Contacts of the helix formed by residues 269 - 281 (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 SER 269 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267H GLN 3.9 1.9 + - - -
268H VAL* 1.3 73.8 - - - +
270H TRP* 1.3 61.8 + - - +
271H LYS* 3.7 6.6 + - - +
272H LEU* 3.3 43.3 + - - +
273H VAL* 3.3 9.0 + - - +
323H ASN* 2.6 32.6 + - - -
336H ILE* 4.6 1.0 - - - +
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Residues in contact with TRP 270 (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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268H VAL* 3.6 20.8 - - + +
269H SER* 1.3 72.1 + - - +
271H LYS* 1.3 61.2 + - - +
272H LEU 3.1 2.2 - - - -
273H VAL* 3.2 3.5 + - - +
274H THR* 2.8 34.1 + - - +
332H ASN* 5.1 8.1 - - + -
335H THR* 3.6 33.4 - - + -
336H ILE* 3.6 46.2 - - + +
339H GLN* 3.2 38.8 - - + +
329I ASP 6.0 3.1 - - - -
330I SER 4.7 6.5 - - - +
331I LYS* 3.0 70.6 - - + +
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Residues in contact with LYS 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H SER* 3.6 6.2 + - - +
270H TRP* 1.3 79.3 - - - +
272H LEU* 1.3 58.3 + - + +
274H THR* 3.7 7.6 - - - -
275H GLU* 2.9 39.0 + - + +
296I GLN* 4.1 12.2 - - - +
328I ALA* 4.0 36.9 + - + +
329I ASP* 3.5 31.5 - - - +
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Residues in contact with LEU 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H SER* 3.3 21.3 + - - +
270H TRP 3.1 0.6 - - - -
271H LYS* 1.3 78.1 - - + +
273H VAL* 1.3 65.4 + - - +
275H GLU* 3.1 20.2 + - - +
276H TYR* 3.0 19.8 + - - +
292H TYR* 4.1 0.4 - - - +
319H LYS* 4.9 8.1 - - + +
320H HIS* 3.2 28.4 - - + +
322H ALA* 5.8 2.9 - - + -
323H ASN* 3.5 35.9 - - + +
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Residues in contact with VAL 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H SER 3.3 9.4 - - - +
270H TRP 3.2 5.5 + - - +
272H LEU* 1.3 75.5 - - - +
274H THR* 1.3 58.4 + - - +
276H TYR* 3.3 5.0 + - - +
277H ALA* 3.0 26.2 + - - +
288H LEU* 5.1 4.4 - - + +
292H TYR* 3.6 29.4 - - + -
323H ASN* 3.2 26.0 - - - +
327H PHE* 4.8 2.5 - - + -
336H ILE* 3.6 33.7 - - + +
337H CYS* 4.2 24.2 - - - -
340H ALA* 4.4 4.3 - - + -
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Residues in contact with THR 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H TRP 2.8 22.1 + - - -
271H LYS* 3.7 8.9 - - - -
273H VAL* 1.3 74.1 - - - +
275H GLU* 1.3 59.9 + - - +
277H ALA* 3.2 2.6 + - - +
278H MET* 2.9 30.2 + - + +
336H ILE 5.3 1.4 + - - -
339H GLN* 4.2 13.0 + - - -
340H ALA* 3.9 17.9 + - - +
343H THR* 3.6 40.5 + - + +
333I GLN* 4.8 9.6 + - - +
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Residues in contact with GLU 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H LYS* 2.9 28.0 + - + +
272H LEU* 3.2 27.7 - - - +
274H THR* 1.3 77.9 - - - +
276H TYR* 1.3 62.9 + - - +
278H MET* 3.1 10.6 + - + +
279H GLU* 3.0 33.4 + - + +
319H LYS* 3.2 35.6 + - - -
320H HIS* 3.9 4.3 - - + -
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Residues in contact with TYR 276 (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 3.0 8.4 + - - +
273H VAL 3.6 7.9 - - - +
275H GLU* 1.3 78.1 - - - +
277H ALA* 1.3 60.9 + - - +
279H GLU* 3.2 6.5 + - - +
280H THR* 3.1 47.7 + - + +
288H LEU* 4.1 22.7 - - + -
291H MET* 3.9 23.1 - - + +
292H TYR* 3.6 21.1 - + + -
295H PHE* 3.8 18.8 - + - -
312H SER* 2.7 36.1 + - - -
316H TYR* 3.6 33.4 - + + -
320H HIS* 3.2 24.4 + + + +
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Residues in contact with ALA 277 (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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273H VAL 3.0 14.0 + - - +
274H THR 3.3 9.6 - - - +
276H TYR* 1.3 78.8 - - - +
278H MET* 1.3 53.6 + - - +
280H THR* 4.2 0.4 - - - -
281H LYS* 2.8 34.5 + - - -
282H CYS 3.3 4.3 + - - +
288H LEU* 3.8 19.7 - - + -
340H ALA* 3.6 24.9 - - + +
344H VAL* 3.7 19.1 - - + +
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Residues in contact with MET 278 (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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274H THR* 2.9 22.0 + - + +
275H GLU* 3.1 10.1 + - - +
277H ALA* 1.3 75.9 - - - +
279H GLU* 1.3 66.7 + - - +
281H LYS* 3.7 17.2 - - - +
343H THR* 3.5 46.0 - - + +
344H VAL* 4.3 7.4 - - - -
347H LYS* 3.9 33.9 - - + +
293I LEU* 5.7 4.0 - - + -
297I TYR* 5.4 7.9 - - - +
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Residues in contact with GLU 279 (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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275H GLU* 3.0 30.5 + - + +
276H TYR* 3.3 9.9 - - - +
277H ALA 3.1 0.2 - - - -
278H MET* 1.3 80.9 - - - +
280H THR* 1.3 61.3 + - + +
281H LYS* 3.0 15.9 + - - +
316H TYR* 3.5 44.5 + - + +
319H LYS* 5.5 6.3 - - - -
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Residues in contact with THR 280 (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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276H TYR* 3.1 40.3 + - + +
277H ALA* 3.8 0.9 + - - -
279H GLU* 1.3 77.2 - - - +
281H LYS* 1.3 72.0 + - - +
282H CYS* 3.1 20.5 + - - +
312H SER* 3.6 32.5 - - - -
316H TYR* 4.6 7.9 - - + +
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Residues in contact with LYS 281 (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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277H ALA 2.8 13.4 + - - -
278H MET 3.7 11.4 - - - +
279H GLU 3.0 13.2 - - - +
280H THR* 1.3 79.1 - - - +
282H CYS* 1.3 63.5 + - - +
283H ASP* 3.1 11.3 + - - +
344H VAL* 3.6 13.8 - - + +
348H LYS* 3.7 17.8 + - - +
363H ASN* 5.7 3.6 - - - +
367H ASP* 3.5 30.8 + - - -
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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