Contacts of the helix formed by residues 314 - 334 (chain D) in PDB entry 6UZA
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 PHE 314 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D PHE* 5.4 12.3 - + - -
270D SER* 3.8 32.3 - - - -
271D ARG* 4.9 5.6 - - + -
274D ILE* 3.7 38.4 - - + -
311D GLU* 3.8 14.6 - - - -
313D GLU* 1.3 106.0 + - + +
315D LYS* 1.3 62.3 + - - +
316D ASN 3.4 2.7 - - - +
317D ASP* 3.6 15.8 + - - +
318D TYR* 3.2 32.6 + - + -
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Residues in contact with LYS 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ALA* 3.4 34.5 - - + +
309D ASN* 5.2 5.2 - - - +
311D GLU 4.5 0.4 - - - -
312D LYS* 3.4 19.7 - - - +
313D GLU* 3.2 2.7 + - - -
314D PHE* 1.3 74.1 - - - +
316D ASN* 1.3 83.7 + - - +
317D ASP 3.1 4.7 + - - -
318D TYR* 3.3 2.3 + - - +
319D LYS* 3.0 48.9 + - + +
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Residues in contact with ASN 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D PHE* 3.4 0.6 - - - +
315D LYS* 1.3 96.4 + - - +
317D ASP* 1.3 61.0 + - - +
319D LYS* 4.2 11.5 - - - +
320D LYS* 3.3 33.5 + - - +
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Residues in contact with ASP 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ILE* 3.7 29.2 - - + +
278D LYS* 6.3 3.1 - - - -
314D PHE* 3.6 17.7 + - - +
315D LYS 3.1 0.8 - - - -
316D ASN* 1.3 82.6 - - - +
318D TYR* 1.3 62.4 + - - +
319D LYS 3.2 1.6 - - - -
320D LYS* 3.2 24.5 + - - +
321D LEU* 3.0 33.0 + - + +
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Residues in contact with TYR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D SER 5.2 0.2 + - - -
273D ARG* 3.4 34.3 - - - +
274D ILE* 4.1 23.1 - - + +
277D TYR* 4.1 12.6 - + + -
304D LEU* 3.6 36.6 - - + +
307D LEU* 3.7 34.5 - - + +
308D ALA* 3.7 20.9 - - + -
311D GLU* 3.9 20.9 + - + -
314D PHE* 3.2 27.9 + - + +
315D LYS 3.3 1.6 + - - +
317D ASP* 1.3 73.8 - - - +
319D LYS* 1.3 61.6 + - - +
321D LEU* 3.9 8.8 - - + +
322D SER* 3.0 30.0 + - - -
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Residues in contact with LYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ALA* 4.9 11.0 + - + +
308D ALA* 4.0 18.9 - - + +
309D ASN* 4.4 17.6 + - - +
315D LYS* 3.0 37.4 + - + +
316D ASN* 4.3 13.2 - - - +
317D ASP 3.2 0.2 - - - -
318D TYR* 1.3 75.9 - - - +
320D LYS* 1.3 58.2 + - + +
322D SER* 3.5 6.1 + - - -
323D MET* 2.9 29.5 + - - +
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Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ASN* 3.3 25.2 + - - +
317D ASP* 3.2 26.3 + - - +
319D LYS* 1.3 75.7 - - + +
321D LEU* 1.3 63.0 + - + +
323D MET* 3.3 7.1 + - - +
324D GLN* 3.0 30.1 + - - +
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ILE* 4.5 9.9 - - + +
277D TYR* 4.1 15.0 - - + -
278D LYS* 3.9 52.0 - - + +
281D ALA* 4.3 3.8 - - + -
304D LEU* 3.7 16.6 - - + -
317D ASP* 3.0 21.7 + - + +
318D TYR* 3.9 17.9 - - + +
320D LYS* 1.3 78.4 - - + +
322D SER* 1.3 56.7 + - - +
324D GLN* 3.4 25.7 - - - +
325D CYS* 3.0 30.5 + - - -
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Residues in contact with SER 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D SER* 3.0 26.1 + - - +
304D LEU* 3.9 13.5 - - - +
305D ALA* 4.1 10.9 - - - +
318D TYR 3.0 17.2 + - - -
319D LYS* 3.9 6.3 - - - -
321D LEU* 1.3 77.0 - - - +
323D MET* 1.3 57.2 + - - +
325D CYS* 3.3 5.8 + - - +
326D LYS* 3.0 48.4 + - - +
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Residues in contact with MET 323 (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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319D LYS 2.9 18.6 + - - +
320D LYS* 3.3 9.4 + - - +
322D SER* 1.3 77.5 - - - +
324D GLN* 1.3 57.0 + - - +
326D LYS* 3.3 26.2 + - + +
327D ASP* 2.9 60.4 + - - +
376D LYS* 4.3 24.0 - - + +
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Residues in contact with GLN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D GLN* 5.3 3.4 + - - +
278D LYS* 4.6 4.2 + - - +
281D ALA 2.4 37.2 + - - +
282D SER* 3.9 8.1 - - - +
283D PRO* 4.9 11.6 - - + +
286D LEU* 5.7 0.2 - - - +
320D LYS 3.0 15.1 + - - +
321D LEU* 3.4 30.0 - - - +
323D MET* 1.3 73.7 - - - +
325D CYS* 1.3 63.0 + - - +
327D ASP* 3.7 10.6 - - + +
328D PHE* 3.0 28.2 + - - +
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Residues in contact with CYS 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ALA* 3.6 27.8 - - - -
286D LEU* 4.4 9.9 - - - -
297D ALA* 3.9 9.7 - - + +
300D LEU* 3.8 28.0 - - - -
301D SER* 3.8 18.2 - - - -
304D LEU* 4.0 4.5 - - - -
321D LEU 3.0 18.0 + - - +
322D SER 3.3 8.5 + - - +
324D GLN* 1.3 78.6 - - - +
326D LYS* 1.3 59.8 + - - +
328D PHE* 3.7 9.1 + - - +
329D VAL* 3.5 20.1 - - - +
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Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 6.4 0.7 - - - -
301D SER* 4.2 12.1 - - - -
305D ALA* 5.6 4.4 - - - +
322D SER* 3.0 37.5 + - - +
323D MET* 3.6 28.8 - - + +
324D GLN 3.2 0.2 - - - -
325D CYS* 1.3 76.1 - - - +
327D ASP* 1.3 60.3 + - - +
329D VAL* 3.2 7.5 + - - +
330D VAL* 3.0 32.3 + - + +
372D TYR 4.1 11.5 + - - -
373D GLU* 3.4 28.5 + - - +
374D VAL* 3.9 31.3 - - + +
375D LYS 5.4 1.3 - - - +
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Residues in contact with ASP 327 (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 MET* 2.9 46.1 + - - +
324D GLN* 3.3 11.2 + - + +
326D LYS* 1.3 74.1 - - - +
328D PHE* 1.3 59.4 + - - +
330D VAL* 4.0 6.7 - - - +
331D GLY* 2.9 26.9 + - - -
376D LYS* 5.0 8.3 - - - +
866D TYR* 5.1 1.3 + - - -
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D PRO* 4.0 18.1 - - + +
286D LEU* 4.2 15.7 - - + -
287D SER* 4.0 22.0 - - - -
293D PRO* 3.7 42.2 - - + -
294D VAL* 4.7 0.4 - - - -
297D ALA* 3.7 18.4 - - + -
324D GLN 3.0 15.6 + - - +
325D CYS 3.8 6.3 - - - +
326D LYS 3.2 0.2 - - - -
327D ASP* 1.3 76.8 - - - +
329D VAL* 1.3 60.2 + - + +
331D GLY 3.7 1.0 - - - -
332D LEU* 2.9 46.5 + - + +
863D ILE* 6.1 0.7 - - + -
866D TYR* 3.5 50.1 - + - +
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Residues in contact with VAL 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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294D VAL* 3.7 31.9 - - + +
297D ALA* 3.7 22.2 - - + -
298D LEU* 4.7 17.0 - - + -
325D CYS 3.5 17.9 - - - +
326D LYS* 3.2 7.5 + - - +
328D PHE* 1.3 75.5 - - + +
330D VAL* 1.3 62.1 + - + +
332D LEU* 3.2 7.1 + - + +
333D LEU* 3.0 28.1 + - - +
345D ILE* 5.0 1.2 - - + +
374D VAL* 5.5 1.3 - - + -
377D PHE* 3.6 31.1 - - + -
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Residues in contact with VAL 330 (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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326D LYS* 3.0 20.6 + - + +
327D ASP* 4.0 7.9 - - - +
328D PHE 3.4 0.2 - - - -
329D VAL* 1.3 76.9 - - - +
331D GLY* 1.3 59.8 + - - +
333D LEU* 3.4 8.0 + - + +
334D ASP* 3.4 20.7 + - - +
374D VAL* 4.6 4.3 - - + -
376D LYS* 3.7 36.6 - - + +
377D PHE* 3.5 32.5 - - + +
380D HIS* 4.4 14.2 - - + +
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Residues in contact with GLY 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 ASP 2.9 17.3 + - - -
328D PHE 3.7 1.8 - - - -
330D VAL* 1.3 76.5 - - - +
332D LEU* 1.3 58.9 + - - +
334D ASP* 3.8 12.8 + - - +
335D LEU* 3.6 21.8 - - - +
866D TYR* 4.1 13.4 - - - -
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Residues in contact with LEU 332 (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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293D PRO* 4.5 9.2 - - + -
294D VAL* 3.8 28.7 - - + -
328D PHE* 2.9 39.8 + - + +
329D VAL* 3.2 6.7 + - - +
331D GLY* 1.3 76.6 - - - +
333D LEU* 1.3 62.7 + - - +
334D ASP 3.2 0.8 + - - -
335D LEU* 3.7 14.8 + - + +
336D CYS* 3.9 9.5 - - - -
345D ILE* 4.3 17.4 - - + +
859D MET* 4.7 3.8 - - + -
862D LEU* 3.9 21.8 - - + +
863D ILE* 5.0 3.8 - - + +
866D TYR* 3.8 33.6 - - + -
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Residues in contact with LEU 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 VAL 3.0 16.3 + - - +
330D VAL* 3.4 5.6 + - - +
332D LEU* 1.3 74.6 - - - +
334D ASP* 1.3 62.5 + - - +
336D CYS* 3.3 17.7 + - - -
342D VAL* 4.9 3.8 - - + -
345D ILE* 3.8 30.9 - - + +
346D LEU* 3.9 23.1 - - + -
377D PHE* 3.7 38.1 - - + +
380D HIS* 3.8 29.8 - - + -
382D ASN* 3.3 27.6 + - + -
383D CYS* 4.8 0.9 - - + -
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Residues in contact with ASP 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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271A ARG* 4.0 15.4 + - - -
330D VAL* 3.4 13.7 + - - +
331D GLY* 3.9 11.9 - - - +
332D LEU 3.2 0.6 - - - -
333D LEU* 1.3 79.7 - - - +
335D LEU* 1.3 60.7 + - + +
336D CYS 3.2 2.2 + - - +
380D HIS* 3.5 28.8 + - + -
382D ASN* 4.5 3.5 + - - +
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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