Contacts of the helix formed by residues 271 - 279 (chain D) in PDB entry 1O97
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 SER 271 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D ASN* 5.7 6.1 - - - -
269D SER* 3.7 6.3 + - - -
270D GLY* 1.3 79.5 - - - +
272D ILE* 1.3 66.0 + - - +
273D GLN* 3.6 5.5 + - - -
274D HIS* 3.0 19.1 + - - +
275D MET* 2.9 21.3 + - - +
294D SER* 5.5 0.2 - - - -
1319D FAD 2.7 51.0 + - - -
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Residues in contact with ILE 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ASP* 5.2 4.5 - - - +
137D GLN* 3.9 27.8 - - + +
156D ARG* 3.4 48.9 - - + +
252D GLN* 5.3 6.1 - - - +
270D GLY 3.7 0.8 + - - +
271D SER* 1.3 73.7 - - - +
273D GLN* 1.3 74.5 + - + +
275D MET* 3.3 20.7 + - + +
276D ALA* 3.0 27.5 + - + +
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Residues in contact with GLN 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLN* 4.0 13.1 + - - +
251D GLY* 3.3 1.4 - - - -
252D GLN* 2.9 54.8 + - + +
271D SER* 3.8 4.9 - - - -
272D ILE* 1.3 95.0 - - + +
274D HIS* 1.3 63.0 + - - +
276D ALA* 3.6 5.8 - - - +
1319D FAD 3.3 77.7 + - + +
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Residues in contact with HIS 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D CYS 3.9 1.3 - - - -
235D SER* 3.6 26.0 - - - -
250D VAL* 3.3 17.0 + - + +
251D GLY* 3.8 2.9 - - - -
263D TYR* 2.7 33.2 + + - -
268D ILE* 3.8 26.5 - - + +
270D GLY* 4.8 1.6 - - - -
271D SER* 3.0 27.1 + - - +
273D GLN* 1.3 75.9 - - - +
275D MET* 1.3 64.7 + - - +
277D GLY* 2.9 16.6 + - - -
278D MET* 3.6 20.1 - - + +
295D ILE* 5.2 4.0 - - + -
1319D FAD 2.9 30.5 + - - +
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Residues in contact with MET 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D GLY* 3.2 27.4 - - - +
271D SER 2.9 16.2 + - - +
272D ILE* 3.6 21.5 - - + +
274D HIS* 1.3 75.7 - - - +
276D ALA* 1.3 59.4 + - - +
277D GLY 3.0 0.5 + - - -
278D MET* 3.8 10.1 - - - -
279D LYS* 2.8 51.6 + - + +
294D SER* 3.4 31.4 - - - +
295D ILE 4.4 0.7 - - - +
297D THR* 4.0 9.0 - - - +
298D ILE* 3.7 34.8 - - + -
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D SER* 6.1 2.2 - - - +
252D GLN* 4.2 24.5 - - + +
256D VAL* 3.9 16.3 - - + +
272D ILE* 3.0 13.8 + - + +
273D GLN* 3.6 13.7 - - - +
274D HIS 3.1 0.4 - - - -
275D MET* 1.3 75.1 - - - +
277D GLY* 1.3 59.0 + - - +
279D LYS* 4.8 9.6 + - - +
280D HIS* 5.1 1.9 + - - -
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Residues in contact with GLY 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D VAL* 3.8 3.4 - - - +
251D GLY* 3.7 19.0 - - - -
255D LYS 3.8 8.5 - - - -
256D VAL* 3.5 8.1 - - - -
257D VAL* 3.0 30.7 + - - +
274D HIS 2.9 10.0 + - - -
276D ALA* 1.3 81.8 - - - +
278D MET* 1.3 57.8 + - - +
280D HIS* 3.3 8.0 - - - -
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Residues in contact with MET 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D VAL* 3.9 3.4 - - + -
257D VAL* 4.0 5.4 - - + -
263D TYR* 3.8 45.3 - - + -
274D HIS* 3.6 34.5 - - + +
275D MET* 3.0 19.7 + - - -
277D GLY* 1.3 80.5 - - - +
279D LYS* 1.3 67.7 + - - +
280D HIS* 3.1 11.0 - - - -
281D VAL* 3.1 18.1 + - + +
284D ILE* 3.6 30.5 - - + +
295D ILE* 4.3 8.7 - - + -
298D ILE* 3.9 14.4 - - + -
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Residues in contact with LYS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D SER* 5.4 14.8 - - - +
275D MET* 2.8 43.6 + - + +
276D ALA* 4.8 6.3 - - - +
278D MET* 1.3 78.5 - - - +
280D HIS* 1.3 65.3 + - + +
281D VAL 3.4 1.7 + - - +
284D ILE* 3.9 9.7 - - - +
298D ILE* 4.0 34.6 - - + +
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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