Contacts of the helix formed by residues 325 - 342 (chain D) in PDB entry 4ZZ7
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 THR 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D PHE* 5.4 12.3 - - + -
176D ARG* 4.3 22.0 + - + +
323D VAL* 3.4 5.7 - - - +
324D ILE* 1.3 96.8 - - + +
326D ARG* 1.3 59.4 + - - +
327D GLN* 3.8 10.7 + - - +
328D HIS* 3.0 24.1 + - - +
329D GLN* 2.9 24.9 + - - +
362D PHE* 3.5 12.9 - - - +
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Residues in contact with ARG 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLY* 5.7 1.0 + - - -
325D THR* 1.3 70.5 - - - +
327D GLN* 1.3 67.9 + - - +
328D HIS 3.1 0.2 + - - -
329D GLN* 3.1 30.2 + - - +
330D GLU* 2.9 47.5 + - - +
360D ASN* 3.4 31.9 + - - +
361D GLY 3.7 10.3 + - - -
362D PHE* 3.6 37.0 - - + -
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Residues in contact with GLN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ARG* 5.2 7.8 + - - -
325D THR* 3.4 9.0 + - - +
326D ARG* 1.3 77.9 - - - +
328D HIS* 1.3 57.6 + - - +
330D GLU* 3.7 13.6 + - - +
331D LYS* 3.1 33.0 + - - +
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Residues in contact with HIS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE* 5.4 2.9 - + - -
176D ARG* 6.0 1.7 + - - +
278D GLU* 3.7 14.8 + - - -
323D VAL* 3.6 25.6 - - + -
324D ILE* 3.9 12.3 - - + +
325D THR* 3.0 23.5 + - - +
327D GLN* 1.3 74.5 - - - +
329D GLN* 1.3 65.4 + - - +
331D LYS* 2.9 30.8 + - + +
332D VAL* 2.8 31.6 + - + +
383D ILE 3.9 14.4 - - - -
384D PHE* 2.8 44.3 + + + -
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Residues in contact with GLN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D VAL* 3.2 13.9 - - + +
325D THR 2.9 14.1 + - - +
326D ARG* 3.1 39.8 + - - +
328D HIS* 1.3 76.4 - - - +
330D GLU* 1.3 65.0 + - - +
332D VAL* 3.2 3.3 + - - +
333D ILE* 2.9 34.6 + - + +
351D ARG 5.6 1.2 + - - -
353D PRO* 5.6 1.6 - - - +
361D GLY 3.9 6.1 + - - -
362D PHE* 3.8 15.4 - - + +
363D PHE 3.0 26.0 + - - +
364D VAL* 3.9 19.6 - - + +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ARG* 2.9 46.4 + - + +
327D GLN* 3.7 11.0 - - - +
329D GLN* 1.3 76.0 - - + +
331D LYS* 1.3 52.4 + - - +
333D ILE* 3.2 10.5 + - - +
334D GLY* 2.8 32.2 + - - -
377E THR* 3.9 25.6 + - + +
381E GLU* 3.8 17.3 - - - +
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Residues in contact with LYS 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLN* 3.1 22.2 + - - +
328D HIS* 2.9 37.1 + - + +
330D GLU* 1.3 70.2 - - - +
332D VAL* 1.3 62.4 + - - +
334D GLY* 3.0 13.1 + - - -
335D TYR* 3.0 46.7 + - + +
382D GLU 5.7 0.7 - - - +
383D ILE 5.3 0.9 - - - +
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D VAL* 4.4 5.4 - - + -
328D HIS* 2.8 44.8 + - + +
329D GLN 3.5 7.0 - - - +
331D LYS* 1.3 70.8 - - + +
333D ILE* 1.3 64.7 + - - +
335D TYR* 3.2 18.7 + - - +
336D ILE* 3.2 20.8 + - + +
364D VAL* 4.0 29.2 - - + -
383D ILE* 4.1 24.2 - - + +
384D PHE 4.2 5.2 - - - +
385D GLY* 4.3 4.3 - - - -
386D PRO* 4.3 11.2 - - + -
387D VAL* 4.4 1.6 - - + -
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Residues in contact with ILE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLN* 2.9 32.1 + - + +
330D GLU* 3.5 11.0 - - - +
332D VAL* 1.3 75.8 - - - +
334D GLY* 1.3 56.7 + - - +
336D ILE* 3.2 9.1 + - - +
337D ASN* 2.9 35.4 + - - +
351D ARG* 3.1 46.7 - - + +
364D VAL* 4.5 16.6 - - + -
341E GLN* 3.6 25.1 - - - +
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D GLU 2.8 18.3 + - - -
331D LYS* 3.0 6.2 + - - -
333D ILE* 1.3 73.8 - - - +
335D TYR* 1.3 56.7 + - - +
337D ASN* 3.3 11.9 + - - +
338D SER* 2.8 30.6 + - - -
334E GLY* 6.1 2.6 - - - -
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Residues in contact with TYR 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D LYS* 3.0 48.8 + - + +
332D VAL 3.2 6.3 + - - +
334D GLY* 1.3 76.1 - - - +
336D ILE* 1.3 57.7 + - + +
338D SER* 3.2 8.2 + - - -
339D ALA* 2.9 29.2 + - - +
377D THR* 4.5 7.0 - - + -
378D SER* 3.6 22.2 - - - -
381D GLU* 2.6 47.4 + - + +
382D GLU 3.8 19.4 + - - -
383D ILE* 3.8 41.1 - - + -
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Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D VAL* 3.2 21.3 + - + +
333D ILE* 3.2 8.2 + - - +
335D TYR* 1.3 78.9 - - + +
337D ASN* 1.3 61.5 + - - +
339D ALA* 3.2 7.7 + - - +
340D GLU* 3.0 21.8 + - - +
346D ILE* 3.9 21.8 - - + +
349D ASP* 4.7 2.7 - - - +
351D ARG* 3.5 38.4 - - + +
364D VAL* 4.5 5.4 - - + -
367D THR* 3.6 38.6 - - + +
369D ILE* 4.6 6.3 - - + -
383D ILE* 5.8 0.2 - - + -
387D VAL* 4.2 16.6 - - + -
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Residues in contact with ASN 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ILE* 2.9 24.2 + - - +
334D GLY* 3.6 10.4 - - - +
336D ILE* 1.3 74.0 - - - +
338D SER* 1.3 60.9 + - - +
340D GLU* 3.4 3.2 + - - +
341D GLN* 3.1 26.0 + - - +
351D ARG* 2.7 44.6 + - - +
334E GLY 5.4 1.0 + - - +
337E ASN* 4.0 20.8 + - + +
338E SER* 4.4 18.8 - - - +
341E GLN* 3.1 26.3 + - - +
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D GLY 2.8 21.2 + - - -
335D TYR* 3.4 12.3 - - - -
337D ASN* 1.3 70.3 - - - +
339D ALA* 1.3 67.1 + - - +
341D GLN* 3.9 1.6 - - - +
342D GLN* 3.0 48.1 + - - +
377D THR* 4.0 13.7 - - - +
378D SER* 4.4 4.7 + - - -
337E ASN* 4.5 9.6 - - - +
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D TYR 2.9 13.8 + - - +
336D ILE 3.5 8.3 - - - +
338D SER* 1.3 72.4 - - - +
340D GLU* 1.3 67.5 + - - +
342D GLN* 3.2 12.3 + - - +
343D GLY 3.2 0.5 + - - -
344D ALA* 3.0 35.3 + - + +
346D ILE* 4.4 0.9 - - + -
369D ILE* 3.9 25.8 - - + -
376D MET* 4.6 3.1 - - - +
378D SER* 3.6 17.5 + - - +
389D GLN* 5.2 1.3 - - - +
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Residues in contact with GLU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ILE 3.0 13.0 + - - +
337D ASN* 3.6 8.4 - - - +
338D SER 3.3 0.2 - - - -
339D ALA* 1.3 75.9 - - - +
341D GLN* 1.3 58.0 + - - +
343D GLY* 3.0 20.8 + - - -
344D ALA 3.7 13.9 + - - +
346D ILE* 4.0 19.7 - - + +
351D ARG* 2.8 40.5 + - - -
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Residues in contact with GLN 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ASN 3.1 14.3 + - - +
338D SER* 3.9 2.9 - - - +
340D GLU* 1.3 80.4 - - - +
342D GLN* 1.3 70.7 + - - +
343D GLY* 3.2 1.7 + - - -
333E ILE* 3.6 21.6 - - - +
337E ASN* 3.7 19.6 + - - +
351E ARG* 3.5 39.8 + - - +
352E GLN* 3.7 21.3 + - - +
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Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D SER* 3.0 36.8 + - - +
339D ALA 3.2 3.3 + - - +
341D GLN* 1.3 86.4 + - - +
343D GLY* 1.3 56.3 + - - +
344D ALA 3.7 2.2 - - - -
375D GLU 4.8 2.8 + - - -
376D MET* 3.7 32.9 - - + +
377D THR* 3.0 39.7 + - - +
378D SER* 4.3 1.6 + - - -
330E GLU* 5.1 4.8 + - - +
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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