Contacts of the helix formed by residues 307 - 322 (chain D) in PDB entry 4PEI
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 THR 307 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304D SER 5.8 0.2 - - - +
305D LYS 3.4 11.7 + - - +
306D ARG* 1.3 81.1 - - - +
308D LYS* 1.3 59.9 + - - +
309D GLU* 3.6 5.3 + - - +
310D LEU* 3.0 31.2 + - + +
311D ASP* 2.8 34.5 + - - -
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Residues in contact with LYS 308 (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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307D THR* 1.3 74.7 - - - +
309D GLU* 1.3 68.6 + - - +
311D ASP* 3.4 9.6 + - + +
312D LYS* 3.0 27.5 + - - +
294E ASP* 6.0 0.4 - - - +
296E SER* 4.6 26.4 - - - +
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Residues in contact with GLU 309 (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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307D THR* 3.3 5.2 + - - +
308D LYS* 1.3 85.4 + - - +
310D LEU* 1.3 68.3 + - + +
312D LYS* 3.5 32.4 + - - +
313D LYS* 3.1 20.8 + - - +
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Residues in contact with LEU 310 (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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281D MET* 4.0 13.7 - - + -
305D LYS* 3.9 19.1 - - + +
306D ARG 5.0 0.2 - - - -
307D THR* 3.0 26.4 + - + +
309D GLU* 1.3 76.9 - - - +
311D ASP* 1.3 62.2 + - - +
313D LYS* 3.0 7.3 + - + +
314D ILE* 2.8 36.3 + - + +
351D LEU* 4.2 42.2 - - + +
353D ILE* 4.5 13.2 - - + -
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Residues in contact with ASP 311 (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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277D CYS* 3.5 20.1 - - - +
306D ARG* 2.7 53.2 + - - +
307D THR 2.8 31.8 + - - +
308D LYS* 3.7 7.0 - - - +
310D LEU* 1.3 72.8 - - - +
312D LYS* 1.3 64.3 + - - +
314D ILE* 3.6 4.4 - - - +
315D ILE* 3.0 31.9 + - + +
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Residues in contact with LYS 312 (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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308D LYS 3.0 18.9 + - - +
309D GLU* 3.7 33.2 + - - +
310D LEU 3.2 0.4 - - - -
311D ASP* 1.3 77.0 - - - +
313D LYS* 1.3 62.5 + - - +
315D ILE* 3.6 4.9 + - - +
316D GLU* 3.1 28.4 + - - +
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Residues in contact with LYS 313 (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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309D GLU 3.1 12.4 + - - +
310D LEU* 3.0 12.4 + - + +
312D LYS* 1.3 74.9 - - - +
314D ILE* 1.3 66.3 + - - +
316D GLU* 3.0 36.6 + - - +
317D LEU* 2.9 44.9 + - + +
350D GLU* 4.8 11.0 + - - -
351D LEU* 3.6 24.0 - - + +
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Residues in contact with ILE 314 (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 VAL* 3.9 16.8 - - + -
277D CYS* 4.1 23.6 - - + +
280D ILE* 3.7 30.1 - - + -
281D MET* 3.8 37.5 - - + -
310D LEU* 2.8 24.4 + - + +
311D ASP* 3.6 7.2 - - - +
313D LYS* 1.3 76.8 - - - +
315D ILE* 1.3 57.5 + - - +
317D LEU* 3.8 0.7 - - - +
318D TRP* 2.8 30.2 + - + +
347D ILE* 4.5 8.9 - - + +
351D LEU* 3.8 20.2 - - + -
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Residues in contact with ILE 315 (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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273D LYS* 3.6 61.0 - - + +
276D VAL* 3.9 18.2 - - + -
277D CYS* 3.9 10.5 - - - -
311D ASP* 3.0 21.4 + - + +
312D LYS* 4.1 4.9 - - - +
314D ILE* 1.3 72.5 - - - +
316D GLU* 1.3 58.3 + - - +
318D TRP* 3.7 3.6 - - + +
319D GLU* 2.9 35.4 + - - +
324D LEU* 4.4 19.5 - - + +
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Residues in contact with GLU 316 (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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312D LYS* 3.1 19.0 + - + +
313D LYS* 3.0 42.7 + - - +
315D ILE* 1.3 78.6 - - - +
317D LEU* 1.3 69.4 + - + +
319D GLU* 3.3 11.5 + - - +
320D LYS* 3.2 20.0 + - + +
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Residues in contact with LEU 317 (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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313D LYS* 2.9 53.3 + - + +
314D ILE 4.0 1.8 - - - +
316D GLU* 1.3 77.8 - - + +
318D TRP* 1.3 67.6 + - - +
320D LYS* 3.1 15.7 + - + +
321D TYR* 3.0 37.9 + - + +
347D ILE* 4.1 28.0 - - + +
350D GLU* 3.3 43.5 - - + +
351D LEU* 4.8 1.8 - - + -
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Residues in contact with TRP 318 (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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271D TYR* 3.4 33.9 - + - +
276D VAL* 3.4 34.3 - - + -
279D LEU* 3.9 29.4 - - + -
280D ILE* 4.6 5.8 - - + -
314D ILE 2.8 22.2 + - - +
315D ILE* 3.7 5.4 - - + +
317D LEU* 1.3 71.8 - - - +
319D GLU* 1.3 61.5 + - - +
322D ILE* 2.8 67.2 + - + +
323D GLY 2.8 35.5 + - - -
324D LEU* 4.2 13.7 - - + -
340D ARG* 4.0 11.9 - - - -
344D ILE* 4.5 10.8 - - + -
347D ILE* 3.7 21.6 - - + +
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Residues in contact with GLU 319 (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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315D ILE* 2.9 21.7 + - - +
316D GLU* 3.3 11.6 - - - +
317D LEU 3.1 0.2 - - - -
318D TRP* 1.3 82.3 - - - +
320D LYS* 1.3 61.2 + - - +
323D GLY* 3.4 21.6 + - - +
324D LEU* 4.3 27.8 - - + +
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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
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316D GLU* 3.2 12.1 + - + +
317D LEU* 3.1 20.6 + - + +
319D GLU* 1.3 81.1 - - - +
321D TYR* 1.3 100.5 + - + +
322D ILE 5.2 0.2 - - - -
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Residues in contact with TYR 321 (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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317D LEU* 3.0 32.4 + - + +
320D LYS* 1.3 112.9 + - + +
322D ILE* 1.3 64.6 + - + +
343D TYR* 3.7 43.3 - + + -
346D LYS* 3.5 27.3 - - + -
347D ILE* 3.8 20.6 - - + -
350D GLU* 2.7 39.1 + - - -
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Residues in contact with ILE 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D TYR* 4.0 5.8 - - + +
318D TRP* 2.8 69.2 + - + +
319D GLU 4.4 0.2 - - - -
321D TYR* 1.3 80.3 - - + +
323D GLY* 1.3 60.7 + - - +
325D LYS 4.7 3.8 - - - +
327D ILE* 4.8 12.5 - - - +
340D ARG* 3.7 38.4 - - - +
343D TYR* 3.8 32.1 - - + -
347D ILE* 4.5 5.2 - - + -
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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