Contacts of the helix formed by residues 316 - 328 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H TYR* 3.6 32.1 - + + -
279H GLU* 3.5 51.8 + - + +
280H THR* 4.6 6.0 - - + +
295H PHE* 4.6 4.3 - - + -
311H PRO 3.3 23.8 - - - -
312H SER* 3.9 17.3 - - - +
313H HIS 3.1 4.4 + - - +
315H LYS* 1.3 99.8 + - + +
317H HIS* 1.3 64.8 + - - +
318H GLU 3.5 1.6 - - - -
319H LYS* 3.7 23.3 - - + +
320H HIS* 3.0 29.2 + - + +
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Residues in contact with HIS 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H GLU 3.7 17.7 - - - -
295H PHE* 3.3 40.7 + + + -
298H SER 3.6 8.9 + - - -
299H PHE* 3.4 30.5 + - + +
302H CYS* 3.9 4.0 - - - -
305H CYS* 5.4 1.1 - - - -
313H HIS* 2.9 16.2 + - - +
314H TYR* 4.5 4.6 - - - +
315H LYS 3.9 0.2 - - - -
316H TYR* 1.3 77.2 - - - +
318H GLU* 1.3 56.4 + - + +
319H LYS 3.0 0.4 + - - -
320H HIS 3.1 0.5 + - - -
321H TYR* 2.6 63.1 + - + +
700H ZN 2.7 29.3 - - - -
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Residues in contact with GLU 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H PHE* 3.6 49.6 - - + -
305H CYS* 5.1 7.9 - - - -
314H TYR 4.8 10.7 + - - +
315H LYS 5.6 0.4 - - - -
316H TYR 3.5 0.2 - - - -
317H HIS* 1.3 76.7 - - + +
319H LYS* 1.3 61.0 + - - +
321H TYR* 4.1 6.2 + - - +
322H ALA 5.3 0.5 + - - -
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Residues in contact with LYS 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H LEU* 4.9 8.9 - - + +
275H GLU* 3.2 37.1 + - - +
279H GLU* 5.5 5.4 - - - -
315H LYS 4.8 4.0 - - - +
316H TYR* 3.3 32.2 + - + +
317H HIS 3.0 0.8 - - - -
318H GLU* 1.3 80.9 - - - +
320H HIS* 1.3 78.3 + - + +
321H TYR 3.6 0.2 - - - -
322H ALA* 5.3 2.3 + - - +
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Residues in contact with HIS 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 3.2 35.4 + - + +
275H GLU* 3.9 17.2 - - - -
276H TYR* 3.2 41.4 - + + +
292H TYR* 3.4 26.8 + + + +
295H PHE* 4.6 6.7 - + + -
316H TYR* 3.0 26.2 + - + +
317H HIS 3.4 1.6 - - - -
319H LYS* 1.3 100.5 + - + +
321H TYR* 1.3 59.3 + - - +
322H ALA* 3.3 3.6 - - - +
323H ASN* 3.6 4.7 + - - +
324H ALA* 3.0 31.5 + - - +
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Residues in contact with TYR 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H PHE 3.2 20.9 - - - -
296H GLN* 4.6 2.2 - - - -
297H TYR 2.9 36.9 + - - -
298H SER* 3.8 11.9 - - - -
299H PHE* 3.5 27.8 - + + -
300H GLU* 4.3 8.4 + - - -
317H HIS* 2.6 33.8 + - + +
318H GLU* 4.1 6.0 - - - +
319H LYS 3.6 1.4 - - - -
320H HIS* 1.3 73.9 - - - +
322H ALA* 1.3 66.5 + - + +
325H ALA* 3.2 29.3 + - + +
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Residues in contact with ALA 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 5.8 3.6 - - + -
318H GLU 5.3 1.0 + - - -
319H LYS 5.3 2.0 + - - +
320H HIS* 3.3 1.7 - - - +
321H TYR* 1.3 85.2 - - - +
323H ASN* 1.3 61.2 + - - +
325H ALA* 3.5 14.4 - - - +
326H ILE* 3.9 13.0 - - - +
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Residues in contact with ASN 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267H GLN 4.8 0.3 - - - +
268H VAL* 3.5 9.5 - - - +
269H SER* 2.6 51.9 + - - -
272H LEU* 3.5 23.0 - - + +
273H VAL* 3.2 12.9 - - - +
292H TYR* 2.8 29.4 + - - +
320H HIS* 3.6 4.2 + - - +
322H ALA* 1.3 75.3 - - - +
324H ALA* 1.3 54.1 + - - +
325H ALA 3.0 1.8 - - - -
326H ILE* 2.9 9.9 + - - +
327H PHE* 2.8 33.5 + - - +
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Residues in contact with ALA 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H TYR* 3.9 20.7 + - + +
295H PHE* 3.1 36.1 - - + +
296H GLN* 3.2 18.5 - - - +
320H HIS 3.0 20.0 + - - +
323H ASN* 1.3 77.4 - - - +
325H ALA* 1.3 60.4 + - - +
327H PHE* 3.2 19.8 + - + +
328H ALA 3.3 5.5 + - - -
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Residues in contact with ALA 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H PHE 4.2 0.4 + - - -
296H GLN* 4.3 11.8 - - - +
321H TYR* 3.2 28.8 + - + +
322H ALA* 3.5 10.3 - - - +
323H ASN 3.0 0.2 - - - -
324H ALA* 1.3 79.5 - - - +
326H ILE* 1.3 63.1 + - + +
328H ALA* 4.0 6.1 - - - +
329H ASP* 4.0 12.3 - - - +
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Residues in contact with ILE 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266H LYS 3.8 21.1 - - - +
267H GLN* 3.7 27.8 - - - +
268H VAL* 3.5 24.5 - - + +
322H ALA 3.9 14.8 - - - +
323H ASN* 2.9 8.1 + - - +
325H ALA* 1.3 77.4 - - + +
327H PHE* 1.3 66.2 + - - +
328H ALA 3.1 2.5 - - - -
329H ASP* 3.0 22.6 + - + +
330H SER 3.5 4.2 + - - -
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Residues in contact with PHE 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H VAL* 4.0 8.3 - - + -
273H VAL* 4.8 2.0 - - + -
289H LEU* 3.7 9.9 - - + -
292H TYR* 3.7 31.4 - + + -
293H LEU* 3.5 33.4 - - + -
323H ASN* 2.8 16.4 + - - +
324H ALA* 3.4 16.6 - - - +
326H ILE* 1.3 78.2 - - - +
328H ALA* 1.3 60.6 + - - +
330H SER* 3.1 17.7 + - - -
333H GLN* 3.3 38.2 - - + +
336H ILE* 3.5 45.8 - - + -
337H CYS* 3.5 15.9 - - - -
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Residues in contact with ALA 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G TRP* 5.5 1.6 - - - +
271G LYS* 4.4 25.8 + - + +
339G GLN* 5.4 0.3 - - - +
296H GLN* 3.2 46.6 + - + +
324H ALA 3.3 2.0 + - - -
325H ALA 4.0 5.8 - - - +
326H ILE 3.1 0.4 - - - -
327H PHE* 1.3 80.0 - - - +
329H ASP* 1.3 67.2 + - - +
330H SER 3.1 3.7 + - - +
333H GLN* 3.0 18.9 - - - +
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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