Contacts of the helix formed by residues 272 - 284 (chain F) in PDB entry 6G2T
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 272 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177F LEU* 4.4 0.9 - - - -
179F LEU* 4.9 0.2 - - - -
260F LEU 3.3 14.1 - - - -
261F PHE 3.7 6.2 + - - -
263F PRO* 3.5 17.2 - - - +
271F CYS* 1.3 77.2 - - - +
273F ILE* 1.3 65.1 + - - -
274F HIS 3.3 2.7 - - - -
275F GLU* 3.1 20.5 + - - -
276F THR* 3.1 18.9 + - - +
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Residues in contact with ILE 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F MET* 3.5 28.1 - - + +
159F THR* 4.7 3.6 - - + +
177F LEU* 3.8 15.7 - - + -
179F LEU* 4.1 3.4 - - + -
260F LEU* 3.1 40.6 + - + +
261F PHE* 3.8 27.1 - - + -
272F GLY* 1.3 71.4 - - - -
274F HIS* 1.3 65.0 + - - +
276F THR* 2.7 22.7 + - - -
277F THR* 3.2 13.3 + - - -
308F ILE* 5.1 5.8 - - + -
312F MET* 3.5 29.5 - - + +
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Residues in contact with HIS 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PHE* 3.7 29.7 + + + -
262F GLN* 5.2 5.1 + - - -
273F ILE* 1.3 80.5 + - - +
275F GLU* 1.3 98.4 + - - +
277F THR* 3.3 11.8 + - - -
278F PHE* 3.0 22.7 + - + -
312F MET* 3.7 21.5 - - + -
315F GLU* 2.9 51.7 + - + +
316F ILE* 4.6 8.2 - - + +
319F LEU* 4.3 15.9 - - + +
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Residues in contact with GLU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PHE 5.0 1.0 - - - +
262F GLN* 5.7 1.6 + - - -
271F CYS* 3.5 28.7 - - + -
272F GLY* 3.1 22.7 + - - -
274F HIS* 1.3 112.5 + - + +
276F THR* 1.3 63.1 + - - +
278F PHE* 3.1 13.4 + - - +
279F ASN* 3.0 20.7 + - - +
319F LEU* 4.8 10.3 - - + +
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Residues in contact with THR 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F MET* 4.9 2.3 - - - +
159F THR* 5.7 0.2 - - - +
161F THR* 4.3 12.0 + - - -
175F LEU* 3.5 25.2 - - + +
177F LEU* 3.7 27.8 - - + +
271F CYS* 3.6 18.8 - - + +
272F GLY 3.1 14.2 + - - +
273F ILE* 2.7 24.9 + - - -
275F GLU* 1.3 76.7 - - - +
277F THR* 1.3 61.6 + - - +
279F ASN* 3.2 6.2 + - - +
280F SER* 3.1 26.3 + - - -
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Residues in contact with THR 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ILE* 3.9 26.5 - - + -
152F MET* 4.2 18.1 - - + +
161F THR* 4.7 6.7 + - + +
273F ILE 3.2 11.4 + - - -
274F HIS* 3.3 11.6 + - - -
275F GLU 3.2 0.4 - - - -
276F THR* 1.3 79.9 + - - +
278F PHE* 1.3 62.7 + - + +
280F SER* 3.3 8.2 + - - -
281F ILE* 3.1 37.4 + - + +
296F THR* 5.0 7.2 - - + +
312F MET* 4.4 7.3 - - - +
316F ILE* 4.8 17.7 - - + -
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Residues in contact with PHE 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F HIS* 3.0 28.8 + - + -
275F GLU* 3.1 9.5 + - - +
277F THR* 1.3 79.7 - - + +
279F ASN* 1.3 56.9 + - - +
281F ILE* 3.2 9.2 + - + +
282F MET* 2.9 45.2 + - + +
293F TYR* 4.1 17.9 - + - -
315F GLU 4.2 0.7 - - - -
316F ILE* 3.1 52.5 - - + -
319F LEU* 3.3 34.5 - - + -
320F ALA* 3.5 27.4 - - + -
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Residues in contact with ASN 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 3.5 26.5 - - + +
275F GLU 3.0 12.3 + - - +
276F THR* 3.2 10.1 + - - +
278F PHE* 1.3 76.0 - - - +
280F SER* 1.3 61.1 - - - +
282F MET* 3.3 9.3 + - - +
283F LYS* 3.1 49.0 + - - +
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Residues in contact with SER 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ILE* 4.2 7.0 - - - -
161F THR* 3.4 29.6 - - - +
163F PRO* 4.4 3.6 - - - -
173F ALA* 3.2 25.8 + - - +
175F LEU* 3.5 13.1 - - - +
276F THR 3.1 11.5 + - - -
277F THR 3.5 9.0 - - - -
279F ASN* 1.3 76.0 - - - +
281F ILE* 1.3 61.8 + - - +
283F LYS* 3.5 7.6 + - - +
284F CYS* 3.2 27.9 + - - -
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Residues in contact with ILE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ILE* 3.9 15.7 - - + -
277F THR* 3.1 31.1 + - + +
278F PHE* 3.2 11.4 + - + +
280F SER* 1.3 75.2 - - - +
282F MET* 1.3 64.6 + - + +
284F CYS* 3.1 18.8 + - - +
289F ARG* 3.2 32.3 + - + +
292F LEU* 4.9 9.2 - - + +
293F TYR* 3.5 64.4 - - + +
296F THR* 5.9 0.7 - - - +
316F ILE* 5.8 2.0 - - + -
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Residues in contact with MET 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ASP* 5.6 2.2 - - - +
278F PHE* 2.9 36.7 + - + +
279F ASN* 3.3 10.3 + - - +
281F ILE* 1.3 77.4 - - + +
283F LYS* 1.3 60.4 + - + +
289F ARG* 2.7 43.4 + - - +
293F TYR* 3.7 22.9 - - - +
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Residues in contact with LYS 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ASP* 5.6 7.5 + - - +
172F HIS* 3.2 49.5 + - + +
173F ALA* 3.8 17.3 - - - +
174F ILE 5.8 0.4 - - - -
175F LEU* 5.5 7.2 - - - -
279F ASN* 3.1 42.8 + - - +
280F SER* 3.6 8.3 - - - +
281F ILE 3.2 0.2 - - - -
282F MET* 1.3 77.8 - - + +
284F CYS* 1.3 62.1 + - - +
285F ASP* 4.0 2.6 + - - +
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Residues in contact with CYS 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F PRO* 3.7 21.8 - - - -
170F LEU* 3.5 20.9 - - + -
173F ALA* 3.4 19.7 - - - -
280F SER 3.2 18.6 - - - -
281F ILE 3.1 12.2 + - - +
283F LYS* 1.3 80.9 - - - +
285F ASP* 1.3 62.6 + - - +
288F ILE* 4.1 9.9 - - + -
289F ARG* 2.8 29.3 + - + -
292F LEU* 4.1 15.0 - - + -
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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