Contacts of the helix formed by residues 245 - 256 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ILE* 5.2 8.3 - - - -
241C LEU 3.9 0.2 - - - -
242C ASN 3.0 15.4 + - - -
243C GLU 3.1 2.6 + - - -
244C GLN* 1.3 78.5 - - - +
246C LEU* 1.3 63.6 + - - +
247C LEU 3.4 2.5 - - - -
248C ASP* 3.3 15.4 + - - +
249C LYS* 3.1 27.8 + - - +
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 4.5 5.4 - - + -
42C GLU* 3.6 37.9 - - + +
241C LEU* 2.9 47.6 + - + +
244C GLN* 3.3 5.5 + - + -
245C GLY* 1.3 76.8 - - - +
247C LEU* 1.3 58.3 + - + +
249C LYS* 3.1 14.4 + - + +
250C LEU* 2.8 55.8 + - + +
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 3.7 21.7 + - + +
39C LEU* 3.9 27.6 - - + -
106C PHE* 3.3 42.4 - - + +
107C MET* 5.3 0.3 - - - +
238C VAL* 4.2 7.2 - - + +
241C LEU* 3.8 4.0 + - + +
242C ASN* 3.5 46.7 - - + +
245C GLY 3.4 0.6 - - - -
246C LEU* 1.3 82.1 - - + +
248C ASP* 1.3 58.9 + - - +
250C LEU* 3.4 5.1 + - + +
251C LYS* 3.0 28.8 + - - +
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Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU 4.9 2.9 - - - +
216A ASP* 4.6 18.1 - - - +
217A SER* 4.5 16.0 + - - -
242C ASN* 4.6 13.7 - - - +
245C GLY* 3.3 18.5 + - - +
246C LEU 3.2 0.4 - - - -
247C LEU* 1.3 74.4 - - - +
249C LYS* 1.3 65.5 + - - +
251C LYS* 3.4 5.2 + - - +
252C ASN* 3.2 34.0 + - - +
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 6.2 3.7 - - - +
244C GLN 5.7 2.2 + - - -
245C GLY 3.1 15.9 + - - +
246C LEU* 3.1 16.0 + - + +
248C ASP* 1.3 79.1 - - - +
250C LEU* 1.3 64.2 + - + +
252C ASN* 3.3 9.1 + - - +
253C LYS* 3.0 23.9 + - + +
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 3.6 25.6 - - + +
38C ASP* 3.5 43.1 - - + +
39C LEU* 4.2 18.6 - - + +
42C GLU* 5.5 0.4 - - + -
246C LEU* 2.8 50.7 + - + +
247C LEU* 3.9 2.9 - - - +
249C LYS* 1.3 81.1 - - + +
251C LYS* 1.3 61.7 + - - +
253C LYS* 3.3 13.5 + - + +
254C TRP* 3.1 30.4 + - + +
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 3.6 3.3 - - - -
107C MET* 3.4 31.0 - - + -
108C SER 5.8 1.1 - - - -
195C THR* 4.3 13.5 - - - -
198C GLU* 3.4 21.2 + - - -
247C LEU 3.0 17.7 + - - +
248C ASP* 3.9 6.5 - - - +
249C LYS 3.3 0.2 - - - -
250C LEU* 1.3 75.5 - - - +
252C ASN* 1.3 60.3 + - - +
255C TRP* 2.8 69.9 + - + +
256C TYR* 3.7 21.8 + - + -
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Residues in contact with ASN 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ASP* 3.2 20.3 + - - +
249C LYS* 3.7 9.1 - - - +
251C LYS* 1.3 80.3 - - - +
253C LYS* 1.3 60.1 + - - +
256C TYR* 3.0 30.7 + - + +
257C ASP* 2.9 39.9 + - - +
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 3.0 26.8 + - - +
249C LYS* 3.0 18.8 + - + +
250C LEU* 3.5 14.0 - - + +
252C ASN* 1.3 79.9 - - - +
254C TRP* 1.3 87.6 + - + +
257C ASP* 3.4 16.5 + - + +
258C LYS* 3.2 43.8 + - - +
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Residues in contact with TRP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 4.1 10.8 - - + +
18C MET* 3.6 31.0 - - + -
33C GLU* 3.8 22.7 - - + -
34C GLY* 3.4 26.5 - - - -
35C TYR* 3.4 26.3 - + - +
38C ASP* 2.9 29.6 + - - -
199C TYR* 3.6 21.8 - - - -
250C LEU* 3.1 26.9 + - + +
253C LYS* 1.3 97.6 - - + +
255C TRP* 1.3 75.2 + - + +
258C LYS* 4.1 37.2 - - + +
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Residues in contact with TRP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 3.7 22.0 - - + -
16C TYR* 3.6 42.6 - + - -
35C TYR* 3.6 28.3 - + + -
107C MET* 4.0 10.1 - - + -
195C THR* 2.9 31.4 + - - +
198C GLU* 4.2 5.6 - - + +
199C TYR* 3.5 32.4 - + + +
202C GLN* 4.0 15.8 - - - +
203C ARG* 5.6 1.2 + - - -
251C LYS* 2.8 61.8 + - + +
254C TRP* 1.3 82.3 - - + +
256C TYR* 1.3 88.4 + + + +
258C LYS* 4.7 1.1 - - - +
259C GLY* 4.0 9.3 + - - -
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Residues in contact with TYR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLU* 4.1 22.7 + - + +
202C GLN* 4.2 28.5 - - + -
251C LYS* 3.7 24.6 + - + -
252C ASN* 3.0 32.4 + - + +
255C TRP* 1.3 100.4 - + + +
257C ASP* 1.3 62.1 + - - +
258C LYS 3.1 2.0 - - - -
259C GLY* 2.8 20.6 + - - +
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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