Contacts of the helix formed by residues 280 - 301 (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 SER 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A THR 3.6 1.5 + - - -
279A PRO* 1.3 76.2 - - - +
281A PRO* 1.3 72.4 - - - +
282A GLU* 3.1 20.1 + - - +
283A ILE* 3.2 19.7 + - - +
284A VAL* 3.0 21.5 + - - +
328A PHE* 5.8 0.2 - - - -
335A GLU* 3.4 14.2 + - - -
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Residues in contact with PRO 281 (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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279A PRO 4.2 2.9 - - - +
280A SER* 1.3 86.7 - - - +
282A GLU* 1.3 61.2 + - - +
284A VAL* 3.8 6.8 - - + +
285A LYS* 2.7 37.9 + - - +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 3.1 21.5 + - - +
281A PRO* 1.3 80.7 - - - +
283A ILE* 1.3 57.9 + - - +
285A LYS* 3.1 9.5 + - - +
286A TYR* 2.9 29.8 + - - +
328A PHE* 4.2 15.2 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 4.2 0.9 - - + -
280A SER* 3.2 36.7 + - - +
282A GLU* 1.3 79.3 - - - +
284A VAL* 1.3 52.3 + - - +
286A TYR* 3.9 0.5 - - - +
287A THR* 2.4 40.4 + - - +
324A LEU* 4.1 4.3 - - + -
328A PHE* 3.7 35.9 - - + -
331A ALA* 4.1 13.2 - - + -
335A GLU* 3.9 17.0 - - + +
336A ILE* 3.7 30.3 - - + -
339A SER* 3.2 24.5 - - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 3.6 33.9 - - + +
280A SER 3.0 21.1 + - - +
281A PRO* 3.8 6.7 - - + +
283A ILE* 1.3 75.4 - - - +
285A LYS* 1.3 60.6 + - - +
287A THR* 3.3 5.3 + - - -
288A HIS* 2.9 29.0 + - + +
339A SER* 3.7 7.6 - - - +
342A VAL* 4.1 25.8 - - + -
343A VAL* 3.5 10.2 - - + +
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Residues in contact with LYS 285 (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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281A PRO 2.7 22.5 + - - +
282A GLU* 3.5 7.2 - - - +
284A VAL* 1.3 75.2 - - - +
286A TYR* 1.3 56.8 + - - +
288A HIS* 3.2 8.4 + - + +
289A LYS* 3.0 41.2 + - - +
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU 2.9 15.8 + - - +
283A ILE 3.9 0.2 - - - +
285A LYS* 1.3 74.1 - - + +
287A THR* 1.3 65.8 + - - +
289A LYS* 3.1 32.5 + - + +
290A LEU* 3.1 52.8 + - + +
323A GLN* 4.4 12.1 + - - +
324A LEU* 3.6 18.2 - - + -
327A LYS* 4.0 47.8 + - + +
328A PHE* 3.9 21.3 - + + -
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Residues in contact with THR 287 (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 2.4 24.5 + - - -
284A VAL* 3.5 7.2 - - - -
286A TYR* 1.3 74.6 - - - +
288A HIS* 1.3 56.7 + - - +
290A LEU* 3.1 5.3 + - - +
291A ALA* 3.0 28.5 + - + +
320A THR* 4.1 15.5 - - + -
324A LEU* 3.4 23.6 - - + +
339A SER* 3.5 8.2 - - - +
340A PHE* 3.7 30.1 - - + +
343A VAL* 3.6 19.7 - - + +
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Residues in contact with HIS 288 (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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284A VAL* 2.9 14.7 + - + +
285A LYS* 3.2 12.1 + - + +
287A THR* 1.3 75.3 - - - +
289A LYS* 1.3 64.7 + - - +
292A MET* 3.1 67.1 + - + +
343A VAL* 3.7 24.1 - - + +
346A GLU* 5.8 8.5 - - + +
347A VAL* 4.6 6.4 - - + +
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Residues in contact with LYS 289 (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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285A LYS* 3.0 28.1 + - - +
286A TYR* 3.1 43.1 + - + +
288A HIS* 1.3 78.6 + - - +
290A LEU* 1.3 64.6 + - + +
292A MET 5.1 0.5 + - - -
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Residues in contact with LEU 290 (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* 3.1 57.0 + - + +
287A THR 3.1 6.9 + - - +
289A LYS* 1.3 89.0 - - + +
291A ALA* 1.3 58.7 + - - +
293A GLU 5.6 0.4 - - - -
294A ARG* 4.2 19.2 + - - +
320A THR* 3.8 30.7 + - + +
323A GLN* 3.6 40.6 - - + +
324A LEU* 4.5 2.0 - - + -
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Residues in contact with ALA 291 (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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287A THR* 3.0 14.1 + - + +
290A LEU* 1.3 78.4 - - - +
292A MET* 1.3 67.7 + - - +
293A GLU 3.4 2.2 - - - -
294A ARG* 3.3 2.7 + - - -
295A LEU* 2.8 45.4 + - + +
316A ILE* 4.1 8.7 - - + -
320A THR* 3.9 16.4 - - + +
340A PHE* 4.0 14.1 - - + -
343A VAL* 4.6 3.4 - - + -
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Residues in contact with MET 292 (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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287A THR 4.4 0.2 + - - -
288A HIS* 3.1 57.4 + - + +
289A LYS 4.9 0.2 - - - -
290A LEU 3.9 0.4 - - - -
291A ALA* 1.3 76.2 - - - +
293A GLU* 1.3 92.1 + - - +
295A LEU* 3.8 1.6 - - - +
296A TYR* 2.8 50.2 + - + +
343A VAL* 4.6 2.0 - - - +
347A VAL* 3.9 21.0 - - + +
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Residues in contact with GLU 293 (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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290A LEU 5.5 0.4 + - - -
291A ALA 3.4 0.2 - - - -
292A MET* 1.3 105.0 - - - +
294A ARG* 1.3 67.0 + - + +
296A TYR* 3.4 12.7 + - - +
297A ALA* 3.1 23.2 + - - +
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Residues in contact with ARG 294 (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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290A LEU 4.2 17.7 + - - +
291A ALA 3.3 6.9 + - - +
293A GLU* 1.3 77.7 - - + +
295A LEU* 1.3 61.9 + - - +
297A ALA* 3.5 6.9 + - - +
298A VAL* 3.3 26.3 + - - +
315A LYS* 4.0 16.2 + - - +
316A ILE* 3.6 49.8 - - + +
319A ASP* 3.5 34.6 + - - +
320A THR* 5.0 2.6 + - - -
323A GLN* 5.3 5.5 - - - +
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Residues in contact with LEU 295 (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* 2.8 39.2 + - + +
292A MET 3.8 2.9 - - - +
294A ARG* 1.3 74.9 - - - +
296A TYR* 1.3 66.1 + - - +
298A VAL* 3.1 3.8 + - + +
299A PHE* 2.9 42.1 + - + -
313A VAL* 4.0 26.5 - - + -
316A ILE* 4.3 13.5 - - + -
340A PHE* 4.0 21.3 - - + -
343A VAL* 4.5 7.4 - - + +
344A ALA* 3.7 31.0 - - + +
347A VAL* 4.1 10.5 - - + -
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Residues in contact with TYR 296 (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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292A MET* 2.8 36.4 + - + +
293A GLU* 3.7 17.7 - - - +
294A ARG 3.3 0.2 - - - -
295A LEU* 1.3 77.3 - - - +
297A ALA* 1.3 63.5 + - + +
299A PHE 3.4 0.5 + - - -
300A THR* 2.9 45.8 + - + +
347A VAL* 3.8 12.7 - - + +
350A SER* 5.4 2.7 - - - -
351A ILE* 3.5 28.0 - - + +
355A GLU* 2.5 38.6 + - - -
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Residues in contact with ALA 297 (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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293A GLU 3.1 16.5 + - - +
294A ARG* 3.9 7.0 - - - +
295A LEU 3.2 0.2 - - - -
296A TYR* 1.3 80.7 - - + +
298A VAL* 1.3 63.1 + - + +
300A THR* 3.3 8.7 + - - -
301A ASP* 3.1 23.0 + - - +
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Residues in contact with VAL 298 (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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294A ARG 3.3 15.8 + - - +
295A LEU* 3.1 10.2 + - - +
297A ALA* 1.3 78.6 - - + +
299A PHE* 1.3 59.6 - - + +
301A ASP* 3.2 24.6 + - - +
304A HIS* 3.5 15.6 - - - +
309A ARG* 4.3 13.6 + - + +
312A ALA* 4.0 25.6 - - + -
313A VAL* 4.0 25.1 - - + -
316A ILE* 3.7 19.3 - - + -
359A CYS 5.2 0.5 - - - +
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Residues in contact with PHE 299 (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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295A LEU* 2.9 37.0 + - + +
298A VAL* 1.3 79.6 - - + +
300A THR* 1.3 62.3 + - - +
301A ASP 3.5 0.2 - - - -
302A TYR* 4.3 1.4 - - - -
309A ARG* 4.5 9.2 - - - +
313A VAL* 3.8 27.8 - - + -
344A ALA* 3.6 27.8 - - + -
347A VAL* 3.9 14.4 - - + -
348A PHE* 3.6 38.4 - + + -
351A ILE* 3.5 22.2 - - + +
358A ARG 4.5 0.5 - - - +
359A CYS* 3.3 33.8 - - + +
536A ILE* 3.7 19.7 - - + -
540A ASN* 5.3 2.0 - - - -
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Residues in contact with THR 300 (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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296A TYR* 2.9 50.0 + - + +
297A ALA* 3.3 11.6 + - - -
298A VAL 3.2 0.2 - - - -
299A PHE* 1.3 78.6 - - - +
301A ASP* 1.3 59.3 - - - +
302A TYR* 3.2 37.8 + - + +
351A ILE* 4.1 16.8 - - + -
355A GLU* 4.5 4.7 - - - +
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Residues in contact with ASP 301 (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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297A ALA 3.1 17.9 + - - +
298A VAL* 3.2 4.5 + - - +
300A THR* 1.3 73.3 - - - +
302A TYR* 1.3 64.7 + - - +
303A GLU* 3.3 22.8 + - - +
304A HIS* 3.2 48.9 + - + +
359A CYS 3.9 5.6 - - - +
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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) + - + + + + + -
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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