Contacts of the helix formed by residues 314 - 329 (chain D) in PDB entry 5U03
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 TYR 314 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU* 3.3 5.2 - - - -
303D LEU* 3.6 28.5 - - + -
305D GLY* 4.7 0.5 - - - -
306D LYS 4.5 1.7 + - - -
307D TYR* 3.4 35.0 + - + +
308D THR* 3.0 38.6 + - - -
311D SER* 4.6 6.9 + - - +
312D ASP* 2.9 1.7 - - - +
313D SER* 1.3 92.1 - - - +
315D ALA* 1.3 53.3 + - - +
316D SER 3.3 0.4 - - - -
317D VAL* 3.0 22.7 + - + -
318D ILE* 2.8 44.7 + - + +
336D TYR* 5.4 3.1 - + + -
370D PRO* 3.6 30.3 - - + +
371D GLY 4.9 6.3 + - - -
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 3.1 5.3 + - - +
69D LEU* 4.3 10.8 - - + -
312D ASP* 3.0 29.6 + - + +
314D TYR* 1.3 75.7 - - - +
316D SER* 1.3 58.9 + - - +
318D ILE* 4.0 6.6 - - - +
319D LYS* 3.0 28.1 + - - +
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Residues in contact with SER 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 2.6 34.8 + - - +
69D LEU* 3.9 24.3 - - - +
76D ARG* 4.2 13.8 + - - +
315D ALA* 1.3 72.1 - - - +
317D VAL* 1.3 58.3 + - - +
319D LYS* 3.6 7.7 - - - +
320D ALA* 2.8 28.1 + - - +
323D HIS* 5.7 0.2 - - - -
528D GLU* 4.0 26.7 - - - +
529D PHE* 4.5 5.0 - - - -
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 4.4 4.5 - - + +
303D LEU* 5.6 1.1 - - + -
313D SER 5.3 0.7 - - - +
314D TYR* 3.0 34.0 + - + +
316D SER* 1.3 77.1 + - - +
318D ILE* 1.3 67.0 + - + +
320D ALA* 3.1 5.5 + - - +
321D LEU* 3.0 24.3 + - + +
368D LEU* 3.8 28.3 - - + -
370D PRO* 6.0 4.0 - - + -
528D GLU* 4.0 29.6 - - + +
540D TYR* 4.2 14.6 - - + +
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Residues in contact with ILE 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D LEU* 5.8 0.9 - - + -
314D TYR* 2.8 34.2 + - + +
315D ALA* 4.1 6.3 - - - +
317D VAL* 1.3 74.0 - - + +
319D LYS* 1.3 57.8 + - - +
321D LEU* 2.9 13.4 + - + +
322D GLU* 2.8 45.4 + - + +
332D LEU* 4.7 2.2 - - + -
334D ILE* 3.9 37.9 - - + -
336D TYR* 3.2 31.9 - - + +
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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
----------------------------------------------------------
76D ARG* 3.6 29.2 - - - +
249D SER* 4.7 10.5 + - - -
250D ILE* 5.4 12.3 - - - +
292D TYR* 5.9 1.1 + - - +
315D ALA 3.0 20.7 + - - +
316D SER* 3.6 8.5 - - - +
317D VAL 3.2 0.2 - - - -
318D ILE* 1.3 77.2 - - - +
320D ALA* 1.3 60.8 + - - +
322D GLU* 2.8 36.3 + - + +
323D HIS* 2.9 52.1 + - + +
533D PRO* 6.1 0.2 - - + -
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Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D SER 2.8 15.0 + - - +
317D VAL 3.1 9.4 + - - +
319D LYS* 1.3 75.4 - - - +
321D LEU* 1.3 61.4 + - - +
323D HIS* 3.0 29.7 + - - +
324D SER* 3.3 9.6 + - - -
528D GLU* 4.0 8.7 - - + +
531D SER* 4.0 14.6 + - - +
536D PRO* 5.2 0.2 - - - +
540D TYR* 3.7 33.1 - - + +
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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
----------------------------------------------------------
301D ILE* 4.1 30.1 - - + -
317D VAL* 3.0 26.5 + - + +
318D ILE* 2.9 14.5 + - + +
320D ALA* 1.3 75.8 - - - +
322D GLU* 1.3 55.5 + - - +
324D SER* 3.0 8.6 + - - -
325D ALA* 2.8 27.4 + - - +
332D LEU* 3.6 18.8 - - + +
334D ILE* 3.7 25.6 - - + -
368D LEU* 5.0 3.6 - - + -
540D TYR* 3.7 38.8 - - + +
543D LEU* 5.0 2.5 - - + -
544D LEU* 4.9 4.4 - - + +
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Residues in contact with GLU 322 (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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249D SER* 5.2 3.1 + - - -
292D TYR* 5.4 13.7 + - + +
318D ILE* 2.8 34.2 + - + +
319D LYS* 2.8 46.2 + - + +
321D LEU* 1.3 71.8 - - - +
323D HIS* 1.3 68.5 + - + +
325D ALA* 3.5 8.0 - - + +
326D LEU* 2.8 25.8 + - - +
332D LEU* 4.4 8.7 - - + -
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Residues in contact with HIS 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 3.7 14.2 + - - -
292D TYR* 5.7 4.0 - - - -
316D SER 5.7 0.2 - - - -
319D LYS* 2.9 47.1 + - + +
320D ALA* 3.0 11.9 + - - +
322D GLU* 1.3 78.9 - - + +
324D SER* 1.3 60.0 + - - +
326D LEU* 3.4 6.7 + - - +
327D ALA* 3.1 20.8 + - - +
528D GLU 5.8 0.9 - - - -
531D SER* 3.0 38.7 + - - +
532D ARG* 3.3 21.1 - - - +
533D PRO* 3.4 40.9 - - + +
536D PRO* 3.9 12.9 - - + +
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Residues in contact with SER 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ALA 3.3 7.9 + - - -
321D LEU* 3.0 10.8 + - - -
323D HIS* 1.3 75.9 - - - +
325D ALA* 1.3 64.6 + - - +
327D ALA* 3.0 14.5 + - - +
328D ILE* 3.0 11.6 + - - +
536D PRO* 4.2 7.4 - - - +
537D SER 4.3 0.2 + - - -
540D TYR* 3.6 7.0 - - - +
541D PHE* 3.1 45.7 + - - +
544D LEU* 3.4 21.9 - - - +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D LEU* 5.9 0.4 - - - -
321D LEU 2.8 12.5 + - - +
322D GLU* 3.1 13.2 + - + +
324D SER* 1.3 75.1 - - - +
326D LEU* 1.3 53.3 + - - +
328D ILE* 3.4 2.1 - - - +
329D ASN* 2.6 28.9 + - - -
330D HIS* 2.9 28.1 + - + +
331D LYS 5.2 0.2 - - - +
332D LEU* 4.2 21.8 - - + -
544D LEU* 3.7 13.6 - - + +
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Residues in contact with LEU 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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288D MET* 4.4 20.2 - - + +
291D ARG* 3.7 40.4 - - + +
292D TYR* 3.5 48.2 - - + +
295D LEU* 5.0 5.8 - - + -
322D GLU 2.8 16.3 + - - +
323D HIS* 3.7 6.3 - - - +
325D ALA* 1.3 76.3 - - - +
327D ALA* 1.3 66.9 + - - +
329D ASN* 2.8 26.7 + - - +
533D PRO* 5.1 14.6 - - + +
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Residues in contact with ALA 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 HIS 3.1 12.9 + - - +
324D SER* 3.0 11.2 + - - +
326D LEU* 1.3 78.7 - - - +
328D ILE* 1.3 61.2 + - - +
329D ASN* 3.3 10.4 + - - -
533D PRO 6.0 0.9 - - - +
536D PRO* 4.7 12.3 - - + -
541D PHE* 3.9 21.1 - - + -
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Residues in contact with ILE 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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324D SER 3.0 7.3 + - - +
325D ALA* 3.4 10.1 - - - +
327D ALA* 1.3 74.3 - - - +
329D ASN* 1.3 72.5 + - - +
330D HIS* 3.4 51.0 + - + +
541D PHE* 4.5 7.2 - - + -
544D LEU* 3.5 27.8 - - + -
545D LEU* 3.8 28.0 - - + -
548D VAL* 4.0 16.8 - - + -
550D ARG* 4.6 7.9 - - + +
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Residues in contact with ASN 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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291D ARG* 3.8 34.8 + - - +
294D ARG 5.2 9.2 - - - +
295D LEU* 4.0 16.2 - - + +
296D LEU* 3.2 14.0 + - - +
325D ALA 2.6 13.3 + - - -
326D LEU* 2.8 22.7 + - - +
327D ALA 3.3 16.0 + - - -
328D ILE* 1.3 79.5 + - - +
330D HIS* 1.3 65.9 + - + +
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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