Contacts of the helix formed by residues 278 - 284 (chain H) in PDB entry 2R9R
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 278 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202H PHE* 3.7 8.1 - - - -
276H ASN 3.0 1.4 + - - -
277H LYS* 1.3 80.2 - - - +
279H VAL* 1.3 58.4 + - - +
280H LEU* 4.1 4.2 + - - +
281H GLN* 2.7 40.8 + - - +
282H PHE* 3.0 30.8 + - - +
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Residues in contact with VAL 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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202H PHE* 3.6 39.7 - - + +
205H TYR* 4.8 12.3 - - + -
278H SER* 1.3 73.3 - - - +
280H LEU* 1.3 74.7 + - + +
282H PHE* 4.0 1.0 - - - +
283H GLN* 3.1 26.9 + - + +
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Residues in contact with LEU 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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278H SER* 3.5 4.3 + - - +
279H VAL* 1.3 91.1 - - + +
281H GLN* 1.3 63.9 + - + +
283H GLN* 3.7 17.4 + - - +
284H ASN* 3.3 21.5 + - - +
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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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275H SER 3.5 21.8 + - - -
276H ASN* 3.6 28.4 + - + +
277H LYS 4.2 3.1 + - - +
278H SER* 2.7 33.3 + - - +
280H LEU* 1.3 77.0 - - + +
282H PHE* 1.3 66.7 + - - +
284H ASN* 2.9 21.7 + - - +
285H VAL* 3.3 9.0 + - - +
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Residues in contact with PHE 282 (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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202H PHE* 3.7 15.3 - + + -
205H TYR* 3.8 24.9 - + - -
206H SER* 3.5 39.0 - - - -
209H THR* 3.8 29.6 - - + -
210H ILE* 4.5 1.3 - - + -
273H THR* 3.8 31.6 - - + -
276H ASN 3.8 12.4 + - - +
278H SER 3.0 18.8 + - - +
279H VAL 4.0 1.6 - - - +
281H GLN* 1.3 75.7 - - - +
283H GLN* 1.3 52.4 + - - +
285H VAL* 2.8 17.5 + - + +
286H ARG* 2.8 37.7 + - + -
289H VAL* 4.2 18.2 - - + -
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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
----------------------------------------------------------
205H TYR* 3.9 29.2 - - + +
279H VAL* 3.1 19.8 + - + +
280H LEU* 3.7 19.8 - - - +
282H PHE* 1.3 78.9 - - - +
284H ASN* 1.3 62.0 + - - +
285H VAL 3.6 0.3 + - - -
286H ARG* 4.0 11.1 + - - +
287H ARG* 6.2 0.2 - - - +
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Residues in contact with ASN 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 LEU 3.3 11.8 + - - +
281H GLN* 2.9 14.1 + - - +
283H GLN* 1.3 83.7 + - - +
285H VAL* 1.3 56.9 + - - +
286H ARG 3.7 0.2 - - - -
287H ARG* 4.4 16.9 + - - -
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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