Contacts of the helix formed by residues 316 - 328 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276I TYR* 3.6 32.1 - + + -
279I GLU* 3.5 50.4 + - + +
280I THR* 4.6 6.0 - - + +
295I PHE* 4.6 4.2 - - + -
311I PRO 3.3 24.5 - - - -
312I SER* 3.9 16.6 - - - +
313I HIS 3.1 3.8 + - - +
315I LYS* 1.3 100.5 + - + +
317I HIS* 1.3 63.4 + - - +
318I GLU 3.5 1.3 - - - -
319I LYS* 3.3 25.2 + - + +
320I HIS* 3.0 28.9 + - + +
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Residues in contact with HIS 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294I GLU 3.7 17.3 - - - -
295I PHE* 3.3 39.9 + + + -
298I SER 3.6 8.3 - - - -
299I PHE* 3.4 30.1 + + + +
302I CYS* 3.9 4.0 - - - -
305I CYS* 5.4 0.9 - - - -
313I HIS* 2.9 15.6 + - - +
314I TYR* 4.5 3.9 - - - -
315I LYS 3.9 0.4 - - - -
316I TYR* 1.3 74.0 - - - +
318I GLU* 1.3 56.3 + - + +
319I LYS 3.0 4.7 + - - -
320I HIS 3.1 0.5 + - - -
321I TYR* 2.6 63.1 + + + +
700I ZN 2.5 30.3 - - - -
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Residues in contact with GLU 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I PHE* 3.6 51.5 - - + -
305I CYS* 5.1 7.1 - - - -
314I TYR 4.8 11.3 + - - +
315I LYS 5.6 0.8 - - - -
317I HIS* 1.3 75.7 - - + +
319I LYS* 1.3 61.0 + - - +
321I TYR* 4.1 6.6 + - - +
322I ALA 5.3 0.7 + - - -
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Residues in contact with LYS 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272I LEU* 4.9 8.4 - - + +
275I GLU* 3.2 36.6 + - - -
279I GLU* 5.5 5.4 - - - -
315I LYS 4.8 4.2 + - - +
316I TYR* 3.5 31.8 - - + +
317I HIS 3.0 1.0 - - - -
318I GLU* 1.3 80.3 - - - +
320I HIS* 1.3 78.9 + - + +
321I TYR 3.6 0.2 - - - -
322I ALA* 5.3 2.3 + - - +
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Residues in contact with HIS 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I LEU* 3.2 35.2 + - + +
275I GLU* 3.9 17.9 - - - -
276I TYR* 3.2 41.4 + + + +
292I TYR* 3.4 26.9 + + + +
295I PHE* 4.6 6.5 - + + -
316I TYR* 3.0 26.9 + - + +
317I HIS 3.4 1.8 - - - -
319I LYS* 1.3 102.5 + - + +
321I TYR* 1.3 59.3 + - - +
322I ALA* 3.3 2.9 - - - +
323I ASN* 3.6 5.2 + - - +
324I ALA* 3.0 30.5 + - - +
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Residues in contact with TYR 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295I PHE 3.2 20.4 - - - +
296I GLN* 4.6 2.0 - - - -
297I TYR 2.9 37.1 + - - -
298I SER* 3.8 11.7 - - - -
299I PHE* 3.6 27.8 - + + -
300I GLU* 4.3 8.7 + - - -
317I HIS* 2.6 34.3 + - + +
318I GLU* 4.1 6.0 + - - +
319I LYS 3.6 1.2 - - - -
320I HIS* 1.3 74.1 - - - +
322I ALA* 1.3 65.0 + - + +
325I ALA* 3.2 28.4 + - + +
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Residues in contact with ALA 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I LEU* 5.8 3.8 - - + -
318I GLU 5.3 0.6 + - - -
319I LYS 5.4 2.0 - - - +
320I HIS* 3.3 1.3 - - - -
321I TYR* 1.3 85.8 - - + +
323I ASN* 1.3 61.9 + - - +
325I ALA* 3.5 14.4 - - - +
326I ILE* 3.9 13.4 - - - +
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Residues in contact with ASN 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267I GLN 4.8 0.5 - - - +
268I VAL* 3.5 8.3 - - - +
269I SER* 2.6 51.4 + - - -
272I LEU* 3.5 23.8 - - + +
273I VAL* 3.2 12.5 - - - +
292I TYR* 2.8 29.1 + - - +
320I HIS 3.6 4.4 + - - +
322I ALA* 1.3 73.8 - - - +
324I ALA* 1.3 54.7 + - - +
325I ALA 3.0 1.8 - - - -
326I ILE* 3.0 9.5 + - - +
327I PHE* 2.7 33.0 + - - +
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Residues in contact with ALA 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292I TYR* 3.9 20.3 + - + +
295I PHE* 3.1 36.6 - - + +
296I GLN* 3.2 18.7 - - + +
320I HIS 3.0 20.2 + - - +
323I ASN* 1.3 77.7 - - - +
325I ALA* 1.3 60.6 + - - +
327I PHE* 3.2 18.5 + - - +
328I ALA 3.3 5.9 + - - -
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Residues in contact with ALA 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295I PHE 4.2 0.2 + - - -
296I GLN* 4.3 12.8 - - - +
321I TYR* 3.2 30.2 + - + +
322I ALA* 3.5 10.1 - - - +
323I ASN 3.0 0.4 - - - -
324I ALA* 1.3 77.7 - - - +
326I ILE* 1.3 62.5 + - + +
328I ALA* 4.0 6.4 - - - +
329I ASP* 4.0 12.6 - - - +
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Residues in contact with ILE 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266I LYS* 4.1 18.4 - - - +
267I GLN* 3.7 28.5 - - - +
268I VAL* 3.5 23.8 - - + +
322I ALA 3.9 14.8 - - - +
323I ASN* 3.0 8.4 + - - +
325I ALA* 1.3 78.6 - - + +
327I PHE* 1.3 66.2 + - - +
328I ALA 3.0 2.7 - - - -
329I ASP* 3.0 22.5 + - + +
330I SER 3.5 4.2 + - - -
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Residues in contact with PHE 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268I VAL* 3.9 9.6 - - + +
273I VAL* 4.8 1.8 - - + -
289I LEU* 3.7 9.9 - - + -
292I TYR* 3.7 32.5 - + + -
293I LEU* 3.5 32.8 - - + -
296I GLN* 5.0 0.4 - - + -
323I ASN* 2.7 15.7 + - - +
324I ALA* 3.4 16.2 - - - +
326I ILE* 1.3 77.9 - - - +
328I ALA* 1.3 61.6 + - - +
330I SER* 3.1 17.5 + - - -
333I GLN* 3.3 39.7 - - + +
336I ILE* 3.5 44.0 - - + -
337I CYS* 3.6 15.9 - - - -
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Residues in contact with ALA 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270H TRP* 5.8 0.5 - - - +
271H LYS* 4.0 26.9 + - + +
296I GLN* 3.2 45.7 + - + +
324I ALA 3.3 2.6 + - - -
325I ALA 4.0 8.5 - - - +
326I ILE 3.0 0.4 - - - -
327I PHE* 1.3 80.2 - - - +
329I ASP* 1.3 67.1 + - - +
330I SER 3.1 4.2 + - - +
333I GLN* 3.0 18.3 - - - +
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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