Contacts of the helix formed by residues 242 - 256 (chain A) in PDB entry 5OF4
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A THR* 1.3 72.5 + - - +
268A VAL* 5.2 1.9 - - - +
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLN* 1.3 85.9 + - - +
268A VAL* 1.3 72.8 + - - +
269A SER* 4.2 2.2 + - - -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLN 5.2 1.3 - - - +
267A THR* 1.3 85.0 - - - +
269A SER* 1.3 66.2 + - - +
270A PHE* 3.6 32.9 + - + -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A THR* 4.2 3.5 + - - -
268A VAL* 1.3 75.6 - - - +
270A PHE* 1.3 69.8 + - - +
271A GLU* 3.9 11.3 + - - +
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A VAL* 3.6 32.9 + - + -
269A SER* 1.3 77.5 - - - +
271A GLU* 1.3 64.6 + - - +
272A VAL* 2.8 25.8 + - + +
273A LYS* 4.9 8.5 - - - +
281A GLN* 5.2 11.0 - - - -
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A SER* 3.9 12.5 + - - +
270A PHE* 1.3 72.2 - - - +
272A VAL* 1.3 62.6 + - - +
273A LYS* 3.2 23.5 + - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 2.8 27.0 + - + +
271A GLU* 1.3 69.0 - - - +
273A LYS* 1.3 72.4 + - - +
274A GLN 4.1 0.7 + - - -
275A GLU 5.0 1.4 + - - -
277A ILE* 4.2 18.4 - - + -
278A GLU* 3.2 29.1 - - + +
281A GLN* 3.2 32.8 - - - +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 4.9 9.1 - - - +
271A GLU 3.2 26.8 + - - +
272A VAL* 1.3 83.8 - - - +
274A GLN* 1.3 77.0 + - + +
275A GLU* 3.0 9.5 + - - -
277A ILE* 3.3 29.5 + - + +
278A GLU* 5.1 0.7 + - - +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL 4.1 1.2 + - - -
273A LYS* 1.3 80.3 - - + +
275A GLU* 1.3 64.4 + - - +
276A MET* 2.9 18.2 + - - +
277A ILE* 3.3 21.5 - - + +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL 5.0 1.8 + - - -
273A LYS 3.0 5.8 + - - -
274A GLN* 1.3 76.2 - - - +
276A MET* 1.3 70.6 + - + +
277A ILE 3.8 0.9 - - - -
278A GLU* 4.8 10.7 - - - +
435A TRP* 6.1 0.9 - - - -
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A GLN 2.9 13.9 + - - +
275A GLU* 1.3 87.4 - - + +
277A ILE* 1.3 68.7 + - + +
278A GLU 3.3 1.8 - - - +
279A GLU* 4.9 16.9 + - - +
280A LEU* 3.8 20.1 - - - +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL* 4.2 19.5 - - + -
273A LYS* 3.3 27.3 + - + +
274A GLN* 3.3 32.8 - - + +
275A GLU 3.8 0.2 - - - -
276A MET* 1.3 82.1 - - + +
278A GLU* 1.3 58.5 + - - +
279A GLU 3.4 0.9 - - - -
280A LEU* 3.1 16.0 + - + +
281A GLN* 2.9 34.4 + - + +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL* 3.2 29.5 - - + +
273A LYS 5.1 0.8 + - - +
275A GLU* 5.2 11.2 - - - +
276A MET* 3.3 3.0 - - - +
277A ILE* 1.3 79.4 - - - +
279A GLU* 1.3 60.7 + - + +
281A GLN* 3.2 15.1 + - - +
282A LYS* 2.9 68.6 + - - +
292A LEU* 5.1 4.7 - - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A MET* 5.5 15.3 - - - +
278A GLU* 1.3 78.1 - - + +
280A LEU* 1.3 71.5 + - + +
282A LYS* 3.3 11.6 + - - +
283A ARG* 3.0 57.0 + - - +
459A GLN* 4.8 16.8 + - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A MET 3.8 22.2 - - - +
277A ILE* 3.1 11.6 + - + +
279A GLU* 1.3 95.3 - - + +
281A GLN* 1.3 57.0 + - - +
283A ARG* 3.2 24.7 - - - +
284A CYS* 3.0 37.0 + - - -
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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