Contacts of the helix formed by residues 319 - 339 (chain D) in PDB entry 5ED1
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D LEU 5.8 0.4 - - - +
318D HIS* 1.3 74.9 - - - +
320D PRO* 1.3 74.8 - - + +
321D GLN 3.4 2.5 - - - +
322D VAL* 3.1 22.5 - - + +
323D LEU* 2.9 23.2 + - - +
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Residues in contact with PRO 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D PRO* 4.2 19.5 - - + -
311D PRO* 5.3 8.5 - - + -
316D GLN* 4.0 22.2 - - + +
318D HIS 3.7 5.4 - - - +
319D LEU* 1.3 86.2 - - + +
321D GLN* 1.3 58.0 + - - +
323D LEU* 3.4 2.8 + - + +
324D ALA* 2.9 29.3 + - - +
580D LEU* 3.7 33.8 - - + +
582D SER* 4.8 2.2 - - - +
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Residues in contact with GLN 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D PRO* 4.6 15.4 - - + +
319D LEU* 3.4 1.6 - - - +
320D PRO* 1.3 78.0 - - + +
322D VAL* 1.3 60.3 + - - +
324D ALA* 3.6 4.6 - - - +
325D ASP* 3.0 62.2 + - - +
582D SER* 3.8 6.5 + - - -
583D GLY 3.4 25.7 + - - +
584D ILE* 3.8 7.0 - - - +
585D SER* 3.9 15.8 + - - +
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Residues in contact with VAL 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D HIS* 4.7 1.1 - - + -
319D LEU* 3.1 43.3 + - + +
321D GLN* 1.3 74.6 - - - +
323D LEU* 1.3 65.3 + - - +
325D ASP* 3.9 4.6 - - + +
326D ALA* 2.9 31.7 + - + +
363D VAL* 4.7 24.9 - - + -
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Residues in contact with LEU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D GLN* 6.2 0.4 - - - +
318D HIS* 3.8 37.2 - - + +
319D LEU 2.9 16.9 + - - +
320D PRO* 3.6 3.6 - - + +
322D VAL* 1.3 77.0 - - - +
324D ALA* 1.3 66.1 + - - +
326D ALA* 3.1 5.2 + - + +
327D VAL* 3.0 41.5 + - + +
358D THR* 4.7 5.2 - - + -
363D VAL* 4.4 9.9 - - + -
443D HIS* 3.7 21.5 - - + +
544D SER* 3.3 27.8 - - - +
546D ILE* 5.3 0.9 - - + -
580D LEU* 3.9 14.8 - - + -
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D PRO 2.9 17.4 + - - +
321D GLN* 3.6 20.0 - - - +
322D VAL 3.4 0.2 - - - -
323D LEU* 1.3 76.8 - - - +
325D ASP* 1.3 63.3 + - - +
327D VAL* 3.4 0.3 + - - -
328D SER* 3.0 27.1 + - - -
546D ILE* 3.6 35.7 - - + +
582D SER* 3.7 10.1 - - - +
583D GLY 3.7 5.8 - - - +
584D ILE* 4.4 1.8 - - + -
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Residues in contact with ASP 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D GLN* 3.0 44.1 + - - +
322D VAL* 4.0 5.2 - - - +
324D ALA* 1.3 74.4 - - - +
326D ALA* 1.3 57.2 + - - +
328D SER* 3.0 7.0 + - - -
329D ARG* 2.9 40.2 + - - +
584D ILE* 4.3 2.8 - - - +
585D SER* 3.3 30.7 + - - -
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D VAL* 2.9 21.1 + - + +
323D LEU* 3.1 8.5 + - + +
325D ASP* 1.3 77.9 - - - +
327D VAL* 1.3 60.4 + - + +
329D ARG* 3.3 16.6 + - - +
330D LEU* 2.9 40.3 + - + +
363D VAL* 4.3 21.3 - - + +
366D ALA* 6.0 1.3 - - + -
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Residues in contact with VAL 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LEU* 3.0 37.9 + - + +
324D ALA 4.2 0.9 - - - +
326D ALA* 1.3 70.8 - - + +
328D SER* 1.3 69.3 + - - +
330D LEU* 4.3 3.4 - - - -
331D VAL* 3.0 26.3 + - - +
356D VAL* 3.9 28.5 - - + -
443D HIS* 4.3 17.9 - - + +
444D LEU 4.9 1.3 - - - +
445D TYR* 3.7 27.4 - - + +
546D ILE* 4.0 20.4 - - + -
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Residues in contact with SER 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D ALA 3.0 16.3 + - - -
325D ASP* 3.0 15.8 + - - -
327D VAL* 1.3 80.3 - - - +
329D ARG* 1.3 75.1 + - - +
331D VAL* 3.9 0.9 - - - +
332D LEU* 3.0 26.7 + - - +
445D TYR* 3.7 33.7 - - - -
584D ILE* 3.9 21.4 - - - +
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Residues in contact with ARG 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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325D ASP* 2.9 18.1 + - - +
326D ALA* 3.8 16.4 + - - +
328D SER* 1.3 82.5 + - - +
330D LEU* 1.3 67.7 + - - +
332D LEU* 4.1 4.2 - - - +
333D GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 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 ALA* 2.9 29.3 + - + +
327D VAL* 3.9 4.0 - - - +
329D ARG* 1.3 88.0 - - + +
331D VAL* 1.3 59.8 + - - +
333D GLY* 3.5 0.8 + - - -
334D LYS* 2.9 30.5 + - - +
356D VAL* 4.5 10.1 - - + -
363D VAL 5.5 1.1 - - - +
366D ALA* 3.8 36.1 - - + +
368D VAL* 3.6 20.3 - - + +
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Residues in contact with VAL 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D VAL 3.0 20.9 + - - +
328D SER 4.0 1.6 - - - +
330D LEU* 1.3 72.0 - - - +
332D LEU* 1.3 68.0 + - - +
334D LYS* 3.9 3.0 - - - +
335D PHE* 3.0 23.0 + - - +
352D LEU* 3.9 14.1 - - + -
353D ALA 4.1 16.2 - - - +
354D GLY* 3.9 23.1 - - - +
355D VAL 4.4 0.9 - - - +
356D VAL* 3.9 20.2 - - + -
368D VAL* 4.5 9.9 - - + -
371D VAL* 4.1 7.4 - - + +
445D TYR* 3.7 26.7 - - + -
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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
----------------------------------------------------------
328D SER 3.0 18.6 + - - +
329D ARG* 4.2 3.6 - - - +
331D VAL* 1.3 77.0 - - - +
333D GLY* 1.3 57.8 + - - +
335D PHE* 3.2 6.9 + - + +
336D GLY 3.0 23.2 + - - -
342D PHE* 3.5 25.9 - - + -
349D ARG* 3.9 18.4 - - - +
352D LEU* 3.6 25.3 - - + +
445D TYR* 5.8 4.3 - - + +
588D GLU* 4.8 8.1 - - - +
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Residues in contact with GLY 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 ARG 2.9 19.0 + - - -
330D LEU* 3.8 1.3 - - - -
332D LEU* 1.3 76.9 - - - +
334D LYS* 1.3 57.3 + - - +
336D GLY* 3.1 4.4 + - - -
337D ASP* 2.9 32.8 + - - +
342D PHE* 5.2 2.5 - - - -
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Residues in contact with LYS 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 LEU 2.9 18.9 + - - +
331D VAL 3.9 3.1 - - - +
332D LEU 3.4 0.2 - - - -
333D GLY* 1.3 72.1 - - - +
335D PHE* 1.3 66.5 + - - +
337D ASP* 3.1 25.2 + - + +
338D LEU* 2.9 34.5 + - + +
368D VAL* 4.0 18.6 - - + -
371D VAL* 3.8 11.0 - - + -
602D TRP* 3.8 44.0 - - + -
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Residues in contact with PHE 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 VAL 3.0 17.8 + - - +
332D LEU* 3.5 6.5 - - + +
334D LYS* 1.3 75.8 - - - +
336D GLY* 1.3 62.6 + - - +
338D LEU* 3.2 6.9 + - + +
339D THR* 3.0 44.1 + - + +
342D PHE* 3.7 20.9 - + - -
346D HIS 3.8 7.6 - - - -
347D ALA* 3.6 40.4 - - - -
349D ARG* 4.2 11.0 - - + -
352D LEU* 3.8 19.1 - - + -
371D VAL* 3.6 27.5 - - + +
373D THR* 3.7 26.0 - - + -
600D VAL* 4.3 14.6 - - + -
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Residues in contact with GLY 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 LEU 3.0 10.9 + - - -
333D GLY 3.4 6.1 - - - -
334D LYS 3.1 0.2 - - - -
335D PHE* 1.3 77.1 - - - +
337D ASP* 1.3 61.2 + - - +
339D THR* 3.1 7.4 + - - -
341D ASN* 2.9 33.2 + - - -
342D PHE* 3.4 31.1 - - - -
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Residues in contact with ASP 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 GLY 2.9 20.5 + - - +
334D LYS* 3.1 34.3 + - + +
336D GLY* 1.3 75.6 - - - +
338D LEU* 1.3 62.4 + - + +
339D THR 3.3 0.9 + - - -
340D ASP* 3.8 7.8 + - - -
341D ASN 5.1 0.7 - - - +
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Residues in contact with LEU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D LYS* 2.9 32.1 + - + +
335D PHE* 3.6 6.5 - - + +
336D GLY 3.2 0.2 - - - -
337D ASP* 1.3 78.7 - - + +
339D THR* 1.3 63.2 + - + +
340D ASP* 3.6 3.1 + - - +
371D VAL* 4.4 13.7 - - + -
602D TRP* 3.5 64.6 - - + +
607D SER 4.4 12.3 - - - +
608D ALA* 5.1 0.6 - - - -
609D ILE* 3.6 30.9 + - + +
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Residues in contact with THR 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 PHE* 3.0 48.5 + - + +
336D GLY 3.1 1.9 + - - -
338D LEU* 1.3 85.4 - - + +
340D ASP* 1.3 69.3 + - - +
342D PHE* 2.9 30.1 + - - -
344D SER* 3.2 25.1 + - - -
346D HIS 4.4 4.3 - - - +
347D ALA* 3.9 17.0 - - - +
609D ILE* 5.0 8.3 - - + -
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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