Contacts of the helix formed by residues 298 - 306 (chain P) in PDB entry 6LTJ
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 ASP 298 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P LEU* 1.3 74.2 - - - +
299P PRO* 1.3 68.3 - - - +
300P ARG* 2.6 45.4 + - - +
301P LEU* 3.8 15.0 - - + +
302P ALA* 2.7 33.6 + - - +
346P ILE* 5.3 4.6 - - - +
364P LEU* 3.5 41.2 + - + +
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Residues in contact with PRO 299 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P LEU 3.4 4.7 - - - +
298P ASP* 1.3 93.6 - - - +
300P ARG* 1.3 59.6 + - + +
302P ALA* 4.3 0.2 - - + -
303P ARG* 2.9 61.7 + - + +
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Residues in contact with ARG 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939O LEU* 5.3 2.2 - - - +
298P ASP* 2.6 22.2 + - - +
299P PRO* 1.3 73.4 - - + +
301P LEU* 1.3 65.6 + - - +
303P ARG* 3.4 4.8 + - - +
304P LEU* 2.9 24.9 + - - +
345P GLN* 2.2 65.2 + - - +
346P ILE* 3.2 32.7 - - + +
348P GLU* 5.8 0.2 + - - -
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Residues in contact with LEU 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P LEU* 3.5 33.4 - - + -
298P ASP* 3.3 17.0 + - + +
300P ARG* 1.3 76.8 - - - +
302P ALA* 1.3 64.6 + - - +
304P LEU* 3.2 8.3 + - + +
305P LEU* 2.9 47.0 + - + +
315P ILE* 5.0 2.0 - - + -
319P LEU* 5.4 4.7 - - + -
343P LEU* 5.3 4.9 - - + -
346P ILE* 3.4 27.0 - - + +
347P PHE* 4.8 9.0 - - + -
361P LEU* 3.5 27.6 - - + -
364P LEU* 4.5 10.8 - - + -
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Residues in contact with ALA 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P LEU* 3.7 22.8 - - + +
298P ASP 2.7 21.9 + - - +
299P PRO* 4.3 0.2 - - + -
301P LEU* 1.3 71.8 - - - +
303P ARG* 1.3 79.1 + - - +
305P LEU 2.9 2.3 + - - -
306P GLY* 2.8 29.5 + - - -
307P ILE 3.1 23.8 - - - +
308P HIS* 4.4 6.7 - - - +
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Residues in contact with ARG 303 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935O HIS* 3.2 36.3 - - + +
938O GLN* 4.8 4.9 + - - +
939O LEU* 4.5 20.8 - - + +
297P LEU 5.6 0.2 + - - -
299P PRO* 2.9 57.3 + - + +
300P ARG* 4.0 4.0 - - - +
302P ALA* 1.3 88.2 - - - +
304P LEU* 1.3 60.1 + - - +
305P LEU 3.6 0.2 + - - -
307P ILE 5.7 0.2 - - - -
308P HIS* 3.8 30.5 + - - -
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Residues in contact with LEU 304 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932O GLN* 4.2 15.2 - - - +
935O HIS* 4.9 3.1 - - - +
936O MET* 3.9 14.0 + - + +
939O LEU* 4.6 14.3 - - + +
300P ARG 2.9 18.8 + - - +
301P LEU* 3.5 9.6 - - + +
303P ARG* 1.3 78.4 - - - +
305P LEU* 1.3 65.5 + - + +
319P LEU* 6.0 0.9 - - + -
322P TYR* 3.7 46.9 - - + +
342P TYR* 3.5 40.8 - - + +
343P LEU* 4.9 9.2 - - + -
346P ILE* 4.1 9.9 - - + -
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Residues in contact with LEU 305 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928O LEU* 4.1 4.7 - - - +
932O GLN* 3.0 28.7 + - - +
297P LEU* 4.5 9.2 - - + -
301P LEU* 2.9 39.8 + - + +
302P ALA 2.9 2.7 + - - +
304P LEU* 1.3 84.1 - - + +
306P GLY* 1.3 57.4 + - - +
307P ILE* 3.2 10.8 + - + +
315P ILE* 3.9 11.0 - - + +
318P ALA* 3.4 34.2 - - + +
319P LEU* 3.6 35.4 - - + +
322P TYR* 3.7 19.5 - - + -
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Residues in contact with GLY 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928O LEU* 5.6 3.1 - - - -
931O ARG* 3.5 30.0 + - - -
932O GLN* 4.9 2.2 - - - -
935O HIS* 3.6 28.2 + - - -
302P ALA 2.8 8.5 + - - -
303P ARG* 4.0 2.0 + - - -
304P LEU 3.6 1.6 - - - -
305P LEU* 1.3 76.5 - - - +
307P ILE* 1.3 64.9 + - - -
308P HIS* 3.5 2.4 + - - +
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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