Contacts of the helix formed by residues 279 - 289 (chain H) in PDB entry 2A27
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 279 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277H PRO* 4.0 4.0 - - - +
278H VAL* 1.3 82.0 - - + +
280H ASN* 1.3 62.5 - - - +
281H GLN* 3.8 19.9 + - - +
282H GLN* 3.1 36.6 + - - +
283H ALA* 3.5 15.2 + - - +
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Residues in contact with ASN 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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279H ASP* 1.3 74.5 - - - +
281H GLN* 1.3 58.8 + - - +
283H ALA* 3.0 12.8 + - - +
284H MET* 3.0 51.1 + - + +
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Residues in contact with GLN 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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247H LEU* 5.4 2.0 - - - +
279H ASP* 3.4 18.6 + - - +
280H ASN* 1.3 78.8 - - - +
282H GLN* 1.3 79.5 + - - +
284H MET* 3.5 9.7 + - - +
285H VAL* 3.2 37.8 + - - +
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Residues in contact with GLN 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H LEU* 3.9 25.6 - - + +
273H PRO* 3.7 22.9 - - - +
277H PRO* 3.6 13.5 - - + +
278H VAL* 2.9 36.0 + - - +
279H ASP* 3.1 29.3 + - - +
281H GLN* 1.3 91.2 - - - +
283H ALA* 1.3 62.3 + - - +
284H MET 3.3 0.2 + - - -
285H VAL* 3.3 4.6 + - - +
286H ARG* 3.1 23.6 + - - +
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Residues in contact with ALA 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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114H GLU* 4.2 4.4 - - - +
277H PRO* 3.9 18.9 - - + +
279H ASP 3.5 10.5 + - - +
280H ASN* 3.0 16.0 + - - +
282H GLN* 1.3 78.9 - - - +
284H MET* 1.3 56.8 + - - +
286H ARG* 3.6 9.0 + - - +
287H ARG* 3.2 40.4 + - - +
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Residues in contact with MET 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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280H ASN* 3.0 38.7 + - + +
281H GLN* 4.1 8.1 - - - +
282H GLN 3.2 0.4 - - - -
283H ALA* 1.3 73.5 - - - +
285H VAL* 1.3 61.4 + - + +
286H ARG 3.2 0.9 - - - -
287H ARG* 3.4 27.2 + - - +
288H GLU* 3.1 44.6 + - - +
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Residues in contact with VAL 285 (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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245H SER* 3.8 24.7 - - - -
246H GLU 5.4 1.3 - - - +
247H LEU* 4.3 13.2 - - + +
281H GLN* 3.2 37.2 + - - +
282H GLN 3.3 5.1 + - - +
284H MET* 1.3 76.6 - - - +
286H ARG* 1.3 57.7 + - - +
288H GLU* 4.1 6.5 - - - +
289H SER* 2.7 39.0 + - - +
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Residues in contact with ARG 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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113H GLU* 3.3 21.4 + - + +
114H GLU* 3.0 54.3 + - - +
117H THR* 3.5 24.5 + - - -
245H SER* 5.4 0.7 - - - -
247H LEU* 5.2 3.4 - - + -
274H TRP* 2.9 48.7 + - + +
275H ILE* 3.3 20.0 + - - +
277H PRO* 3.6 26.6 - - - +
282H GLN 3.1 15.6 + - - +
283H ALA* 3.8 8.8 + - - +
284H MET 3.2 0.2 - - - -
285H VAL* 1.3 79.1 - - - +
287H ARG* 1.3 59.2 + - - +
289H SER 3.8 1.3 - - - +
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Residues in contact with ARG 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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112H SER* 3.6 19.7 - - - +
114H GLU* 2.9 47.1 + - + +
283H ALA* 3.2 24.0 + - - +
284H MET* 3.4 40.1 + - - +
285H VAL 3.3 0.4 - - - -
286H ARG* 1.3 79.2 - - - +
288H GLU* 1.3 62.8 + - + +
289H SER 4.2 0.4 - - - -
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Residues in contact with GLU 288 (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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284H MET* 3.1 28.5 + - - +
285H VAL* 4.4 6.1 + - - +
287H ARG* 1.3 77.7 - - + +
289H SER* 1.3 63.7 + - - +
290H VAL* 3.6 13.2 - - - +
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Residues in contact with SER 289 (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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112H SER* 3.6 7.3 - - - -
113H GLU* 3.0 53.1 + - - +
243H GLN 3.6 9.5 + - - -
244H THR 4.5 0.3 - - - -
245H SER* 3.4 17.6 + - - -
285H VAL* 2.7 25.9 + - - +
286H ARG 3.8 1.0 - - - +
287H ARG 3.5 0.2 - - - -
288H GLU* 1.3 79.4 - - - +
290H VAL* 1.3 60.2 + - - +
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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