Contacts of the helix formed by residues 277 - 287 (chain H) in PDB entry 2OME
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 ASP 277 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251H HIS* 3.3 32.8 + - + -
253H ILE 2.9 19.6 + - - +
254H ASN* 4.0 7.5 - - + +
255H ASP* 4.1 10.0 + - - +
258H ILE* 5.1 0.5 - - - +
276H VAL* 1.3 67.8 - - - +
278H GLU* 1.3 58.6 + - - +
279H LYS* 3.3 19.8 + - - +
280H ALA* 3.0 38.9 + - + +
281H LEU* 3.0 12.6 + - - +
299H GLU* 4.4 1.9 - - - +
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Residues in contact with GLU 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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273H GLY* 4.8 2.4 - - - -
276H VAL* 3.3 20.9 + - + +
277H ASP* 1.3 71.7 - - - +
279H LYS* 1.3 57.3 + - - +
281H LEU* 3.7 3.6 - - + +
282H ALA* 2.8 31.2 + - - +
295H LEU* 4.6 6.5 - - + +
297H VAL 4.2 2.3 - - - +
298H HIS* 3.3 19.5 - - - +
299H GLU* 3.0 56.3 + - - +
300H SER 4.6 1.4 + - - -
303H PHE* 5.8 0.3 - - - -
309H PRO* 4.1 19.0 - - + +
310H LEU* 3.8 37.5 - - + +
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Residues in contact with LYS 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ASP* 3.2 13.2 + - - +
278H GLU* 1.3 78.7 - - - +
280H ALA* 1.3 60.8 + - - +
282H ALA* 3.4 5.0 + - - +
283H GLN* 3.3 25.4 + - - +
299H GLU* 4.5 1.0 + - - -
309H PRO* 4.0 17.3 - - + +
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Residues in contact with ALA 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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254H ASN* 3.8 2.0 - - - -
255H ASP* 3.6 39.0 + - - +
258H ILE* 3.6 14.9 - - + +
277H ASP* 3.0 27.6 + - + +
279H LYS* 1.3 77.3 - - - +
281H LEU* 1.3 64.4 + - - +
283H GLN* 3.3 7.7 + - - +
284H ALA* 3.0 21.3 + - - +
289H ARG* 5.4 0.9 + - - -
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Residues in contact with LEU 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H ILE* 5.9 0.2 - - + -
258H ILE* 3.5 10.0 - - + +
267H LEU* 4.2 17.0 - - + -
276H VAL* 4.3 16.2 - - + -
277H ASP 3.0 12.0 + - - +
278H GLU* 3.7 9.4 - - + +
280H ALA* 1.3 76.0 - - - +
282H ALA* 1.3 65.1 + - - +
284H ALA* 3.1 2.8 + - - +
285H LEU* 2.9 40.1 + - + +
290H ILE* 3.8 27.8 - - + -
293H ALA* 4.1 17.0 - - + -
295H LEU* 3.8 28.7 - - + -
310H LEU* 4.2 9.6 - - + -
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Residues in contact with ALA 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H GLU 2.8 22.3 + - - +
279H LYS* 3.6 7.0 - - - +
280H ALA 3.3 0.2 - - - -
281H LEU* 1.3 73.3 - - - +
283H GLN* 1.3 61.9 + - - +
285H LEU* 3.4 3.4 + - - +
286H LYS* 3.1 41.5 + - - +
309H PRO 3.3 26.5 - - - +
310H LEU* 4.3 11.4 - - + +
313H ALA* 4.5 8.0 - - + +
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Residues in contact with GLN 283 (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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255H ASP* 4.6 16.4 + - - +
279H LYS 3.3 10.5 + - - +
280H ALA* 3.3 9.1 + - - +
281H LEU 3.2 0.4 - - - -
282H ALA* 1.3 79.0 - - - +
284H ALA* 1.3 58.0 + - - +
286H LYS* 3.3 12.6 + - + +
287H GLU* 2.9 59.8 + - - +
289H ARG* 5.2 4.8 + - - +
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Residues in contact with ALA 284 (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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258H ILE* 3.8 29.8 - - + -
280H ALA 3.0 13.7 + - - +
281H LEU 3.4 7.6 - - - +
283H GLN* 1.3 78.1 - - - +
285H LEU* 1.3 61.4 + - - +
287H GLU* 3.5 1.0 + - - -
288H GLY 3.2 2.9 + - - -
289H ARG* 3.0 43.6 + - + +
290H ILE* 3.3 20.5 + - + +
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Residues in contact with LEU 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H LEU* 2.9 45.4 + - + +
282H ALA* 3.7 3.8 - - - +
284H ALA* 1.3 74.0 - - - +
286H LYS* 1.3 66.5 + - - +
288H GLY* 3.1 13.5 + - - -
290H ILE* 3.7 26.4 - - + +
292H GLY* 3.8 22.2 - - - -
293H ALA* 3.9 10.5 - - + +
310H LEU* 4.8 1.3 - - + -
313H ALA* 4.2 15.3 - - + -
314H PRO* 3.6 40.1 - - + +
315H ASN* 3.9 7.8 - - + +
316H LEU* 4.5 10.1 - - + -
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Residues in contact with LYS 286 (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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282H ALA* 3.1 34.1 + - - +
283H GLN* 3.8 8.8 - - + +
285H LEU* 1.3 75.9 - - - +
287H GLU* 1.3 62.3 + - + +
288H GLY 3.4 0.5 + - - -
309H PRO 4.9 5.1 + - - -
312H ASP* 4.5 19.5 - - - +
313H ALA* 4.6 5.6 - - - +
314H PRO* 3.9 23.1 - - + +
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Residues in contact with GLU 287 (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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263H GLN* 5.1 1.4 + - - -
283H GLN* 2.9 44.6 + - - +
284H ALA* 4.1 4.0 - - - +
285H LEU 3.2 0.2 - - - -
286H LYS* 1.3 76.9 - - + +
288H GLY* 1.3 56.4 + - - +
289H ARG* 3.1 41.5 + - + +
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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