Contacts of the helix formed by residues 316 - 328 (chain D) in PDB entry 4E2I
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 316 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276D TYR* 3.7 31.6 - + + -
279D GLU* 3.5 49.4 + - + +
280D THR* 4.6 7.3 - - + +
295D PHE* 4.6 4.1 - - + -
311D PRO 3.3 23.6 - - - -
312D SER* 3.9 16.8 - - - +
313D HIS 3.1 3.8 + - - +
315D LYS* 1.3 102.7 + - + +
317D HIS* 1.3 64.2 + - - +
318D GLU 3.5 2.0 - - - -
319D LYS* 3.3 25.0 + - + -
320D HIS* 3.0 29.4 + - + +
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Residues in contact with HIS 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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294D GLU 3.7 17.7 - - - -
295D PHE* 3.3 39.6 + + + -
298D SER 3.6 8.5 - - - -
299D PHE* 3.4 28.3 + + + +
302D CYS* 3.9 5.2 - - - -
305D CYS* 5.4 0.7 - - - -
313D HIS* 2.9 15.8 + - - +
314D TYR* 4.5 3.3 - - - -
315D LYS 3.9 0.2 - - - -
316D TYR* 1.3 77.3 - - - +
318D GLU* 1.3 56.9 + - + +
319D LYS 3.1 0.2 + - - -
320D HIS 3.1 0.3 + - - -
321D TYR* 2.6 63.0 + - + +
700D ZN 2.5 30.4 - - - -
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Residues in contact with GLU 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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299D PHE* 3.6 51.6 - - + -
305D CYS* 5.1 8.2 - - - -
314D TYR 4.8 9.8 + - - +
315D LYS 5.6 0.6 - - - -
316D TYR 3.5 0.2 - - - -
317D HIS* 1.3 77.1 - - + +
319D LYS* 1.3 59.8 + - - +
321D TYR* 4.1 6.0 + - - +
322D ALA 5.3 0.9 + - - -
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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
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272D LEU* 4.9 8.8 - - + +
275D GLU* 3.2 37.1 + - - +
279D GLU* 5.5 5.4 - - - -
315D LYS 4.8 3.6 - - - +
316D TYR* 3.3 33.3 + - + +
317D HIS 3.0 0.8 - - - -
318D GLU* 1.3 81.6 - - - +
320D HIS* 1.3 78.5 + - + +
321D TYR 3.6 0.4 - - - -
322D ALA* 5.3 2.3 + - - +
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Residues in contact with HIS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LEU* 3.2 35.2 + - + +
275D GLU* 3.9 17.9 - - - -
276D TYR* 3.2 40.8 - + + +
279D GLU* 5.6 0.4 - - - +
292D TYR* 3.4 26.7 + + + +
295D PHE* 4.6 6.7 - + + -
316D TYR* 3.0 26.4 + - + +
317D HIS 3.4 1.6 - - - -
319D LYS* 1.3 101.6 + - + +
321D TYR* 1.3 58.4 + - - +
322D ALA* 3.3 2.7 - - - -
323D ASN* 3.6 4.4 + - - +
324D ALA* 3.0 32.0 + - - +
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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
----------------------------------------------------------
295D PHE 3.2 20.2 - - - -
296D GLN 4.6 1.8 - - - -
297D TYR 2.9 37.3 + - - -
298D SER* 3.8 12.8 - - - -
299D PHE* 3.6 27.8 - + + -
300D GLU* 4.3 8.1 + - - -
317D HIS* 2.6 34.7 + - + +
318D GLU* 4.1 5.5 + - - +
319D LYS 3.6 1.4 - - - -
320D HIS* 1.3 72.9 - - - +
322D ALA* 1.3 66.1 + - - +
325D ALA* 3.2 29.3 + - + +
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Residues in contact with ALA 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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272D LEU* 5.8 3.4 - - + -
318D GLU 5.3 0.6 + - - -
319D LYS 5.3 2.2 + - - +
320D HIS* 3.3 1.3 - - - -
321D TYR* 1.3 85.2 - - - +
323D ASN* 1.3 62.0 + - - +
325D ALA* 3.5 14.8 - - - +
326D ILE* 3.9 13.8 - - - +
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Residues in contact with ASN 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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267D GLN 4.8 0.5 - - - +
268D VAL* 3.5 9.1 - - - +
269D SER* 2.6 52.3 + - - -
272D LEU* 3.5 22.7 - - + +
273D VAL* 3.2 13.1 - - - +
292D TYR* 2.8 28.9 + - - +
320D HIS 3.6 2.9 + - - +
322D ALA* 1.3 75.2 - - - +
324D ALA* 1.3 55.7 + - - +
325D ALA 3.0 2.2 - - - -
326D ILE* 2.9 8.9 + - - +
327D PHE* 2.7 33.6 + - - +
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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
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292D TYR* 3.9 19.4 + - + +
295D PHE* 3.1 35.9 - - + +
296D GLN* 3.2 20.2 - - + +
320D HIS 3.0 20.6 + - - +
323D ASN* 1.3 76.3 - - - +
325D ALA* 1.3 62.6 + - - +
327D PHE* 3.2 19.5 + - - +
328D ALA 3.3 5.5 + - - -
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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
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295D PHE 4.2 0.2 + - - -
296D GLN* 4.3 12.9 - - - +
321D TYR* 3.2 29.3 + - + +
322D ALA* 3.5 10.3 - - - +
323D ASN 3.0 0.6 - - - -
324D ALA* 1.3 78.9 - - - +
326D ILE* 1.3 62.1 + - + +
328D ALA* 4.1 6.1 - - - +
329D ASP* 4.0 12.5 - - - +
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Residues in contact with ILE 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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266D LYS* 3.2 39.0 - - - +
267D GLN 3.7 17.5 - - - +
268D VAL* 3.5 22.0 - - + +
322D ALA 3.9 15.3 - - - +
323D ASN* 2.9 9.5 + - - +
325D ALA* 1.3 77.2 - - + +
327D PHE* 1.3 65.3 + - - +
328D ALA 3.1 2.9 - - - -
329D ASP* 3.0 21.8 + - + +
330D SER 3.5 4.2 + - - -
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Residues in contact with PHE 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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268D VAL* 3.9 8.7 - - + +
273D VAL* 4.7 2.5 - - + -
289D LEU* 3.7 10.5 - - + -
292D TYR* 3.7 30.7 - + + -
293D LEU* 3.5 32.3 - - + -
296D GLN* 5.0 0.4 - - + -
323D ASN* 2.7 16.2 + - - +
324D ALA* 3.4 15.9 - - - +
326D ILE* 1.3 78.5 - - - +
328D ALA* 1.3 61.3 + - - +
330D SER* 3.1 17.7 + - - -
333D GLN* 3.3 41.0 - - + +
336D ILE* 3.5 42.2 - - + -
337D CYS* 3.5 15.7 - - - -
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Residues in contact with ALA 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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270C TRP* 5.3 2.1 - - - +
271C LYS* 4.3 26.8 + - + +
293D LEU* 4.9 0.2 - - - -
296D GLN* 3.2 48.2 + - + +
324D ALA 3.3 2.2 + - - -
325D ALA 4.1 6.1 - - - +
326D ILE 3.1 0.8 - - - -
327D PHE* 1.3 79.2 - - - +
329D ASP* 1.3 66.3 + - - +
330D SER 3.1 3.9 + - - +
333D GLN* 3.0 18.8 - - - +
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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