Contacts of the helix formed by residues 283 - 290 (chain B) in PDB entry 4RUH
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 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B ASP* 5.4 2.4 + - - +
282B PHE* 1.3 77.2 - - - +
284B ILE* 1.3 57.2 + - - +
285B GLU* 3.0 17.3 + - - +
286B GLU* 3.0 35.3 + - + +
287B PHE* 2.9 28.1 + - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PHE* 3.7 13.2 + - + -
283B ASP* 1.3 73.1 + - - +
285B GLU* 1.3 70.3 + - + +
287B PHE* 3.2 9.0 + - + +
288B ALA* 3.0 26.2 + - - +
296B LEU* 4.0 17.9 - - + +
298B HIS 4.7 0.9 - - - +
299B SER 3.3 28.5 - - - +
300B HIS 3.9 3.4 - - - -
301B LYS* 3.7 36.3 - - + +
304B ILE* 4.1 13.2 - - + -
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ASP* 3.0 10.3 + - - +
284B ILE* 1.3 83.4 - - + +
286B GLU* 1.3 62.2 + - - +
288B ALA* 3.2 7.8 + - - +
289B LYS* 2.9 30.9 + - - +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LYS* 3.9 22.0 + - - +
283B ASP* 3.0 32.3 + - + +
285B GLU* 1.3 76.5 - - - +
287B PHE* 1.3 62.1 + - - +
289B LYS* 4.5 9.0 - - - +
290B ASP* 3.0 55.6 + - - +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A VAL* 4.6 4.3 - - + -
232A TYR* 3.3 47.0 + + - -
235A SER* 4.1 24.5 - - - -
236A VAL* 5.2 0.4 - - + -
199B LEU 5.8 0.4 - - - -
282B PHE* 3.5 30.1 - + + -
283B ASP 2.9 13.9 + - - +
284B ILE* 3.3 8.7 - - - +
286B GLU* 1.3 80.4 - - - +
288B ALA* 1.3 61.3 + - - +
290B ASP* 4.0 8.2 + - - +
291B VAL* 3.6 15.0 + - + +
296B LEU* 4.0 24.7 - - + -
304B ILE* 4.4 7.9 - - + -
308B ARG* 3.3 27.1 - - - -
440B ALA* 6.4 2.2 - - + -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ILE 3.0 12.3 + - - +
285B GLU* 3.2 10.3 + - - +
287B PHE* 1.3 76.7 - - - +
289B LYS* 1.3 62.4 + - - +
291B VAL* 3.1 12.7 + - - +
293B ALA* 3.0 45.6 + - - +
294B GLN 5.3 2.9 - - - +
295B ILE* 5.9 0.4 - - - -
296B LEU* 4.2 21.3 - - + -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASN* 4.2 3.8 + - - -
285B GLU 2.9 16.8 + - - +
286B GLU* 4.4 10.5 - - - +
288B ALA* 1.3 72.6 - - + +
290B ASP* 1.3 65.9 + - - +
291B VAL 3.0 3.0 + - - -
292B GLY* 3.2 12.9 + - - +
293B ALA 4.7 1.8 - - - +
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASN* 3.5 12.8 + - - +
225A LYS* 5.0 2.9 - - - +
232A TYR* 5.6 2.9 - - - +
201B LYS* 3.2 30.3 + - - -
286B GLU* 3.0 45.6 + - - +
287B PHE* 4.2 6.7 - - - +
288B ALA 3.3 0.4 - - - -
289B LYS* 1.3 76.8 - - - +
291B VAL* 1.3 64.3 + - + +
440B ALA* 5.8 2.3 - - - +
441B ASP* 4.4 16.5 - - + +
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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