Contacts of the helix formed by residues 285 - 296 (chain C) in PDB entry 3Q2K
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 LYS 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C LEU* 4.3 13.2 - - + -
281C PRO* 4.3 15.2 + - - +
282C ASP* 2.6 49.8 + - - +
284C ASP* 1.3 76.3 - - + +
286C ILE* 1.3 57.1 + - - +
287C ARG 3.6 1.3 - - - -
288C GLU* 3.7 25.7 + - - +
289C ALA* 2.9 28.7 + - + +
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Residues in contact with ILE 286 (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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140C LEU* 4.3 12.1 - - + -
271C ILE* 3.7 23.3 - - + -
274C TRP* 3.7 33.4 - - + -
282C ASP 4.2 5.8 - - - +
283C ASP 3.4 21.5 - - - +
284C ASP 3.4 2.6 - - - -
285C LYS* 1.3 75.7 - - - +
287C ARG* 1.3 64.3 + - - +
288C GLU 3.1 1.3 - - - -
289C ALA* 2.9 1.0 + - - -
290C ASN* 2.8 44.9 + - - +
287M ARG* 3.3 41.7 - - - +
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Residues in contact with ARG 287 (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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284C ASP 5.2 1.2 + - - -
286C ILE* 1.3 82.2 - - - +
288C GLU* 1.3 64.1 + - - +
290C ASN* 3.3 9.7 + - + +
291C TYR* 2.9 27.1 + - - +
271M ILE* 4.7 7.5 + - - -
272M ASP 3.9 22.0 + - - -
273M GLU* 4.3 3.2 + - - +
274M TRP* 4.0 32.1 + - - +
283M ASP 5.4 0.8 + - - -
286M ILE* 3.5 41.2 - - - +
287M ARG* 4.9 17.7 - - + +
290M ASN* 5.4 2.5 - - - +
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Residues in contact with GLU 288 (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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284C ASP 5.5 1.5 + - - +
285C LYS* 3.7 31.4 + - + +
286C ILE 3.1 0.2 - - - -
287C ARG* 1.3 81.3 - - - +
289C ALA* 1.3 63.0 + - - +
291C TYR* 4.0 5.2 - - - +
292C GLU* 3.1 29.2 + - - +
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Residues in contact with ALA 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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136C ALA* 3.8 26.2 - - + -
137C THR* 4.1 4.5 - - + +
140C LEU* 3.6 22.7 - - + -
285C LYS* 2.9 19.7 + - + +
286C ILE 2.9 4.4 + - - +
288C GLU* 1.3 75.8 - - + +
290C ASN* 1.3 62.5 + - - +
292C GLU* 3.3 2.7 + - - +
293C THR* 2.8 36.3 + - - -
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Residues in contact with ASN 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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137C THR* 3.4 12.2 - - - +
269C ASN 3.5 10.9 - - - +
270C ARG* 3.9 11.0 - - + +
271C ILE* 3.0 50.7 + - - +
286C ILE* 2.8 26.1 + - - +
287C ARG* 3.5 12.6 - - + +
289C ALA* 1.3 76.2 - - - +
291C TYR* 1.3 64.1 + - - +
294C THR* 2.9 30.7 + - - +
287M ARG* 4.6 5.0 - - - +
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Residues in contact with TYR 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 ARG* 2.9 18.8 + - + +
288C GLU* 4.1 5.4 - - - +
290C ASN* 1.3 77.6 - - - +
292C GLU* 1.3 63.8 + - + +
294C THR* 3.8 5.8 - - + -
295C SER* 3.0 45.6 + - - -
272M ASP 5.8 3.8 - - - -
273M GLU* 5.5 9.4 - - - -
270N ARG* 4.7 13.2 + - - -
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Residues in contact with GLU 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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134C ARG 5.5 1.4 - - - +
136C ALA* 3.8 24.1 + - + +
288C GLU* 3.1 23.3 + - + +
289C ALA* 3.7 3.8 - - - +
291C TYR* 1.3 82.5 - - + +
293C THR* 1.3 67.8 + - - +
295C SER* 3.1 17.2 + - - +
296C VAL* 3.5 16.6 + - + +
303C LEU* 5.2 11.1 - - - +
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Residues in contact with THR 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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135C ASN* 3.2 45.3 - - + +
136C ALA 3.2 7.4 + - - +
137C THR* 3.0 33.2 + - - +
269C ASN* 4.0 16.4 - - + +
289C ALA 2.8 20.9 + - - -
292C GLU* 1.3 73.9 - - - +
294C THR* 1.3 63.3 + - - +
296C VAL* 3.2 18.9 + - + +
297C TYR* 3.3 10.6 + - - +
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Residues in contact with THR 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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269C ASN* 3.1 34.1 + - - +
270C ARG* 5.0 1.9 - - - +
290C ASN* 2.9 19.0 + - - +
291C TYR* 3.8 6.1 - - + -
293C THR* 1.3 78.5 - - - +
295C SER* 1.3 57.3 + - - +
297C TYR* 3.0 29.3 + - + +
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Residues in contact with SER 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 TYR* 3.0 40.9 + - - -
292C GLU* 3.1 10.0 + - - +
294C THR* 1.3 77.4 - - - +
296C VAL* 1.3 66.5 + - - +
297C TYR 3.5 0.8 - - - +
299C PHE* 4.9 6.4 - - - -
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Residues in contact with VAL 296 (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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135C ASN* 5.2 9.9 - - - +
292C GLU* 3.5 12.7 + - + +
293C THR* 3.2 15.0 + - - +
294C THR 3.2 0.4 - - - -
295C SER* 1.3 86.1 - - - +
297C TYR* 1.3 57.5 + - - +
298C GLY 3.1 0.7 + - - -
299C PHE* 2.7 51.3 + - + +
300C GLY* 3.5 6.9 + - - -
302C PRO* 6.0 2.7 - - + -
303C LEU* 4.4 25.6 - - + -
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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