - - + +
323A GLN* 1.3 77.7 - - - +
325A LYS* 1.3 53.1 + - - +
327A LYS* 4.7 0.7 - - - -
328A PHE* 2.7 53.7 + - + +
336A ILE* 3.7 46.0 - - + +
339A SER* 4.4 4.0 - - - -
340A PHE* 4.9 0.9 - - + +
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Residues in contact with LYS 325 (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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321A GLU* 3.3 16.5 + - + +
322A GLU* 3.3 30.3 + - - +
324A LEU* 1.3 78.1 - - - +
326A GLU* 1.3 68.6 + - - +
328A PHE 3.9 7.0 - - - -
329A PRO* 3.1 26.7 - - + +
331A ALA 6.1 0.7 - - - +
333A PRO* 6.1 5.4 - - + -
336A ILE* 4.3 18.6 - - + -
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Residues in contact with GLU 326 (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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322A GLU* 3.3 36.9 - - + +
323A GLN* 3.3 8.7 + - - +
324A LEU 3.2 0.6 - - - -
325A LYS* 1.3 80.1 - - - +
327A LYS* 1.3 65.0 + - - +
329A PRO* 3.5 13.3 - - - +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 4.0 38.5 + - + +
323A GLN 2.9 16.9 + - - +
326A GLU* 1.3 77.1 - - - +
328A PHE* 1.3 90.3 + - + +
329A PRO* 3.5 6.2 - - - +
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Residues in contact with PHE 328 (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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280A SER* 5.8 0.2 - - - -
282A GLU* 4.2 12.1 - - + -
283A ILE* 3.7 50.3 - - + -
286A TYR* 3.9 26.2 - + + -
324A LEU* 2.7 26.3 + - + +
325A LYS* 3.3 10.8 - - - +
327A LYS* 1.3 100.4 - - + +
329A PRO* 1.3 66.9 - - - +
330A GLU* 3.2 3.1 - - - +
331A ALA* 3.2 31.0 + - + +
336A ILE* 4.4 0.5 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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