Contacts of the helix formed by residues 285 - 296 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I LEU* 3.9 17.7 - - + -
281I PRO* 3.5 24.7 - - - -
282I ASP* 2.8 29.4 + - + +
284I ASP* 1.3 92.1 + - - +
286I ILE* 1.3 67.6 + - - +
287I ARG 2.9 4.0 + - - -
288I GLU* 3.2 27.1 + - + +
289I ALA* 2.9 22.4 + - + +
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Residues in contact with ILE 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I LEU* 4.1 9.6 - - + -
271I ILE* 3.7 33.9 - - + +
274I TRP* 3.7 46.2 - - + -
282I ASP 4.0 2.4 + - - +
283I ASP 3.7 21.5 + - - +
284I ASP 3.6 1.6 - - - -
285I LYS* 1.3 78.6 - - - +
287I ARG* 1.3 54.8 + - + +
289I ALA* 3.3 1.6 - - - +
290I ASN* 2.8 50.3 + - - +
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Residues in contact with ARG 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284I ASP 5.0 10.6 + - - +
285I LYS 3.0 1.0 - - - -
286I ILE* 1.3 82.2 - - + +
288I GLU* 1.3 59.6 + - + +
290I ASN* 3.4 9.0 + - - +
291I TYR* 2.9 27.7 + - - +
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Residues in contact with GLU 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284I ASP 5.0 3.0 - - - +
285I LYS* 3.4 38.9 + - - +
287I ARG* 1.3 77.7 - - + +
289I ALA* 1.3 66.1 + - - +
291I TYR* 3.1 8.8 + - + +
292I GLU* 2.8 39.8 + - - +
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Residues in contact with ALA 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ALA* 3.7 27.1 - - + +
137I THR* 4.2 4.0 - - - +
140I LEU* 3.0 37.9 - - + -
285I LYS* 2.9 8.3 + - + +
286I ILE 3.3 6.7 - - - +
288I GLU* 1.3 78.1 + - - +
290I ASN* 1.3 57.5 + - - +
292I GLU* 5.5 0.2 - - - -
293I THR* 2.9 35.4 + - - -
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Residues in contact with ASN 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I THR* 3.6 3.9 - - - +
269I ASN 3.4 11.1 - - - +
270I ARG* 3.9 11.7 - - + +
271I ILE* 2.9 53.5 + - - +
286I ILE* 2.8 33.9 + - - +
287I ARG* 3.5 7.9 - - - +
289I ALA* 1.3 70.6 - - - +
291I TYR* 1.3 68.4 + - - +
294I THR* 2.9 29.0 + - - +
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Residues in contact with TYR 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I ARG 2.9 20.5 + - - +
288I GLU* 3.1 9.2 + - + +
290I ASN* 1.3 75.0 - - - +
292I GLU* 1.3 56.5 + - + +
294I THR* 3.3 6.4 + - - -
295I SER* 2.8 57.9 + - - -
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Residues in contact with GLU 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ALA* 3.8 18.6 - - + +
288I GLU* 2.8 28.4 + - + +
289I ALA* 3.8 2.7 - - - +
291I TYR* 1.3 80.7 - - + +
293I THR* 1.3 64.8 + - - +
295I SER* 3.0 18.7 + - - +
296I VAL* 3.1 25.8 + - + +
303I LEU* 6.3 2.2 - - + -
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Residues in contact with THR 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I ASN* 3.7 25.8 - - - +
136I ALA* 3.4 10.5 + - - +
137I THR* 3.1 23.5 + - - +
269I ASN* 3.1 38.6 - - + -
289I ALA 2.9 18.3 + - - -
292I GLU* 1.3 76.5 - - - +
294I THR* 1.3 63.2 + - - +
296I VAL* 3.4 11.0 + - + +
297I TYR* 3.3 19.2 + - - +
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Residues in contact with THR 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269I ASN* 3.4 28.2 + - - +
270I ARG* 5.1 1.4 - - - +
290I ASN* 2.9 18.6 + - - +
291I TYR* 3.5 7.0 - - - -
293I THR* 1.3 77.0 - - - +
295I SER* 1.3 57.2 + - - +
297I TYR* 2.9 32.7 + - + +
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Residues in contact with SER 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I TYR* 2.8 45.9 + - - -
292I GLU* 3.0 18.4 + - - +
294I THR* 1.3 71.5 - - - +
296I VAL* 1.3 63.0 + - - +
297I TYR 5.3 0.2 - - - +
299I PHE* 6.0 1.2 - - - -
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Residues in contact with VAL 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I ASN* 5.9 4.3 - - - +
292I GLU* 3.1 22.3 + - + +
293I THR* 3.6 12.1 - - + +
295I SER* 1.3 82.0 - - - +
297I TYR* 1.3 66.4 + - - +
298I GLY 3.4 0.2 + - - -
299I PHE* 2.9 38.6 + - - +
300I GLY* 4.0 3.2 + - - -
303I LEU* 4.2 26.7 - - + -
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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