Contacts of the helix formed by residues 267 - 278 (chain L) in PDB entry 5IJO
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 GLN 267 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263L ALA 3.6 5.7 + - - +
264L HIS* 3.0 19.6 + - - +
265L PHE 2.8 2.0 - - - -
266L GLU* 1.3 84.7 - - - +
268L ALA* 1.4 47.0 + - - +
269L ASN* 3.4 3.1 - - + +
270L ILE* 4.2 9.9 - - + +
271L LYS* 2.6 34.6 + - - +
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Residues in contact with ALA 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266L GLU 3.3 3.4 + - - -
267L GLN* 1.4 68.2 - - - +
269L ASN* 1.4 56.7 + - + +
271L LYS* 3.4 6.6 - - - +
272L THR* 2.7 32.3 + - - -
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Residues in contact with ASN 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L GLN* 5.4 2.2 - - + -
268L ALA* 1.4 74.0 - - + +
270L ILE* 1.3 65.3 + - - +
272L THR* 3.0 7.6 + - - +
273L GLN* 2.7 30.4 + - - +
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Residues in contact with ILE 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L VAL* 5.2 16.9 - - + +
264L HIS 3.8 22.7 - - - +
265L PHE* 3.9 9.4 - - - +
267L GLN* 3.5 8.2 + - + +
268L ALA 3.3 0.2 - - - -
269L ASN* 1.3 84.0 - - - +
271L LYS* 1.3 50.6 + - - +
273L GLN* 3.0 8.9 + - + +
274L LEU* 2.6 35.9 + - - +
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Residues in contact with LYS 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265L PHE 3.4 11.4 + - - +
266L GLU* 4.3 6.5 - - - +
267L GLN 2.6 24.8 + - - +
268L ALA* 3.4 7.4 - - - +
270L ILE* 1.3 72.4 - - - +
272L THR* 1.4 56.2 + - - +
274L LEU* 3.1 6.5 + - - +
275L GLN* 2.8 30.2 + - - +
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Residues in contact with THR 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268L ALA 2.7 18.8 + - - -
269L ASN* 3.0 8.2 + - - -
271L LYS* 1.4 75.2 - - - +
273L GLN* 1.3 61.7 + - - +
275L GLN* 3.1 9.5 + - - +
276L GLN* 3.1 19.9 + - - +
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Residues in contact with GLN 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L VAL* 5.2 12.8 - - + -
269L ASN 2.7 18.7 + - - +
270L ILE* 3.3 11.0 - - + +
272L THR* 1.3 70.0 - - - +
274L LEU* 1.3 65.3 + - - +
276L GLN* 3.2 16.4 + - - +
277L LEU* 3.4 10.0 + - - +
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Residues in contact with LEU 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L VAL* 6.2 1.1 - - - +
265L PHE* 5.5 6.1 - - + +
270L ILE 2.6 19.1 + - - +
271L LYS* 3.6 8.7 - - - +
273L GLN* 1.3 73.5 - - - +
275L GLN* 1.3 56.8 + - - +
277L LEU* 3.0 29.0 + - - +
279L VAL* 3.1 27.6 + - + +
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Residues in contact with GLN 275 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271L LYS 2.8 13.0 + - - +
272L THR* 3.1 13.7 + - - +
274L LEU* 1.3 71.9 - - - +
276L GLN* 1.3 61.5 + - - +
278L GLY* 2.9 19.2 + - - -
279L VAL 3.5 17.5 + - - +
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Residues in contact with GLN 276 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272L THR 3.1 12.3 + - - +
273L GLN* 3.6 11.7 - - - +
274L LEU 3.2 0.6 - - - -
275L GLN* 1.3 76.2 - - - +
277L LEU* 1.3 60.3 + - - +
278L GLY* 3.3 0.9 + - - -
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Residues in contact with LEU 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L LYS* 6.1 0.9 - - - +
212L SER* 5.7 8.7 - - - -
273L GLN 3.4 5.8 + - - +
274L LEU* 3.0 19.4 + - - +
276L GLN* 1.3 78.7 - - - +
278L GLY* 1.3 54.9 - - - -
279L VAL* 4.5 2.5 - - + +
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Residues in contact with GLY 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L PHE* 3.3 7.3 - - - -
196L ASN* 3.0 38.7 + - - +
197L LYS* 5.9 2.2 - - - -
275L GLN 2.9 12.4 + - - -
276L GLN 3.1 1.5 - - - -
277L LEU* 1.3 78.5 - - - +
279L VAL* 1.4 63.8 + - - +
280L THR 3.3 0.9 + - - -
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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