Contacts of the helix formed by residues 297 - 304 (chain C) in PDB entry 1AIH
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 ILE 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C MET* 4.0 24.1 - - - +
295C GLY 3.6 4.8 + - - -
296C ASN* 1.3 69.4 - - - +
298C LEU* 1.3 69.0 + - + +
300C LEU* 3.5 2.0 + - + -
301C LYS* 3.1 19.4 + - - +
309C ILE* 4.4 12.7 - - + +
312C THR* 3.5 45.2 - - + +
313C MET* 4.7 1.1 - - - +
316C ALA* 4.3 19.5 - - + +
296D ASN* 3.5 27.0 - - - +
297D ILE* 3.5 28.5 - - + +
298D LEU* 4.5 9.9 - - + -
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ASN* 2.9 24.7 - - - +
297C ILE* 1.3 82.1 - - + +
299C VAL* 1.3 65.7 + - + +
301C LYS* 3.1 24.5 - - + +
302C GLU* 3.4 6.9 + - - +
309C ILE* 5.2 5.4 - - + -
291D MET* 3.5 34.3 - - + -
297D ILE* 3.5 30.5 - - + +
313D MET* 4.9 5.2 - - + -
316D ALA* 3.7 34.8 - - + +
319D ALA* 4.2 6.5 - - + -
321D SER* 4.7 9.1 + - - +
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C PHE* 4.2 4.5 - - + -
296C ASN* 3.0 26.8 + - + +
298C LEU* 1.3 72.3 - - - +
300C LEU* 1.3 67.3 + - - +
301C LYS 3.0 1.6 - - - -
302C GLU* 3.0 17.2 + - - +
303C ILE* 3.0 31.2 + - + +
319D ALA* 6.3 0.9 - - + -
320D PRO 5.3 1.3 - - - +
321D SER* 4.0 28.5 - - - +
322D HIS 3.7 22.0 - - - +
323D LEU* 3.8 11.4 - - + -
325D SER* 3.7 14.8 - - - +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C PHE* 4.2 10.3 - - + -
287C ALA* 3.8 18.4 - - + +
290C PHE* 3.5 35.2 - - + -
291C MET* 3.6 36.1 - - + -
296C ASN 3.1 6.2 + - - +
297C ILE 3.7 7.6 - - - +
299C VAL* 1.3 75.7 - - - +
301C LYS* 1.3 63.1 + - - +
303C ILE* 3.2 5.6 + - + +
304C LEU* 2.9 56.4 + - + +
312C THR* 3.9 15.5 - - + -
315C TYR* 4.3 11.4 - - + -
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Residues in contact with LYS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ILE 3.1 11.8 + - - +
298C LEU* 3.1 16.8 - - + +
300C LEU* 1.3 77.4 - - - +
302C GLU* 1.3 65.0 + - - +
304C LEU* 3.4 0.7 + - - -
305C GLY 3.0 18.7 + - - -
306C HIS* 2.7 39.5 + - - +
307C SER* 3.1 24.5 + - - +
308C THR* 3.5 10.5 - - - +
309C ILE* 3.8 21.7 - - + +
312C THR* 3.4 27.3 - - + +
313D MET* 5.1 9.2 - - + -
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Residues in contact with GLU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ARG* 3.7 14.0 - - - +
298C LEU 3.4 5.3 + - - +
299C VAL* 3.0 10.3 + - - +
301C LYS* 1.3 81.5 - - - +
303C ILE* 1.3 62.5 + - - +
305C GLY* 3.2 12.5 + - - -
306C HIS 5.7 0.2 - - - -
321D SER* 5.8 5.6 - - - +
323D LEU* 4.4 16.2 - - + -
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Residues in contact with ILE 303 (chain C).
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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204C THR 3.6 23.6 - - - +
205C GLY 5.5 0.2 - - - +
235C ARG* 2.6 32.5 + - - +
236C THR 5.8 0.9 - - - -
237C VAL* 4.0 25.6 - - + +
286C PHE* 3.8 15.5 - - + -
290C PHE* 3.9 21.8 - - + -
299C VAL* 3.0 33.9 + - + +
300C LEU* 3.2 8.7 + - - +
302C GLU* 1.3 76.7 - - - +
304C LEU* 1.3 54.0 + - + +
323D LEU* 3.7 19.1 - - + +
326D ALA* 4.0 19.3 - - + -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLY* 3.8 20.9 - - - +
207C ARG* 3.9 4.0 + - - -
235C ARG* 3.5 13.2 + - - +
283C ARG* 2.9 40.9 + - + +
286C PHE* 4.0 26.2 - - + -
287C ALA* 4.0 5.2 - - + -
300C LEU* 2.9 41.5 + - + +
301C LYS 4.2 0.2 - - - +
303C ILE* 1.3 76.9 - - + +
305C GLY* 1.3 62.4 + - - +
306C HIS* 3.5 30.7 - - + +
312C THR* 5.0 0.2 - - + -
315C TYR* 3.9 17.3 - - + +
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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