Contacts of the helix formed by residues 316 - 328 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L TYR* 3.7 31.4 - + + -
279L GLU* 3.5 51.1 + - + +
280L THR* 4.6 6.6 - - + +
295L PHE* 4.6 4.7 - - + -
311L PRO 3.3 23.8 - - - -
312L SER* 3.9 16.6 - - - +
313L HIS 3.1 3.8 + - - +
315L LYS* 1.3 103.4 + - + +
317L HIS* 1.3 64.6 + - - +
318L GLU 3.5 2.0 - - - -
319L LYS* 3.3 23.1 + - + -
320L HIS* 3.0 29.4 + - + +
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Residues in contact with HIS 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294L GLU 3.7 17.3 - - - -
295L PHE* 3.3 40.3 + + + -
298L SER 3.6 9.1 + - - -
299L PHE* 3.4 30.5 + + + +
302L CYS* 3.9 4.7 - - - -
305L CYS* 5.4 0.7 - - - -
313L HIS* 2.9 16.8 + - - +
314L TYR* 4.5 3.7 - - - +
315L LYS 3.9 0.2 - - - -
316L TYR* 1.3 77.6 - - - +
318L GLU* 1.3 55.1 + - + +
319L LYS 3.0 0.4 + - - -
320L HIS 3.1 0.5 + - - -
321L TYR* 2.6 63.0 + + + +
700L ZN 2.8 28.2 - - - -
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Residues in contact with GLU 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299L PHE* 3.6 50.6 - - + -
305L CYS* 5.1 7.1 - - - -
314L TYR 4.8 10.7 + - - +
315L LYS 5.6 0.6 - - - -
317L HIS* 1.3 77.3 - - + +
319L LYS* 1.3 59.0 + - - +
321L TYR* 4.1 6.2 + - - +
322L ALA 5.3 0.5 + - - -
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Residues in contact with LYS 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L LEU* 4.9 8.4 - - + +
275L GLU* 3.2 36.9 + - - +
279L GLU* 5.5 5.8 - - - -
315L LYS 4.8 4.7 + - - +
316L TYR* 3.5 30.5 - - + +
317L HIS 3.0 0.8 - - - -
318L GLU* 1.3 81.1 - - - +
320L HIS* 1.3 78.7 + - + +
321L TYR 3.6 0.2 - - - -
322L ALA* 5.3 2.3 + - - +
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Residues in contact with HIS 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L LEU* 3.2 36.1 + - + +
275L GLU* 3.9 17.3 - - + -
276L TYR* 3.2 41.6 - + + +
292L TYR* 3.4 27.8 + + + +
295L PHE* 4.6 5.8 - + + -
316L TYR* 3.0 26.9 + - + +
317L HIS 3.4 1.3 - - - -
319L LYS* 1.3 101.5 + - + +
321L TYR* 1.3 59.8 + - - +
322L ALA* 3.3 2.9 - - - +
323L ASN* 3.6 4.2 + - - +
324L ALA* 3.0 30.6 + - - +
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Residues in contact with TYR 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295L PHE 3.2 21.0 - - - +
296L GLN* 4.6 1.8 - - - -
297L TYR 2.9 38.7 + - - -
298L SER* 3.8 11.6 - - - -
299L PHE* 3.6 28.0 - + + -
300L GLU* 4.3 8.3 + - - -
317L HIS* 2.6 33.9 + - + +
318L GLU* 4.1 5.3 - - - +
319L LYS 3.6 1.4 - - - -
320L HIS* 1.3 73.2 - - - +
322L ALA* 1.3 65.7 + - - +
325L ALA* 3.2 29.5 + - + +
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Residues in contact with ALA 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L LEU* 5.8 3.8 - - + -
318L GLU 5.3 1.0 + - - -
319L LYS 5.3 1.7 + - - +
320L HIS* 3.3 1.7 - - - -
321L TYR* 1.3 85.2 - - - +
323L ASN* 1.3 62.1 + - - +
325L ALA* 3.5 14.5 - - - +
326L ILE* 3.9 13.3 - - - +
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Residues in contact with ASN 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L GLN 4.8 0.7 - - - +
268L VAL* 3.5 9.1 - - - +
269L SER* 2.6 50.9 + - - -
272L LEU* 3.5 23.1 - - + +
273L VAL* 3.2 13.5 - - - +
292L TYR* 2.8 28.3 + - - +
320L HIS* 3.6 3.8 + - - +
321L TYR 3.4 0.2 - - - -
322L ALA* 1.3 75.1 - - - +
324L ALA* 1.3 55.2 + - - +
325L ALA 3.0 2.0 - - - -
326L ILE* 3.0 9.9 + - - +
327L PHE* 2.8 33.3 + - - +
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Residues in contact with ALA 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292L TYR* 3.9 19.8 + - + +
295L PHE* 3.1 36.6 - - + +
296L GLN* 3.2 19.4 - - + +
320L HIS 3.0 20.2 + - - +
323L ASN* 1.3 77.2 - - - +
325L ALA* 1.3 60.4 + - - +
327L PHE* 3.2 20.2 + - + +
328L ALA 3.3 5.5 + - - -
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Residues in contact with ALA 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295L PHE 4.2 0.2 + - - -
296L GLN* 4.3 12.4 - - - +
321L TYR* 3.2 30.5 + - + +
322L ALA* 3.5 9.9 - - - +
323L ASN 3.0 0.4 - - - -
324L ALA* 1.3 78.3 - - - +
326L ILE* 1.3 61.3 + - + +
328L ALA* 4.1 6.1 - - - +
329L ASP* 4.0 12.6 - - - +
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Residues in contact with ILE 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266L LYS* 3.0 46.2 - - + +
267L GLN 3.7 17.9 - - - +
268L VAL* 3.5 22.0 - - + +
322L ALA 3.9 15.5 - - - +
323L ASN* 3.0 8.4 + - - +
325L ALA* 1.3 77.1 - - + +
327L PHE* 1.3 66.2 + - - +
328L ALA 3.0 2.7 - - - -
329L ASP* 3.0 21.6 + - + +
330L SER 3.5 4.5 + - - -
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Residues in contact with PHE 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268L VAL* 3.9 9.4 - - + +
273L VAL* 4.7 2.0 - - + -
289L LEU* 3.7 10.8 - - + -
292L TYR* 3.7 30.7 - + + -
293L LEU* 3.5 33.7 - - + -
323L ASN* 2.8 15.6 + - - +
324L ALA* 3.2 17.0 + - - +
326L ILE* 1.3 78.1 - - - +
328L ALA* 1.3 60.7 + - - +
330L SER* 3.1 17.3 + - - -
333L GLN* 3.3 41.9 - - + +
336L ILE* 3.5 42.6 - - + -
337L CYS* 3.5 15.0 - - - -
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Residues in contact with ALA 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270K TRP* 5.4 0.9 - - - +
271K LYS* 4.1 27.1 + - + +
274K THR* 5.7 0.5 + - - -
296L GLN* 3.2 47.0 + - + +
324L ALA 3.3 3.4 + - - -
325L ALA 4.1 6.1 - - - +
326L ILE 3.0 0.2 - - - -
327L PHE* 1.3 79.4 - - - +
329L ASP* 1.3 67.9 + - - +
330L SER 3.1 3.7 + - - +
333L GLN* 3.0 19.9 - - - +
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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