Contacts of the helix formed by residues 323 - 341 (chain D) in PDB entry 5IJO
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 PRO 323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D GLU* 5.3 14.4 - - + +
320D TRP* 3.5 26.7 - - + +
321D LYS 3.3 2.1 - - - +
322D LEU* 1.3 76.6 - - - +
324D GLY* 1.3 64.5 + - - +
325D LEU 3.4 1.3 - - - +
326D GLN* 3.5 24.3 + - + +
327D ALA* 3.5 6.1 + - - +
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Residues in contact with GLY 324 (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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263D SER* 5.9 3.8 - - - -
321D LYS 4.2 6.5 - - - -
322D LEU 3.0 9.7 + - - -
323D PRO* 1.3 71.2 - - - +
325D LEU* 1.3 53.7 + - - +
327D ALA* 2.6 35.7 + - - +
328D THR* 2.9 5.7 + - - -
366D ASP 5.1 5.6 - - - -
367D ASN* 5.3 5.1 - - - +
371D PHE* 5.2 11.2 - - - +
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Residues in contact with LEU 325 (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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263D SER* 6.0 2.7 - - - +
268D ASN* 5.7 9.6 - - + -
323D PRO 3.4 0.4 - - - -
324D GLY* 1.3 71.4 - - - +
326D GLN* 1.3 67.9 + - - +
328D THR* 3.7 10.5 - - - +
329D VAL* 3.2 18.9 + - - +
371D PHE* 5.2 7.9 - - + +
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Residues in contact with GLN 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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254D GLU* 6.1 3.8 - - + -
320D TRP* 5.2 7.4 - - + +
323D PRO* 3.5 27.0 + - + +
324D GLY 3.1 0.8 - - - -
325D LEU* 1.3 78.1 - - - +
327D ALA* 1.3 62.5 + - - +
329D VAL* 3.0 5.8 + - - +
330D ARG* 2.9 24.9 + - - +
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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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320D TRP 5.1 5.4 + - - +
321D LYS 6.0 0.2 - - - +
323D PRO 3.5 5.9 + - - +
324D GLY* 2.6 22.0 + - - +
326D GLN* 1.3 74.7 - - - +
328D THR* 1.3 60.0 + - - +
330D ARG* 3.4 5.3 + - - +
331D LEU* 3.0 22.7 + - - +
363D ALA* 4.3 8.2 - - + +
366D ASP* 4.2 29.2 - - + +
368D VAL* 4.2 11.6 - - + +
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Residues in contact with THR 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 GLY 2.9 9.7 + - - -
325D LEU* 3.9 12.3 - - - -
326D GLN 3.2 0.4 - - - -
327D ALA* 1.3 78.0 - - - +
329D VAL* 1.3 66.6 + - - +
331D LEU* 2.9 5.0 + - - +
332D ALA* 2.9 21.7 + - - +
368D VAL* 4.3 21.9 - - - +
371D PHE* 5.4 9.9 - - - -
372D LEU* 5.6 3.6 - - - -
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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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250D ILE* 6.6 0.2 - - + -
275D LEU* 5.4 11.7 - - + -
325D LEU 3.2 12.6 + - - +
326D GLN* 3.0 5.0 + - - +
328D THR* 1.3 82.0 - - - +
330D ARG* 1.3 64.4 + - - +
332D ALA* 3.1 10.6 + - - +
333D TRP* 2.9 20.4 + - - +
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Residues in contact with ARG 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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314D LEU* 4.5 22.4 - - + +
317D SER* 6.5 0.7 - - - -
326D GLN 2.9 16.9 + - - +
327D ALA* 3.9 5.4 - - - +
329D VAL* 1.3 78.6 - - - +
331D LEU* 1.3 62.6 + - - +
333D TRP* 2.8 20.0 + - - +
334D ALA* 3.0 11.3 + - - +
363D ALA* 6.1 0.9 - - + -
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Residues in contact with LEU 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 ALA 3.0 13.4 + - - +
328D THR 2.9 9.3 + - - +
330D ARG* 1.3 75.7 - - - +
332D ALA* 1.3 63.3 + - - +
334D ALA* 3.1 11.6 + - - +
335D LEU* 3.0 19.2 + - - +
360D ALA* 5.6 4.5 - - + +
363D ALA* 3.9 14.3 - - + +
368D VAL* 3.9 20.9 - - + -
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Residues in contact with ALA 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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276D LEU* 6.3 2.9 - - - -
279D PHE* 4.8 7.5 - - + +
328D THR* 2.9 12.3 + - - +
329D VAL* 3.1 14.6 - - - +
331D LEU* 1.3 74.7 - - - +
333D TRP* 1.3 65.4 + - - +
335D LEU* 3.0 17.6 + - - +
336D ALA* 3.1 12.3 + - - +
395D LEU* 6.3 3.6 - - + -
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Residues in contact with TRP 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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279D PHE* 4.3 17.7 - - + +
329D VAL 2.9 10.8 + - - +
330D ARG* 2.8 14.3 + - - +
332D ALA* 1.3 75.1 - - - +
334D ALA* 1.3 52.0 + - - +
336D ALA* 3.1 5.7 + - - +
337D LEU* 2.7 34.9 + - - +
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Residues in contact with ALA 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 ARG 3.0 10.5 + - - +
331D LEU* 3.3 13.5 - - - +
332D ALA 3.1 0.2 - - - -
333D TRP* 1.3 74.3 - - - +
335D LEU* 1.3 65.6 + - - +
337D LEU* 3.1 17.8 + - - +
338D ARG* 3.2 14.4 + - - +
356D ASP* 5.5 10.7 - - + +
359D MET* 6.0 3.4 - - + -
360D ALA* 5.0 17.0 - - + +
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Residues in contact with LEU 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 LEU 3.0 11.3 + - - +
332D ALA* 3.0 13.6 + - - +
334D ALA* 1.3 76.9 - - - +
336D ALA* 1.3 61.6 + - - +
338D ARG* 3.9 5.9 + - - +
339D GLY* 4.2 1.0 + - - -
395D LEU 5.7 0.9 - - - +
398D ASP* 4.9 12.6 - - + +
399D PHE* 4.8 20.6 - - + -
402D LEU* 3.9 22.0 - - + +
403D MET* 5.6 7.2 - - + -
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Residues in contact with ALA 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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279D PHE* 3.5 32.5 - - + +
280D ASP* 4.9 3.6 - - - +
282D SER* 5.5 3.4 - - - -
332D ALA 3.1 10.0 + - - +
333D TRP 3.1 8.6 + - - +
335D LEU* 1.3 73.8 - - - +
337D LEU* 1.3 65.3 + - - +
338D ARG 3.1 2.0 - - - -
339D GLY* 2.9 14.9 + - - -
340D ILE* 3.2 9.7 + - - +
398D ASP* 5.6 5.1 - - + +
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Residues in contact with LEU 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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282D SER* 6.0 2.7 - - - -
311D HIS* 6.1 5.6 - - + -
333D TRP 2.7 19.5 + - - +
334D ALA* 3.1 9.4 + - - +
336D ALA* 1.3 71.3 - - - +
338D ARG* 1.3 64.3 + - - +
340D ILE* 2.8 20.9 + - - +
341D SER* 2.9 14.3 + - - -
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Residues in contact with ARG 338 (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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334D ALA 3.2 8.2 + - - +
335D LEU* 4.0 11.0 - - - +
336D ALA 3.1 0.2 - - - -
337D LEU* 1.3 80.1 - - - +
339D GLY* 1.3 61.7 + - - +
341D SER* 3.3 17.6 + - - -
342D GLN* 3.9 3.5 + - - -
356D ASP* 6.0 7.2 - - + -
402D LEU* 4.7 14.6 - - + +
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Residues in contact with GLY 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 LEU 4.2 2.9 + - - -
336D ALA 2.9 10.0 + - - -
338D ARG* 1.3 80.0 - - - +
340D ILE* 1.3 61.5 + - - +
342D GLN* 3.0 24.5 + - - +
402D LEU* 5.2 5.3 - - - +
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Residues in contact with ILE 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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282D SER* 4.9 16.4 - - - -
283D PHE* 5.8 4.7 - - + +
336D ALA 3.2 7.6 + - - +
337D LEU* 2.8 14.8 + - - +
339D GLY* 1.3 70.6 - - - +
341D SER* 1.3 56.0 + - - +
342D GLN* 2.7 16.1 + - - +
343D LEU* 3.3 13.9 + - - +
346D VAL* 5.1 2.2 - - - +
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Residues in contact with SER 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 LEU 2.9 10.3 + - - -
338D ARG* 3.6 14.4 - - - -
339D GLY 3.2 0.4 - - - -
340D ILE* 1.3 72.4 - - - +
342D GLN* 1.3 65.2 + - - +
343D LEU 3.0 6.1 - - - +
346D VAL* 4.1 15.7 - - - -
347D THR* 2.8 47.0 - - - -
350D ALA* 6.4 0.9 - - - -
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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
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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