Contacts of the helix formed by residues 280 - 299 (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 SER 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B THR 3.6 2.2 + - - -
279B PRO* 1.3 72.7 - - - +
281B PRO* 1.3 73.8 - - - +
282B GLU* 3.6 16.3 + - - -
283B ILE* 3.2 29.0 + - - +
284B VAL* 3.0 22.2 + - - +
335B GLU* 3.3 14.8 + - - -
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO 4.2 2.7 - - - +
280B SER* 1.3 87.6 - - - +
282B GLU* 1.3 66.1 + - - +
284B VAL* 3.7 8.5 - - + +
285B LYS* 2.7 37.6 + - - +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 3.2 19.7 + - - +
281B PRO* 1.3 93.4 - - - +
283B ILE* 1.3 62.6 + - + +
285B LYS* 3.4 5.2 + - - +
286B TYR* 3.0 23.9 + - - +
328B PHE* 3.9 16.8 - - + -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 3.2 15.9 + - - +
282B GLU* 1.3 73.1 - - + +
284B VAL* 1.3 56.1 + - - +
286B TYR* 3.9 0.5 - - - +
287B THR* 2.3 42.3 + - - +
324B LEU* 4.2 6.3 - - + -
328B PHE* 3.8 37.2 - - + -
331B ALA* 3.7 22.2 - - + -
335B GLU* 3.4 34.1 - - + +
336B ILE* 4.5 9.9 - - + -
339B SER* 3.2 25.1 - - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO* 3.8 31.0 - - + +
280B SER 3.0 20.3 + - - +
281B PRO* 3.7 7.2 - - + +
282B GLU 3.3 0.2 - - - -
283B ILE* 1.3 77.5 - - - +
285B LYS* 1.3 56.8 + - - +
287B THR* 3.3 5.1 + - - -
288B HIS* 2.9 27.1 + - + +
339B SER* 3.9 6.5 - - - +
342B VAL* 4.2 20.4 - - + -
343B VAL* 3.5 18.0 - - + +
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO 2.7 21.6 + - - +
282B GLU* 3.8 4.9 - - - +
284B VAL* 1.3 74.2 - - - +
286B TYR* 1.3 61.0 + - - +
288B HIS* 3.2 11.9 + - + +
289B LYS* 3.1 22.0 + - - +
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU 3.0 16.3 + - - +
283B ILE 4.1 0.2 - - - +
285B LYS* 1.3 74.1 - - - +
287B THR* 1.3 65.2 + - - +
289B LYS* 3.4 23.7 + - + +
290B LEU* 3.1 58.1 + - + +
323B GLN* 4.3 13.7 + - - +
324B LEU* 3.5 22.9 - - + -
327B LYS* 3.7 42.3 - - + +
328B PHE* 3.8 23.3 - + + -
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE 2.3 28.5 + - - -
284B VAL 3.6 4.5 - - - -
286B TYR* 1.3 77.1 - - - +
288B HIS* 1.3 61.7 + - - +
290B LEU* 3.4 4.0 + - - +
291B ALA* 3.1 24.2 + - + +
320B THR* 5.4 2.9 - - - -
324B LEU* 3.5 32.3 - - + +
339B SER* 3.7 8.4 - - - +
340B PHE* 3.8 39.9 - - + +
343B VAL* 3.7 13.0 - - + +
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Residues in contact with HIS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 2.9 14.9 + - + +
285B LYS* 3.2 16.4 + - + +
287B THR* 1.3 73.7 - - - +
289B LYS* 1.3 65.3 + - - +
292B MET* 2.8 70.4 + - + +
343B VAL* 3.6 23.4 - - + +
346B GLU* 3.8 22.4 + - - -
347B VAL* 4.5 4.0 - - + -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS 3.1 9.4 + - - +
286B TYR* 3.8 32.9 - - + +
288B HIS* 1.3 84.9 - - + +
290B LEU* 1.3 65.8 + - + +
291B ALA 3.6 0.2 + - - -
292B MET* 4.5 3.1 + - - +
293B GLU 5.5 1.0 + - - -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B TYR* 3.1 62.9 + - + +
287B THR* 3.8 5.6 - - - +
288B HIS 3.1 0.2 - - - -
289B LYS* 1.3 90.2 - - + +
291B ALA* 1.3 57.3 + - - +
294B ARG* 4.5 13.2 + - - +
320B THR* 3.7 40.2 - - + +
323B GLN* 3.8 31.2 - - + +
324B LEU* 4.5 6.1 - - + -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B THR 3.1 15.1 + - - +
290B LEU* 1.3 77.3 - - - +
292B MET* 1.3 60.9 + - - +
293B GLU 3.5 1.8 - - - -
294B ARG* 3.4 4.0 + - - +
295B LEU* 2.8 50.7 + - + +
316B ILE* 4.1 7.4 - - + -
320B THR* 3.9 17.7 - - + -
340B PHE* 4.0 15.0 - - + -
343B VAL* 4.6 1.3 - - + -
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Residues in contact with MET 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B HIS* 2.8 55.9 + - + +
289B LYS* 4.5 3.0 + - - +
290B LEU 3.9 0.2 - - - -
291B ALA* 1.3 77.3 - - - +
293B GLU* 1.3 71.6 + - + +
295B LEU* 3.6 1.3 - - - +
296B TYR* 2.6 56.2 + - + +
343B VAL* 4.9 0.9 - - - +
347B VAL* 4.0 20.3 - - + +
350B SER* 5.6 5.4 - - - +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LYS 5.5 1.4 + - - -
291B ALA 3.5 0.2 - - - -
292B MET* 1.3 91.6 - - - +
294B ARG* 1.3 59.4 + - + +
296B TYR* 3.7 22.9 - - - +
297B ALA* 2.9 28.2 + - - +
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU 4.5 13.1 + - - +
291B ALA 3.4 4.5 + - - +
292B MET 3.2 0.6 - - - -
293B GLU* 1.3 77.0 - - + +
295B LEU* 1.3 63.6 + - - +
297B ALA* 3.3 8.9 + - - +
298B VAL* 3.2 17.7 + - - +
315B LYS* 4.1 10.1 + - - +
316B ILE* 3.3 63.5 - - + +
319B ASP* 3.4 37.9 + - - +
320B THR* 4.6 7.5 - - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 2.8 41.8 + - + +
292B MET 3.7 2.5 - - - +
294B ARG* 1.3 71.3 - - - +
296B TYR* 1.3 65.8 + - - +
298B VAL* 3.1 3.6 + - - +
299B PHE* 3.0 40.9 + - + -
313B VAL* 4.1 20.9 - - + -
316B ILE* 4.1 9.6 - - + -
340B PHE* 3.9 23.8 - - + -
343B VAL* 4.0 12.1 - - + +
344B ALA* 3.7 33.0 - - + +
347B VAL* 3.9 14.6 - - + -
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B MET* 2.6 37.9 + - + +
293B GLU* 3.7 22.0 - - - +
295B LEU* 1.3 72.3 - - - +
297B ALA* 1.3 62.0 + - - +
299B PHE 3.5 0.7 + - - -
300B THR* 2.8 48.9 + - + +
347B VAL* 3.7 12.7 - - + +
350B SER* 5.6 2.0 - - - -
351B ILE* 3.7 27.8 - - + -
355B GLU* 2.6 36.7 + - - -
357B LYS* 4.0 1.7 + - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU 2.9 18.7 + - - +
294B ARG* 3.4 10.8 - - - +
295B LEU 3.1 0.4 - - - -
296B TYR* 1.3 79.5 - - - +
298B VAL* 1.3 63.5 + - + +
300B THR* 3.1 16.5 + - - -
301B ASP* 3.3 15.2 + - - +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG 3.2 13.2 + - - +
295B LEU* 3.1 8.3 + - - +
297B ALA* 1.3 77.3 - - + +
299B PHE* 1.3 61.5 + - + +
300B THR 3.1 4.7 + - - -
301B ASP* 3.2 19.7 + - - +
304B HIS* 3.7 15.5 - - - +
309B ARG* 3.7 28.3 + - + +
312B ALA* 3.9 25.1 - - + -
313B VAL* 3.9 18.4 - - + +
316B ILE* 3.7 18.2 - - + -
359B CYS 4.9 0.9 - - - +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.0 38.7 + - + +
296B TYR 3.5 0.4 + - - -
297B ALA 3.4 0.4 - - - -
298B VAL* 1.3 74.8 - - + +
300B THR* 1.3 62.5 + - - +
302B TYR* 4.7 0.2 - - - -
309B ARG* 4.0 13.7 - - + -
313B VAL* 3.8 28.3 - - + -
344B ALA* 3.9 23.1 - - + -
347B VAL* 4.1 6.1 - - + -
348B PHE* 3.5 44.2 - + + -
351B ILE* 3.6 24.1 - - + +
357B LYS* 5.2 0.2 - - - -
358B ARG 4.3 2.9 - - - +
359B CYS* 3.6 29.5 - - + -
536B ILE* 3.8 18.2 - - + -
540B ASN* 5.1 2.2 - - - -
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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