Contacts of the helix formed by residues 288 - 295 (chain C) in PDB entry 5NTI
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 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C ARG* 3.5 29.9 + - - +
285C CYS* 4.1 13.6 + - - +
286C GLN 4.2 4.7 + - - +
287C LEU* 1.3 75.8 + - - +
289C LEU* 1.3 67.1 + - - +
290C GLU* 4.3 6.7 - - + +
291C ASP* 3.4 30.8 + - - +
292C LEU* 3.1 25.6 + - - +
367C ARG* 4.1 17.9 - - - +
310D ARG* 4.0 26.6 - - - +
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Residues in contact with LEU 289 (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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288C ARG* 1.3 76.1 - - - +
290C GLU* 1.3 66.9 + - - +
292C LEU* 3.4 9.6 + - + +
293C LEU* 3.0 45.7 + - + +
367C ARG* 3.5 43.1 - - + +
414C GLU* 3.4 31.9 - - + +
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Residues in contact with GLU 290 (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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288C ARG* 3.3 4.6 - - + +
289C LEU* 1.3 87.9 - - - +
291C ASP* 1.3 62.3 + - - +
293C LEU* 3.3 11.5 + - - +
294C ARG* 3.0 35.3 + - + +
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Residues in contact with ASP 291 (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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287C LEU* 6.3 1.1 - - + -
288C ARG* 3.4 34.4 + - - +
289C LEU 3.3 0.4 - - - -
290C GLU* 1.3 77.9 - - - +
292C LEU* 1.3 60.7 + - + +
294C ARG* 3.2 3.8 + - - -
295C GLN* 2.9 49.2 + - + +
377C PHE* 5.8 5.8 - - + -
303D GLU* 5.4 9.2 - - - +
307D GLY* 5.9 1.4 - - - -
310D ARG* 4.4 16.8 + - - -
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Residues in contact with LEU 292 (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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287C LEU* 3.8 29.6 - - + -
288C ARG 3.1 20.7 + - - +
289C LEU* 3.7 13.5 - - + +
290C GLU 3.4 0.2 - - - -
291C ASP* 1.3 76.0 - - + +
293C LEU* 1.3 62.9 + - + +
295C GLN* 5.0 0.9 - - - -
296C ARG* 3.2 12.3 + - - +
367C ARG* 3.5 37.2 - - + +
368C ALA* 3.9 8.3 - - - -
377C PHE* 3.7 38.1 - - + -
382C TYR* 2.8 33.5 + - - +
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Residues in contact with LEU 293 (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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289C LEU* 3.0 35.4 + - + +
290C GLU* 3.4 13.5 - - - +
291C ASP 3.2 0.2 - - - -
292C LEU* 1.3 78.7 - - + +
294C ARG* 1.3 63.1 + - + +
296C ARG* 3.4 37.1 - - - +
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Residues in contact with ARG 294 (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 GLU* 3.0 20.8 + - + +
291C ASP* 3.2 5.6 + - - +
293C LEU* 1.3 78.9 - - + +
295C GLN* 1.3 64.5 + - + +
296C ARG 3.3 3.5 + - - -
297C SER* 4.7 6.4 + - - -
298C ASN 5.4 0.2 + - - -
303D GLU* 5.3 12.3 + - - +
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Residues in contact with GLN 295 (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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291C ASP* 2.9 34.9 + - + +
293C LEU 3.3 0.2 - - - -
294C ARG* 1.3 81.1 - - + +
296C ARG* 1.3 57.9 + - - +
297C SER 3.2 3.1 - - - -
298C ASN* 2.9 49.6 + - + +
377C PHE* 3.6 31.1 - - + -
380C GLY 4.7 1.8 - - - -
382C TYR* 3.1 16.7 - - + -
301D SER* 4.9 2.6 + - - -
303D GLU* 5.7 4.6 - - - +
304D GLU* 3.5 34.5 + - - +
381D LYS* 5.3 0.3 + - - -
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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