Contacts of the helix formed by residues 320 - 336 (chain B) in PDB entry 3EZZ
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 ASN 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ASP* 3.3 29.4 + - - +
250B ASN 2.8 26.9 + - - +
251B HIS* 4.5 0.8 - - - +
285B SER* 3.1 10.9 + - - +
318B SER* 3.2 5.0 + - - -
319B PRO* 1.3 74.0 - - - +
321B PHE* 1.3 64.5 + - - +
322B SER* 2.9 26.5 + - - -
323B PHE* 2.9 28.2 + - - +
324B MET 3.0 4.9 + - - -
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PRO 5.0 3.1 - - - -
320B ASN* 1.3 72.7 - - + +
322B SER* 1.3 64.9 + - - +
324B MET* 2.7 23.5 + - + +
325B GLY 2.8 11.3 + - - -
303D LEU* 4.1 20.4 - - + -
304D GLU* 3.8 36.8 - - + -
307D PHE* 3.5 39.9 - + + -
324D MET* 4.0 31.6 - - + -
328D LEU* 3.9 25.9 - - + +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN 3.8 2.3 + - - -
251B HIS* 3.0 42.7 + - - +
320B ASN* 2.9 14.9 + - - -
321B PHE* 1.3 75.9 - - - +
323B PHE* 1.3 63.5 + - - +
325B GLY* 3.0 9.9 + - - -
326B GLN* 2.9 34.9 + - - +
328D LEU* 4.3 12.1 - - - +
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 4.3 5.2 - - + -
248B GLU 3.2 23.8 - - - -
249B ASP* 3.7 0.7 - - - -
250B ASN 3.0 18.6 - - - -
253B ALA* 3.5 22.4 - - + -
255B ILE* 3.9 15.3 - - + -
285B SER* 3.4 14.8 - - - -
286B ARG* 3.5 27.6 - - + -
289B THR* 3.2 33.3 - - + +
319B PRO* 4.2 3.8 - - + -
320B ASN* 2.9 23.8 + - - +
322B SER* 1.3 74.6 - - - +
324B MET* 1.3 53.0 + - - +
326B GLN* 3.1 18.2 + - - +
327B LEU* 2.7 40.1 + - - +
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 3.9 8.2 - - + +
307B PHE* 4.0 17.9 - - + -
318B SER* 4.7 0.9 - - - -
319B PRO* 2.9 55.4 - - + +
320B ASN 3.0 4.8 + - - +
321B PHE* 2.7 26.9 + - + +
323B PHE* 1.3 77.1 - - - +
325B GLY* 1.3 60.7 + - - +
327B LEU* 3.2 15.7 + - - +
328B LEU* 3.2 25.8 + - + +
321D PHE* 3.9 36.6 - - + -
324D MET* 5.2 11.2 - - + -
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Residues in contact with GLY 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE 2.8 11.8 + - - -
322B SER 3.0 3.3 + - - -
324B MET* 1.3 76.0 - - - +
326B GLN* 1.3 57.8 + - - +
328B LEU* 2.9 17.3 + - - +
329B GLN* 2.9 27.8 + - - +
325D GLY* 5.2 7.4 - - - -
328D LEU* 5.0 9.4 - - - +
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B HIS 4.6 1.0 + - - -
253B ALA 2.8 22.8 + - - +
254B ASP* 3.6 4.6 - - - -
255B ILE* 3.2 30.7 + - + +
256B SER* 3.2 27.8 + - - +
259B PHE* 4.0 5.1 - - + -
322B SER* 2.9 33.0 + - - +
323B PHE* 3.5 11.7 - - - +
325B GLY* 1.3 75.9 - - - +
327B LEU* 1.3 55.8 + - - +
329B GLN* 3.6 15.9 - - - +
330B PHE* 3.0 29.5 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 4.2 3.8 - - + -
289B THR* 3.4 46.9 - - + +
292B LEU* 3.8 23.8 - - + -
293B ALA* 3.8 10.3 - - + +
296B MET* 3.1 45.1 - - + +
303B LEU* 3.9 16.5 - - + +
319B PRO* 4.2 9.6 - - + -
323B PHE 2.7 25.3 + - - +
324B MET* 3.3 11.7 - - - +
325B GLY 3.1 0.2 - - - -
326B GLN* 1.3 74.2 - - - +
328B LEU* 1.3 57.3 + - - +
330B PHE* 3.9 2.8 - - - +
331B GLU* 3.1 14.9 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 3.6 17.3 - - + -
324B MET* 3.2 15.4 + - + +
325B GLY* 2.9 15.8 + - - +
327B LEU* 1.3 75.8 - - - +
329B GLN* 1.3 61.4 + - - +
330B PHE 3.0 1.1 - - - -
331B GLU* 2.6 55.5 + - - +
332B SER* 3.1 5.9 + - - -
321D PHE* 3.7 43.7 - - + +
322D SER* 4.2 6.1 - - - +
324D MET* 5.9 0.2 - - + -
325D GLY* 5.1 5.2 - - - +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B SER* 5.4 6.8 + - - -
325B GLY 2.9 12.1 + - - +
326B GLN* 3.6 19.1 - - - +
328B LEU* 1.3 73.5 - - - +
330B PHE* 1.3 58.4 + - - +
332B SER* 2.7 26.2 + - - -
333B GLN* 3.1 15.4 + - - +
254E ASP* 2.4 49.0 + - - +
256E SER* 3.1 15.6 + - - +
257E SER* 4.5 5.8 - - - +
326E GLN* 4.3 12.1 + - - +
329E GLN* 4.7 12.2 + - - +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 3.7 29.6 - + + -
260B MET* 4.3 11.0 - - + -
263B ILE* 3.9 22.0 - - + -
293B ALA* 3.3 36.1 - - + -
296B MET* 4.1 14.1 - - + -
297B MET* 4.1 4.0 - - - -
326B GLN 3.0 14.8 + - - +
327B LEU 3.9 2.5 - - - +
328B LEU 3.0 0.6 - - - -
329B GLN* 1.3 79.1 - - - +
331B GLU* 1.3 64.4 + - - +
333B GLN* 3.3 10.8 + - - +
334B VAL* 3.0 43.9 + - + +
329E GLN* 4.1 11.6 - - + +
333E GLN* 3.3 30.1 - - + -
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B MET* 4.1 16.4 - - + -
301B VAL 4.7 3.8 - - - +
302B ARG* 2.9 34.7 + - - -
303B LEU* 3.3 20.7 + - - +
327B LEU 3.1 15.3 + - - +
328B LEU* 2.6 45.7 + - - +
330B PHE* 1.3 70.4 - - - +
332B SER* 1.3 64.5 + - - +
334B VAL* 3.0 16.8 + - - +
335B LEU* 3.2 23.5 + - + +
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Residues in contact with SER 332 (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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328B LEU 3.1 3.8 + - - -
329B GLN* 2.7 24.7 + - - -
331B GLU* 1.3 79.2 - - - +
333B GLN* 1.3 70.3 + - - +
335B LEU* 3.2 9.6 + - - +
336B ALA 3.1 18.4 + - - -
256E SER 4.5 0.2 + - - -
257E SER* 3.8 28.2 + - - -
260E MET* 3.7 17.5 - - - +
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Residues in contact with GLN 333 (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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329B GLN* 3.1 26.4 + - - +
330B PHE* 3.3 5.8 - - - +
332B SER* 1.3 84.4 + - - +
334B VAL* 1.3 61.7 + - - +
336B ALA* 3.2 25.2 + - - +
256E SER* 3.0 43.8 + - - +
259E PHE* 5.0 0.4 - - + -
260E MET* 5.0 1.3 - - - -
329E GLN* 3.1 24.6 + - - +
330E PHE* 4.1 23.9 + - + -
333E GLN* 2.3 56.2 + - - +
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Residues in contact with VAL 334 (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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296B MET* 3.5 28.7 - - + +
297B MET* 3.5 35.1 - - + +
300B ARG* 4.6 16.1 + - + +
301B VAL 5.9 0.2 - - - +
330B PHE* 3.0 57.5 + - + +
331B GLU* 3.0 8.5 + - - +
333B GLN* 1.3 74.9 - - - +
335B LEU* 1.3 67.1 + - + +
336B ALA* 3.9 4.9 - - - +
333E GLN* 3.9 2.6 - - - +
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Residues in contact with LEU 335 (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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300B ARG* 4.9 14.5 + - + +
301B VAL* 4.8 22.2 - - - +
302B ARG* 4.3 23.8 - - + +
331B GLU* 3.2 27.8 + - + +
332B SER* 3.2 11.3 + - - +
334B VAL* 1.3 81.6 - - + +
336B ALA* 1.3 68.5 + - - +
260E MET* 6.0 0.4 - - + -
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Residues in contact with ALA 336 (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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332B SER 3.1 5.1 + - - -
333B GLN 3.2 17.9 + - - +
334B VAL 3.9 4.3 - - - +
335B LEU* 1.3 82.2 - - - +
260E MET* 2.5 52.8 - - + +
297E MET* 3.8 27.9 - - - +
330E PHE* 3.9 14.4 - - + -
333E GLN* 4.8 8.7 - - - +
334E VAL* 5.2 1.4 - - - -
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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
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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