Contacts of the helix formed by residues 255 - 266 (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 SER 255 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14I ASP* 3.1 16.8 - - - -
17I VAL* 4.9 7.1 - - - +
253I ILE 3.5 5.8 + - - -
254I LEU* 1.3 78.9 - - - +
256I ALA* 1.3 63.5 + - - +
257I GLN* 3.7 4.2 + - - +
258I LEU* 2.8 39.2 + - - +
259I ILE* 3.1 18.8 + - - +
370I VAL* 5.3 1.1 - - - -
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Residues in contact with ALA 256 (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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10I HIS* 3.3 36.8 + - + +
13I SER* 4.3 1.6 - - - -
14I ASP* 2.9 25.6 + - - +
17I VAL* 5.4 0.2 - - - +
255I SER* 1.3 71.8 - - - +
257I GLN* 1.3 61.0 + - - +
259I ILE* 3.4 13.8 + - - +
260I SER* 3.4 13.0 + - - -
368I GLY* 4.2 6.9 - - - +
370I VAL* 4.2 25.6 - - + +
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Residues in contact with GLN 257 (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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10I HIS* 4.2 14.2 + - - +
14I ASP* 4.7 2.4 + - - +
255I SER* 3.3 3.8 + - - +
256I ALA* 1.3 76.3 - - - +
258I LEU* 1.3 62.5 + - - +
260I SER* 3.6 22.0 + - - -
261I HIS* 3.2 19.3 + - - +
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Residues in contact with LEU 258 (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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213I PHE* 3.7 31.2 - - + -
250I LEU* 4.3 9.4 - - + -
253I ILE* 3.8 23.6 - - + +
254I LEU* 3.9 16.4 - - + -
255I SER* 2.8 28.5 + - - +
257I GLN* 1.3 76.5 - - - +
259I ILE* 1.3 65.4 + - + +
261I HIS* 3.1 26.5 + - + +
262I TRP* 3.2 34.5 + - + +
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Residues in contact with ILE 259 (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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236I PHE* 3.9 22.2 - - + -
254I LEU* 5.0 5.6 - - + -
255I SER 3.1 16.6 + - - +
256I ALA* 3.6 10.1 - - - +
257I GLN 3.3 0.2 - - - -
258I LEU* 1.3 75.6 - - + +
260I SER* 1.3 64.4 + - - +
262I TRP* 2.9 53.2 + - + +
263I LYS* 3.2 11.3 + - - +
361I VAL* 4.2 28.0 - - + -
363I ARG* 3.7 30.3 - - + +
368I GLY 6.1 0.7 - - - +
370I VAL* 4.9 8.3 - - + -
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Residues in contact with SER 260 (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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10I HIS* 4.5 9.5 - - - -
256I ALA 3.4 10.2 + - - -
257I GLN* 3.6 27.8 + - - -
259I ILE* 1.3 80.1 - - - +
261I HIS* 1.3 60.7 + - - +
262I TRP 3.2 0.2 + - - -
263I LYS* 3.3 7.9 + - - +
264I GLY* 3.0 20.4 + - - -
363I ARG* 3.9 20.0 + - - +
368I GLY* 5.5 1.6 - - - -
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Residues in contact with HIS 261 (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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213I PHE* 3.7 33.4 - + - -
257I GLN* 3.2 14.3 + - - +
258I LEU* 3.1 21.6 + - + +
260I SER* 1.3 76.3 - - - +
262I TRP* 1.3 58.7 + + - +
264I GLY* 3.6 2.5 + - - -
265I ASN* 3.1 52.7 + - - +
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Residues in contact with TRP 262 (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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211I THR* 3.8 9.9 - - + +
213I PHE* 3.4 38.7 - + + +
223I ILE* 3.5 40.6 - - + -
236I PHE* 4.4 16.2 - + + -
238I ALA* 4.8 6.5 - - + -
250I LEU* 4.0 22.9 - - + -
254I LEU* 3.8 18.8 - - + -
258I LEU* 3.2 30.1 + - + +
259I ILE* 2.9 49.3 + - + +
261I HIS* 1.3 77.5 - + - +
263I LYS* 1.3 66.4 + - - +
264I GLY 3.1 1.6 - - - -
265I ASN* 3.1 4.2 + - - -
266I MET* 3.0 33.5 + - + +
359I LEU* 6.1 0.4 - - + -
361I VAL* 5.4 3.6 - - + -
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Residues in contact with LYS 263 (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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209I ASN* 2.9 33.9 - - - +
225I GLU* 3.1 23.7 + - - +
236I PHE* 4.2 2.4 - - + -
259I ILE 3.2 5.0 + - - +
260I SER* 3.8 8.3 - - - +
262I TRP* 1.3 78.2 - - - +
264I GLY* 1.3 64.1 + - - +
266I MET* 3.5 23.3 + - - +
363I ARG* 3.7 28.3 - - - +
365I ASN* 6.5 0.4 - - - -
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Residues in contact with GLY 264 (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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260I SER 3.0 13.3 + - - -
261I HIS* 3.8 5.4 - - - -
262I TRP 3.1 0.6 - - - -
263I LYS* 1.3 79.2 - - - +
265I ASN* 1.3 64.2 + - - +
266I MET 3.4 4.5 + - - +
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Residues in contact with ASN 265 (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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210I TYR 4.1 0.3 - - - +
211I THR* 3.4 26.6 + - - +
212I GLU 5.5 1.4 - - - +
213I PHE* 5.5 2.1 - - - -
261I HIS* 3.1 43.7 + - - +
262I TRP* 3.1 7.4 + - - +
264I GLY* 1.3 78.1 - - - +
266I MET* 1.3 63.2 + - - +
267I THR* 3.6 8.4 + - - +
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Residues in contact with MET 266 (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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209I ASN* 3.6 29.6 - - + +
210I TYR 3.1 18.8 - - - +
211I THR* 4.0 5.6 - - + -
223I ILE* 3.9 15.9 - - + +
224I LEU* 3.7 28.0 - - - +
225I GLU* 3.8 23.8 - - - +
236I PHE* 3.8 21.3 - - + -
262I TRP* 3.0 18.0 + - + +
263I LYS* 3.7 15.7 - - - +
264I GLY 3.2 7.0 - - - +
265I ASN* 1.3 81.1 - - - +
267I THR* 1.3 63.2 + - - +
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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