Contacts of the helix formed by residues 286 - 293 (chain I) in PDB entry 5BRR
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 LEU 286 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19I VAL* 5.1 5.8 - - + -
34I PHE* 4.6 7.4 - - + -
39I VAL* 4.5 22.2 - - + -
42I VAL* 5.4 4.9 - - + -
43I LEU* 5.1 6.3 - - + -
165I LEU* 5.8 2.0 - - + -
167I ASN* 6.1 0.9 - - + -
284I VAL* 3.5 36.3 - - + +
285I ASP* 1.3 72.3 - - - +
287I ARG* 1.3 55.8 + - - +
289I PRO* 3.1 6.8 - - + +
290I LEU* 2.7 61.8 + - + +
320I ALA* 3.0 22.1 + - + +
321I LEU 4.2 17.0 - - - +
322I GLN* 3.8 16.4 - - + +
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Residues in contact with ARG 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285I ASP* 3.3 24.9 - - - +
286I LEU* 1.3 76.4 - - - +
288I LYS* 1.3 68.1 + - + +
290I LEU* 3.7 1.4 - - - +
291I GLU* 2.7 60.5 + - - +
299I PHE* 3.9 57.6 + - + +
300I ARG* 5.9 3.4 - - - +
301I GLN* 6.1 0.8 - - - +
317I VAL 4.9 0.4 + - - -
318I ALA* 3.8 24.4 + - - +
319I LEU* 5.5 1.1 - - - +
320I ALA 4.5 6.2 + - - +
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Residues in contact with LYS 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I ASP* 4.4 5.1 + - - +
287I ARG* 1.3 91.3 - - + +
289I PRO* 1.3 69.3 - - + +
291I GLU* 3.0 24.1 + - + +
292I ASN* 2.6 48.7 + - - +
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Residues in contact with PRO 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I VAL* 4.4 14.1 - - + -
22I GLN* 3.9 24.7 - - + +
23I VAL* 4.0 25.8 - - + +
284I VAL* 4.5 2.5 - - + -
285I ASP 3.3 21.8 - - - +
286I LEU* 3.1 13.5 - - + +
288I LYS* 1.3 98.2 - - + +
290I LEU* 1.3 61.4 + - - +
292I ASN* 3.1 18.2 + - + +
293I LEU* 3.4 12.6 + - - +
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Residues in contact with LEU 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 4.4 11.9 - - + -
19I VAL* 4.7 12.1 - - + -
39I VAL* 4.7 3.4 - - + -
43I LEU* 4.4 25.6 - - + -
165I LEU* 5.9 0.2 - - + -
286I LEU* 2.7 46.4 + - + +
287I ARG 3.8 2.9 - - - +
289I PRO* 1.3 73.5 - - + +
291I GLU* 1.3 59.5 + - - +
293I LEU* 3.2 19.1 + - + +
295I MET* 3.0 48.0 + - + +
298I MET* 4.5 8.3 - - + -
299I PHE* 3.8 25.8 - - + -
320I ALA* 4.9 4.3 - - + -
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Residues in contact with GLU 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287I ARG* 2.7 52.1 + - - +
288I LYS* 3.5 27.1 + - + +
290I LEU* 1.3 68.4 - - - +
292I ASN* 1.3 66.8 + - - +
293I LEU 3.1 1.8 - - - -
294I GLY* 3.0 14.9 + - - -
295I MET 3.6 21.3 + - - +
296I THR* 4.0 28.3 - - + +
299I PHE* 3.8 16.9 - - + +
300I ARG* 5.3 8.3 + - - +
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Residues in contact with ASN 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN* 3.0 38.8 + - - +
25I GLN* 4.2 11.1 - - - +
288I LYS* 2.6 34.4 + - - +
289I PRO* 3.1 14.3 + - - +
291I GLU* 1.3 73.1 - - - +
293I LEU* 1.3 58.1 + - - +
294I GLY 3.4 0.7 + - - -
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Residues in contact with LEU 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I PHE* 4.0 18.8 - - + -
18I ARG* 4.4 17.0 - - + +
19I VAL* 4.2 21.3 - - + +
22I GLN* 3.5 34.1 - - + +
61I ALA* 4.6 9.1 - - + +
289I PRO 3.5 11.2 - - - +
290I LEU* 3.2 7.4 + - + +
291I GLU 3.1 1.2 - - - -
292I ASN* 1.3 78.1 - - - +
294I GLY* 1.3 58.8 + - - +
295I MET* 3.5 31.1 - - + +
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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