Contacts of the helix formed by residues 269 - 275 (chain I) in PDB entry 6K71
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 ARG 269 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131I LEU* 4.6 19.8 - - + +
150I LEU* 4.8 17.9 - - + +
152I TYR* 6.1 4.7 - - + -
181I MET* 4.6 7.5 - - - +
183I MET* 3.5 10.3 - - - -
248I HIS* 3.0 56.9 + - + +
250I SER* 2.5 37.2 + - - -
268I THR* 1.3 78.6 + - - +
270I ASP* 1.3 56.1 + - - +
271I ASP 3.1 4.7 - - - -
272I PHE* 2.8 46.7 + - + +
273I VAL* 4.1 22.9 + - - +
299I ARG* 5.8 2.0 - - - +
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Residues in contact with ASP 270 (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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201I VAL* 6.1 0.3 - - - +
215I PHE* 3.2 29.9 - - - -
217I LYS* 3.1 31.3 + - - +
248I HIS* 6.2 0.8 - - - -
268I THR* 3.3 15.2 + - + +
269I ARG* 1.3 78.8 - - - +
271I ASP* 1.3 60.1 + - - +
272I PHE 3.4 0.6 + - - -
273I VAL* 4.4 6.7 + - - +
274I ARG* 2.3 54.8 + - - +
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Residues in contact with ASP 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I ASP 4.6 2.6 - - - +
266I TYR* 3.2 38.1 + - + -
267I GLN* 3.6 21.7 + - - +
268I THR* 3.7 22.3 + - - +
269I ARG 3.0 0.6 + - - -
270I ASP* 1.3 78.4 - - - +
272I PHE* 1.3 63.2 + - - +
274I ARG* 2.7 35.6 + - - +
275I GLY* 4.3 7.8 + - - -
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Residues in contact with PHE 272 (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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131I LEU* 4.2 11.2 - - + -
132I GLY* 3.5 31.0 - - - -
135I LEU* 4.4 20.2 - - + -
150I LEU* 6.2 1.3 - - + -
260I PHE* 3.4 29.4 - + - -
266I TYR* 3.9 26.0 + + + -
268I THR 3.7 12.6 - - - -
269I ARG* 2.8 43.9 + - + +
271I ASP* 1.3 80.5 - - - +
273I VAL* 1.3 65.3 + - + +
276I LEU* 3.3 24.8 + - + +
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Residues in contact with VAL 273 (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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181I MET* 6.5 0.7 - - + -
183I MET* 6.2 6.3 - - + -
212I VAL* 5.2 9.0 - - + -
213I LEU 4.5 6.0 - - - +
215I PHE* 3.5 34.5 - - + -
269I ARG* 4.6 23.6 - - - +
270I ASP* 4.4 6.3 - - - +
272I PHE* 1.3 77.7 - - + +
274I ARG* 1.3 70.5 + - - +
276I LEU* 3.3 19.6 - - + +
277I LEU* 3.6 10.1 - - + +
287I ILE* 3.7 27.6 - - + -
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Residues in contact with ARG 274 (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 LEU 5.3 0.2 - - - -
214I HIS* 3.5 30.0 + - + -
215I PHE* 4.1 34.9 - - + +
216I GLN* 6.1 2.6 - - - +
217I LYS* 4.6 5.3 - - - +
270I ASP* 2.3 46.4 + - - +
271I ASP* 2.7 32.2 + - - +
272I PHE 3.4 0.6 - - - -
273I VAL* 1.3 81.0 - - - +
275I GLY* 1.3 60.6 + - - +
276I LEU 3.2 2.6 + - - -
277I LEU 3.5 8.1 + - - -
278I VAL* 5.7 0.2 - - - +
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Residues in contact with GLY 275 (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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266I TYR* 4.7 11.8 + - - -
271I ASP 4.3 5.2 + - - -
272I PHE 4.1 3.7 + - - -
274I ARG* 1.3 74.8 - - - +
276I LEU* 1.3 61.3 + - - +
277I LEU 3.1 2.5 + - - -
278I VAL* 4.2 21.0 + - - +
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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