Contacts of the helix formed by residues 312 - 329 (chain K) in PDB entry 1ZUM
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 GLU 312 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310K VAL 3.4 1.0 + - - -
311K GLN* 1.3 72.3 - - + +
313K ASP* 1.3 73.0 + - - +
314K ILE 3.2 1.0 + - - -
315K TYR* 3.4 13.4 + - - +
316K ASP* 4.8 2.3 + - - -
409K LYS* 3.9 29.0 - - + +
410K PHE 2.9 17.0 + - - +
411K LYS* 3.2 46.6 - - + +
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Residues in contact with ASP 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279K SER* 4.4 21.1 + - - -
311K GLN* 3.1 5.5 + - + +
312K GLU* 1.3 87.8 - - - +
314K ILE* 1.3 61.9 + - + +
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Residues in contact with ILE 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ILE* 3.8 19.3 - - + +
278K MET 3.2 29.4 - - - +
279K SER* 3.5 30.1 - - - +
281K ALA* 5.3 2.0 - - + +
283K MET* 3.6 28.0 - - + -
310K VAL* 3.8 9.9 - - + -
311K GLN 3.0 12.1 + - - +
313K ASP* 1.3 82.4 - - + +
315K TYR* 1.3 65.2 + - - +
316K ASP 3.5 1.8 - - - -
317K GLU* 3.4 10.8 + - - +
318K PHE* 2.9 22.9 + - + +
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Residues in contact with TYR 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310K VAL* 3.7 19.7 - - + -
311K GLN 3.1 9.4 + - - +
312K GLU* 3.4 19.3 + - - +
314K ILE* 1.3 76.4 - - - +
316K ASP* 1.3 73.8 + - - +
318K PHE* 3.6 1.0 - - - +
319K VAL* 2.9 58.6 + - + +
387K GLY* 3.7 6.6 - - - -
388K ASP* 2.7 47.1 + - - -
407K ILE* 4.0 7.9 + - + -
408K LEU 4.0 4.9 - - - -
409K LYS* 3.5 55.6 - - + -
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Residues in contact with ASP 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312K GLU 4.8 2.7 + - - -
314K ILE 3.5 0.6 - - - -
315K TYR* 1.3 94.4 - - - +
317K GLU* 1.3 63.5 + - - +
319K VAL* 3.8 3.8 - - - +
320K GLU* 3.0 26.7 + - - +
409K LYS* 5.3 2.8 + - - -
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Residues in contact with GLU 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K MET* 3.8 20.5 - - + +
314K ILE* 3.4 11.9 + - - +
315K TYR 3.4 0.4 - - - -
316K ASP* 1.3 75.1 - - - +
318K PHE* 1.3 66.3 + - - +
320K GLU* 3.2 12.3 + - + +
321K ARG* 3.0 65.8 + - + +
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Residues in contact with PHE 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ILE* 3.9 29.2 - - + -
283K MET* 4.0 17.4 - - + -
286K ALA* 4.0 3.4 - - + -
287K VAL* 3.6 34.3 - - + +
290K ALA* 3.5 26.5 - - + -
308K THR* 3.8 15.9 - - + -
310K VAL* 3.5 31.0 - - + -
314K ILE* 2.9 19.2 + - + +
315K TYR 3.6 3.1 - - - +
317K GLU* 1.3 76.9 - - - +
319K VAL* 1.3 56.4 + - + +
321K ARG* 3.3 3.1 + - - +
322K SER* 2.8 53.0 + - - -
405K MET* 5.6 1.3 - - - -
407K ILE* 4.5 10.3 - - + -
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Residues in contact with VAL 319 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315K TYR* 2.9 53.6 + - + +
316K ASP* 3.8 4.7 - - - +
318K PHE* 1.3 76.9 - - + +
320K GLU* 1.3 57.7 + - - +
322K SER* 3.3 6.9 + - - -
323K VAL* 2.9 38.0 + - + +
368K LEU* 3.4 34.1 - - + -
407K ILE* 3.9 24.5 - - + -
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Residues in contact with GLU 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316K ASP 3.0 19.3 + - - +
317K GLU* 3.2 11.6 + - - +
319K VAL* 1.3 80.5 - - - +
321K ARG* 1.3 62.2 + - + +
323K VAL* 3.4 5.9 + - - +
324K ALA* 3.1 22.2 + - - +
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Residues in contact with ARG 321 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K MET* 3.4 28.0 - - - +
284K ASP* 2.9 30.9 + - - +
287K VAL* 3.8 23.3 - - + +
317K GLU* 3.0 50.0 + - + +
318K PHE 3.6 3.4 - - - +
320K GLU* 1.3 74.5 - - + +
322K SER* 1.3 60.0 + - - +
324K ALA* 3.4 8.2 + - - +
325K ARG* 3.0 28.9 + - - +
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Residues in contact with SER 322 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287K VAL* 4.3 12.2 + - - +
290K ALA* 5.5 0.5 - - - +
291K HIS* 5.0 3.0 + - - -
318K PHE* 2.8 46.5 + - - -
319K VAL* 3.3 8.0 + - - -
321K ARG* 1.3 74.3 - - - +
323K VAL* 1.3 60.1 + - - +
325K ARG* 3.3 5.0 + - - +
326K ALA* 2.9 30.3 + - - +
405K MET* 3.6 28.7 - - - +
407K ILE* 4.2 3.1 - - - -
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Residues in contact with VAL 323 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319K VAL* 2.9 24.2 + - + +
320K GLU* 3.8 6.7 - - - +
322K SER* 1.3 75.6 - - - +
324K ALA* 1.3 62.3 + - - +
326K ALA* 3.4 6.5 + - - +
327K LYS* 3.0 43.8 + - + +
368K LEU* 3.7 54.3 - - + +
369K CYS* 4.1 6.5 - - + -
385K VAL* 4.3 9.2 - - + -
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Residues in contact with ALA 324 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320K GLU 3.1 13.8 + - - +
321K ARG* 3.5 11.2 - - - +
322K SER 3.2 0.2 - - - -
323K VAL* 1.3 78.6 - - - +
325K ARG* 1.3 62.1 + - - +
327K LYS* 3.3 9.4 + - - +
328K SER* 3.2 23.0 + - - -
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Residues in contact with ARG 325 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287K VAL* 4.7 10.1 - - + +
288K GLU* 2.9 39.9 + - - +
291K HIS* 3.2 50.5 + - + +
321K ARG 3.0 16.2 + - - +
322K SER* 3.3 8.5 + - - +
324K ALA* 1.3 76.7 - - - +
326K ALA* 1.3 60.5 + - - +
328K SER* 2.9 32.1 + - - -
329K ARG* 3.3 9.9 + - - +
340K GLU* 2.8 36.6 + - - -
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Residues in contact with ALA 326 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291K HIS* 3.9 10.7 - - - -
295K PHE* 4.2 17.0 - - + -
322K SER 2.9 16.7 + - - +
323K VAL 3.8 3.8 - - - +
324K ALA 3.3 0.2 - - - -
325K ARG* 1.3 76.8 - - - +
327K LYS* 1.3 63.4 + - - +
329K ARG* 3.5 9.0 + - - +
369K CYS* 4.0 7.0 - - - -
383K PRO* 3.4 26.3 - - + +
385K VAL* 3.6 26.7 - - + -
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Residues in contact with LYS 327 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323K VAL* 3.0 31.7 + - + +
324K ALA* 3.8 7.6 - - - +
325K ARG 3.3 0.4 - - - -
326K ALA* 1.3 77.8 - - - +
328K SER* 1.3 61.4 + - - +
329K ARG 3.6 4.3 + - - +
368K LEU 4.2 4.8 + - - -
369K CYS* 3.6 30.7 - - + +
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Residues in contact with SER 328 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324K ALA 3.2 12.3 + - - -
325K ARG* 2.9 34.8 + - - -
327K LYS* 1.3 75.5 - - - +
329K ARG* 1.3 63.9 + - - +
330K VAL* 3.2 12.5 + - - +
340K GLU* 3.7 6.2 - - - +
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Residues in contact with ARG 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291K HIS* 3.2 37.7 + - + +
292K PHE* 6.0 1.0 - - - +
295K PHE* 3.1 39.9 + - - +
296K PHE* 4.2 4.8 - - - +
297K ASN 4.9 1.2 - - - +
298K GLN* 4.9 2.0 + - - +
325K ARG* 3.3 13.3 + - - +
326K ALA 3.6 12.9 - - - +
327K LYS 3.3 4.5 - - - +
328K SER* 1.3 74.2 - - - +
330K VAL* 1.3 63.5 + - - +
331K VAL* 3.5 11.3 + - - +
340K GLU* 3.5 49.6 + - + +
341K GLN* 3.0 34.4 + - + +
383K PRO* 4.0 11.9 - - + +
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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
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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