Contacts of the helix formed by residues 319 - 338 (chain B) in PDB entry 1ZY7
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 LEU 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B HIS* 1.3 71.4 - - - +
320B PRO* 1.3 77.9 - - + +
321B GLN 3.4 1.8 - - - +
322B VAL* 3.3 28.3 + - + +
323B LEU* 2.9 21.8 + - - +
363B VAL* 5.6 1.4 - - - +
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Residues in contact with PRO 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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309B PRO* 4.1 17.3 - - + -
311B PRO* 5.4 11.0 - - + -
318B HIS 3.3 9.6 - - - +
319B LEU* 1.3 88.8 - - + +
321B GLN* 1.3 58.3 + - - +
323B LEU* 3.4 2.9 + - + +
324B ALA* 2.9 29.9 + - - +
580B LEU* 3.7 40.5 - - + +
582B SER* 4.8 1.6 - - - -
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Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG 5.3 3.4 + - - -
309B PRO* 3.8 19.1 - - + +
319B LEU* 3.4 1.0 - - - +
320B PRO* 1.3 80.9 - - + +
322B VAL* 1.3 58.5 + - + +
324B ALA* 3.7 2.0 - - - +
325B ASP* 2.9 56.8 + - - +
582B SER* 3.7 12.7 + - - -
583B GLY 3.0 24.1 + - - +
584B ILE* 3.6 3.5 - - - -
585B SER* 3.8 21.1 - - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.3 34.1 + - + +
321B GLN* 1.3 76.2 - - + +
323B LEU* 1.3 60.1 + - - +
325B ASP* 3.5 4.7 + - - +
326B ALA* 3.0 30.8 + - + +
363B VAL* 4.4 22.9 - - + -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B HIS* 3.9 34.7 - - + +
319B LEU 2.9 15.9 + - - +
320B PRO* 3.7 3.6 - - + +
322B VAL* 1.3 76.2 - - - +
324B ALA* 1.3 60.4 + - - +
326B ALA* 3.3 3.7 + - - +
327B VAL* 2.8 55.1 + - + +
358B THR* 4.3 19.5 - - + -
363B VAL* 4.7 11.9 - - + -
443B HIS* 3.8 13.5 - - + +
544B SER* 3.5 25.6 - - - +
546B ILE* 5.0 1.1 - - + -
580B LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 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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320B PRO 2.9 17.6 + - - +
321B GLN* 3.7 6.1 - - - +
323B LEU* 1.3 77.6 - - - +
325B ASP* 1.3 60.4 + - - +
327B VAL* 3.5 0.3 + - - +
328B SER* 3.0 27.3 + - - -
546B ILE* 3.7 29.5 - - + +
580B LEU* 5.5 0.6 - - + +
582B SER* 3.4 25.6 - - - +
583B GLY 3.4 13.7 - - - +
584B ILE* 4.3 0.7 - - - -
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Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN* 2.9 32.1 + - - +
322B VAL* 4.0 4.3 - - - +
324B ALA* 1.3 78.0 - - - +
326B ALA* 1.3 55.9 + - - +
328B SER* 2.9 18.3 + - - -
329B ARG* 3.0 20.9 + - - +
584B ILE* 3.5 5.0 - - - +
585B SER* 2.7 50.0 + - - -
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Residues in contact with ALA 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 VAL* 3.0 20.2 + - + +
323B LEU* 3.7 2.9 - - + +
325B ASP* 1.3 72.7 - - - +
327B VAL* 1.3 62.2 + - + +
329B ARG* 3.3 26.8 + - - +
330B LEU* 2.9 42.2 + - + +
363B VAL* 3.7 24.5 - - + -
366B ALA* 6.1 0.2 - - + -
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 2.8 42.5 + - + +
324B ALA 3.9 0.2 - - - +
326B ALA* 1.3 73.7 - - + +
328B SER* 1.3 62.6 + - - +
330B LEU* 3.3 3.7 + - + +
331B VAL* 3.0 24.6 + - - +
356B VAL* 4.0 36.6 - - + -
366B ALA* 6.0 0.9 - - + -
443B HIS* 4.1 11.4 - - + +
445B TYR* 3.7 23.8 - - + +
546B ILE* 3.6 28.0 - - + -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ALA 3.0 14.5 + - - -
325B ASP* 2.9 18.4 + - - -
327B VAL* 1.3 74.9 - - - +
329B ARG* 1.3 60.2 + - - +
331B VAL* 4.0 1.0 - - - +
332B LEU* 3.1 26.2 + - - +
445B TYR* 3.4 43.2 - - - -
584B ILE* 3.4 20.6 - - - +
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Residues in contact with ARG 329 (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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325B ASP 3.0 17.3 + - - +
326B ALA* 3.6 32.5 + - - +
328B SER* 1.3 76.8 + - - +
330B LEU* 1.3 85.4 + - - +
332B LEU* 3.5 5.9 + - - +
333B GLY* 2.9 26.9 + - - -
363B VAL* 5.7 1.2 - - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ALA* 2.9 29.3 + - + +
327B VAL* 3.7 3.8 - - + +
329B ARG* 1.3 101.7 - - - +
331B VAL* 1.3 65.3 + - - +
333B GLY* 3.4 1.2 + - - -
334B LYS* 3.0 25.5 + - - +
356B VAL* 4.4 11.4 - - + -
363B VAL 5.4 0.7 - - - +
366B ALA* 3.7 37.0 - - + +
368B VAL* 3.7 22.6 - - + +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B VAL 3.0 16.2 + - - +
328B SER 4.0 3.8 - - - +
330B LEU* 1.3 74.8 - - - +
332B LEU* 1.3 64.1 + - - +
334B LYS* 3.3 3.3 + - - +
335B PHE* 3.0 22.7 + - - +
352B LEU* 4.1 12.8 - - + -
353B ALA 3.7 28.9 - - - +
354B GLY* 4.0 17.0 - - - -
355B VAL 4.6 0.4 - - - +
356B VAL* 3.7 20.9 - - + -
368B VAL* 4.7 6.7 - - + -
371B VAL* 4.1 11.3 - - + +
445B TYR* 3.9 24.5 - - + -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER 3.1 17.9 + - - +
329B ARG* 3.9 4.9 - - - +
331B VAL* 1.3 78.1 - - - +
333B GLY* 1.3 57.1 + - - +
335B PHE* 3.2 5.0 + - + +
336B GLY 2.9 25.1 + - - -
342B PHE* 3.4 36.7 - - + -
349B ARG* 4.4 13.7 - - - +
352B LEU* 3.7 26.2 - - + +
445B TYR* 6.2 0.4 - - + -
588B GLU* 5.5 2.5 - - - +
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Residues in contact with GLY 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 ARG 2.9 20.5 + - - -
330B LEU* 3.8 1.8 - - - -
331B VAL 3.4 0.2 - - - -
332B LEU* 1.3 72.3 - - - +
334B LYS* 1.3 57.2 + - - +
336B GLY* 3.2 2.8 + - - -
337B ASP* 2.9 36.0 + - - +
342B PHE* 5.0 3.4 - - - -
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Residues in contact with LYS 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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330B LEU 3.0 18.3 + - - +
331B VAL 3.7 3.8 - - - +
333B GLY* 1.3 76.5 - - - +
335B PHE* 1.3 63.9 + - - +
337B ASP* 3.0 20.3 + - + +
338B LEU* 3.0 47.3 + - + +
368B VAL* 4.1 12.1 - - + -
371B VAL* 3.8 12.8 - - + -
602B TRP* 3.4 54.3 - - + +
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Residues in contact with PHE 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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331B VAL 3.0 14.4 + - - +
332B LEU* 3.5 10.1 - - + +
334B LYS* 1.3 75.5 - - - +
336B GLY* 1.3 59.2 + - - +
338B LEU* 3.2 14.7 + - + +
339B THR* 2.8 37.0 + - + +
342B PHE* 3.9 20.9 - + - -
346B HIS 3.9 3.4 - - - -
347B ALA* 3.5 40.6 - - - -
349B ARG* 4.0 13.5 - - + -
352B LEU* 3.7 20.2 - - + -
371B VAL* 3.9 24.5 - - + +
373B THR* 3.6 28.7 - - + -
600B VAL* 3.9 15.0 - - + -
609B ILE* 5.7 1.6 - - + -
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Residues in contact with GLY 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 LEU 2.9 11.3 + - - -
333B GLY 3.5 2.9 - - - -
335B PHE* 1.3 77.0 - - - +
337B ASP* 1.3 61.5 + - - +
339B THR* 3.2 9.9 + - - -
341B ASN* 2.9 30.1 + - - -
342B PHE* 3.2 35.5 - - - -
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Residues in contact with ASP 337 (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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333B GLY 2.9 20.4 + - - +
334B LYS* 3.0 27.8 + - - +
336B GLY* 1.3 76.9 - - - +
338B LEU* 1.3 59.7 + - - +
339B THR 3.3 0.8 + - - -
340B ASP* 4.1 5.2 + - - -
341B ASN* 5.0 7.0 + - - +
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Residues in contact with LEU 338 (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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334B LYS* 3.0 38.6 + - + +
335B PHE* 3.2 10.3 + - + +
337B ASP* 1.3 76.5 - - - +
339B THR* 1.3 63.5 + - + +
340B ASP 3.7 0.9 - - - -
344B SER* 5.3 0.7 - - - -
371B VAL* 4.4 7.9 - - + -
602B TRP* 3.5 58.3 - - + +
607B SER 4.9 4.0 - - - +
608B ALA* 4.5 6.1 - - - -
609B ILE* 3.6 38.9 + - + +
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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