Contacts of the helix formed by residues 316 - 328 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TYR* 3.6 31.6 - + + -
279B GLU* 3.5 50.6 + - + +
280B THR* 4.6 7.1 - - + +
295B PHE* 4.6 3.4 - - + -
311B PRO 3.3 23.8 - - - -
312B SER* 3.9 16.2 - - - +
313B HIS 3.1 3.6 + - - +
315B LYS* 1.3 101.0 + - + +
317B HIS* 1.3 64.0 + - - +
318B GLU 3.5 1.8 - - - -
319B LYS* 3.3 23.9 + - + -
320B HIS* 3.0 28.6 + - + +
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU 3.7 16.6 - - - -
295B PHE* 3.3 40.8 - + + -
298B SER 3.6 8.7 + - - -
299B PHE* 3.4 29.5 + - + +
302B CYS* 3.9 3.1 - - - -
305B CYS* 5.4 1.1 - - - -
313B HIS 2.9 15.8 + - - +
314B TYR* 4.5 4.8 - - - +
315B LYS 3.9 0.4 - - - -
316B TYR* 1.3 77.6 - - - +
318B GLU* 1.3 55.5 + - + +
319B LYS 3.1 0.3 + - - -
320B HIS 3.1 0.5 + - - -
321B TYR* 2.6 62.9 + + + +
700B ZN 2.5 35.9 - - - -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 3.6 50.7 - - + -
305B CYS* 5.1 6.6 - - - -
314B TYR 4.8 10.8 + - - +
315B LYS 5.6 0.4 - - - -
316B TYR 3.5 0.2 - - - -
317B HIS* 1.3 76.9 - - + +
319B LYS* 1.3 59.8 + - - +
321B TYR* 4.1 5.6 + - - +
322B ALA 5.3 0.9 + - - -
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 4.9 8.2 - - + +
275B GLU* 3.2 36.9 + - - +
279B GLU* 5.5 6.1 - - - -
315B LYS 4.8 3.8 - - - +
316B TYR* 3.3 31.8 + - + +
317B HIS 3.0 0.6 - - - -
318B GLU* 1.3 81.6 - - - +
320B HIS* 1.3 77.5 + - + +
321B TYR 3.6 0.4 - - - -
322B ALA* 5.3 2.3 + - - +
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Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.2 35.2 + - + +
275B GLU* 3.9 17.7 - - + -
276B TYR* 3.2 40.9 - + + +
279B GLU* 5.6 0.2 - - - +
292B TYR* 3.4 26.8 + + + +
295B PHE* 4.6 6.7 - + + -
316B TYR* 3.0 26.2 + - + +
317B HIS 3.4 1.6 - - - -
319B LYS* 1.3 101.8 + - + +
321B TYR* 1.3 60.0 + - - +
322B ALA* 3.3 3.6 - - - +
323B ASN* 3.6 4.4 + - - +
324B ALA* 3.0 31.4 + - - +
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PHE 3.2 21.3 - - - +
296B GLN* 4.6 2.2 - - - -
297B TYR 2.9 37.1 + - - -
298B SER* 3.8 11.0 - - - -
299B PHE* 3.5 29.2 - + + -
300B GLU* 4.3 8.5 + - - +
317B HIS* 2.6 32.6 + - + +
318B GLU* 4.1 5.5 - - - +
319B LYS 3.6 1.2 - - - -
320B HIS* 1.3 73.1 - - - +
322B ALA* 1.3 65.8 + - - +
325B ALA* 3.2 28.9 + - + +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 5.8 3.6 - - + -
318B GLU 5.3 0.8 + - - -
319B LYS 5.3 1.5 + - - +
320B HIS* 3.3 1.1 - - - -
321B TYR* 1.3 85.3 - - - +
323B ASN* 1.3 61.3 + - - +
325B ALA* 3.5 14.8 - - - +
326B ILE* 3.9 13.8 - - - +
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B GLN 4.8 0.3 - - - +
268B VAL* 3.5 9.3 - - - +
269B SER* 2.6 50.9 + - - -
272B LEU* 3.5 23.6 - - + +
273B VAL* 3.2 12.5 - - - +
292B TYR* 2.8 29.7 + - - +
320B HIS 3.6 3.6 + - - +
322B ALA* 1.3 74.7 - - - +
324B ALA* 1.3 55.3 + - - +
325B ALA 3.0 1.8 - - - -
326B ILE* 3.0 9.4 + - - +
327B PHE* 2.8 32.9 + - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 3.9 19.7 + - + +
295B PHE* 3.1 36.1 - - + +
296B GLN* 3.2 19.0 - - + +
320B HIS 3.0 20.9 + - - +
323B ASN* 1.3 78.1 - - - +
325B ALA* 1.3 60.1 + - - +
327B PHE* 3.2 19.6 + - - +
328B ALA 3.3 5.7 + - - -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B PHE 4.2 0.2 + - - -
296B GLN* 4.3 12.0 - - - +
321B TYR* 3.2 29.2 + - + +
322B ALA* 3.5 10.3 - - - +
323B ASN 3.0 0.8 - - - -
324B ALA* 1.3 77.9 - - - +
326B ILE* 1.3 61.7 + - + +
328B ALA* 4.1 5.9 - - - +
329B ASP* 4.0 12.8 - - - +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LYS* 4.1 26.7 - - + +
267B GLN* 3.7 28.3 - - - +
268B VAL* 3.5 23.7 - - + +
322B ALA 3.9 15.0 - - - +
323B ASN* 3.0 9.0 + - - +
325B ALA* 1.3 76.9 - - + +
327B PHE* 1.3 66.5 + - - +
328B ALA 3.1 2.7 - - - -
329B ASP* 3.0 22.7 + - + +
330B SER 3.5 3.8 + - - -
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.9 8.7 - - + +
273B VAL* 4.8 2.0 - - + -
289B LEU* 3.7 11.0 - - + -
292B TYR* 3.7 31.2 - + + -
293B LEU* 3.5 33.4 - - + -
323B ASN* 2.8 16.0 + - - +
324B ALA* 3.2 17.0 + - - +
326B ILE* 1.3 78.2 - - - +
328B ALA* 1.3 60.7 + - - +
330B SER* 3.1 17.8 + - - -
333B GLN* 3.3 40.0 - - + +
336B ILE* 3.5 44.0 - - + -
337B CYS* 3.5 15.9 - - - -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP* 5.8 1.6 - - - +
271A LYS* 4.4 26.4 + - + +
296B GLN* 3.2 47.7 + - + +
324B ALA 3.3 3.0 + - - -
325B ALA 4.1 5.8 - - - +
326B ILE 3.1 0.4 - - - -
327B PHE* 1.3 79.4 - - - +
329B ASP* 1.3 67.6 + - - +
330B SER 3.3 2.8 + - - +
333B GLN* 3.0 19.3 - - - +
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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
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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