Contacts of the helix formed by residues 245 - 256 (chain B) in PDB entry 3BFT
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 GLY 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B ASN 2.9 14.5 + - - -
243B GLU 3.2 2.2 + - - -
244B GLN* 1.3 78.8 - - - +
246B LEU* 1.3 63.8 + - - +
247B LEU 3.3 2.5 - - - -
248B ASP* 3.4 17.7 + - - +
249B LYS* 3.1 26.1 + - - +
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Residues in contact with LEU 246 (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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39B LEU* 5.3 0.4 - - + -
42B GLU* 3.3 44.0 - - + +
241B LEU* 3.1 41.0 + - + +
244B GLN* 3.1 9.7 + - + +
245B GLY* 1.3 77.7 - - - +
247B LEU* 1.3 60.1 + - + +
249B LYS* 3.2 21.1 + - + +
250B LEU* 2.9 48.4 + - + +
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Residues in contact with LEU 247 (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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35B TYR* 3.7 24.4 + - + +
39B LEU* 3.8 27.4 - - + -
105B PRO 5.2 0.7 - - - +
106B PHE* 3.4 37.0 - - + +
107B MET* 5.5 0.2 - - - +
238B VAL* 4.2 6.3 - - + +
241B LEU* 3.8 10.5 + - + -
242B ASN* 3.4 49.1 - - + +
245B GLY 3.3 0.6 - - - -
246B LEU* 1.3 79.8 - - + +
248B ASP* 1.3 63.9 + - - +
250B LEU* 3.3 5.8 + - + +
251B LYS* 3.0 22.5 + - - +
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Residues in contact with ASP 248 (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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242B ASN* 4.6 13.2 - - - +
245B GLY* 3.4 20.0 + - - +
246B LEU 3.3 0.2 - - - -
247B LEU* 1.3 75.5 - - - +
249B LYS* 1.3 67.0 + - - +
251B LYS* 3.1 8.2 + - - +
252B ASN* 3.1 34.6 + - - +
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Residues in contact with LYS 249 (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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244B GLN 5.7 2.6 + - - -
245B GLY 3.1 15.9 + - - +
246B LEU* 3.3 22.9 - - + +
248B ASP* 1.3 77.2 - - - +
250B LEU* 1.3 61.0 + - + +
252B ASN* 3.6 6.4 + - - +
253B LYS* 3.1 30.2 + - + +
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Residues in contact with LEU 250 (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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35B TYR* 3.5 29.3 - - + +
38B ASP* 3.7 43.1 - - + +
39B LEU* 4.0 22.0 - - + +
42B GLU* 5.4 0.9 - - + -
246B LEU* 2.9 43.7 + - + +
247B LEU* 3.7 3.4 - - - +
249B LYS* 1.3 78.3 - - + +
251B LYS* 1.3 65.1 + - - +
253B LYS* 4.3 9.9 - - + +
254B TRP* 3.2 29.8 + - - +
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Residues in contact with LYS 251 (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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35B TYR* 3.7 4.4 - - + -
107B MET* 3.4 29.6 - - + +
108B SER 5.7 1.4 + - - -
195B THR* 4.6 8.1 - - - +
198B GLU* 3.7 17.1 + - - -
247B LEU 3.0 13.6 + - - +
248B ASP* 3.1 12.5 + - - +
250B LEU* 1.3 78.5 - - - +
252B ASN* 1.3 61.1 + - - +
255B TRP* 2.8 84.2 + - + +
256B TYR* 4.6 12.1 + - + -
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Residues in contact with ASN 252 (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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248B ASP* 3.1 24.6 + - - +
249B LYS* 4.0 5.6 - - - +
251B LYS* 1.3 79.0 - - - +
253B LYS* 1.3 60.7 + - - +
256B TYR* 3.1 29.9 + - + +
257B ASP* 2.8 37.9 + - - +
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Residues in contact with LYS 253 (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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38B ASP* 3.0 24.1 + - - +
249B LYS* 3.1 21.2 + - + +
250B LEU* 3.8 13.6 - - + +
251B LYS 3.3 0.2 - - - -
252B ASN* 1.3 78.3 - - - +
254B TRP* 1.3 88.6 + - + +
257B ASP* 3.3 19.7 + - + +
258B LYS* 2.8 39.8 + - - +
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Residues in contact with TRP 254 (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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15B PRO* 3.9 12.8 - - + +
18B MET* 3.7 29.8 - - + -
33B GLU* 3.6 23.8 - - + -
34B GLY* 3.4 31.1 - - - -
35B TYR* 3.5 18.6 - - + -
38B ASP* 2.7 29.2 + - - -
199B TYR* 3.4 23.6 - - - -
250B LEU* 3.2 27.1 + - + +
253B LYS* 1.3 100.6 - - + +
255B TRP* 1.3 73.0 + - + +
258B LYS* 3.9 37.2 - - + +
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Residues in contact with TRP 255 (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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15B PRO* 3.8 20.4 - - + -
16B TYR* 3.6 42.2 - + - -
35B TYR* 3.7 24.2 - + + -
107B MET* 4.0 7.2 - - + -
195B THR* 2.8 29.7 + - - -
198B GLU* 4.1 7.1 - - + +
199B TYR* 3.4 33.7 - + + +
202B GLN* 4.2 9.7 - - - +
203B ARG* 5.8 0.5 + - - -
251B LYS* 2.8 59.6 + - + +
254B TRP* 1.3 85.5 - - + +
256B TYR* 1.3 89.5 + + + +
258B LYS* 4.4 0.9 - - - +
259B GLY* 3.7 15.8 + - - -
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Residues in contact with TYR 256 (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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198B GLU* 3.9 30.7 + - + +
202B GLN* 4.3 26.9 - - + -
251B LYS* 4.6 13.3 + - + -
252B ASN* 3.1 29.7 + - + +
255B TRP* 1.3 101.3 - + + +
257B ASP* 1.3 68.5 + - - +
258B LYS 3.1 1.8 - - - -
259B GLY* 3.0 14.1 + - - +
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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