Contacts of the helix formed by residues 296 - 306 (chain T) in PDB entry 5GJQ
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 PRO 296 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284T PHE* 4.3 9.7 - - + -
288T THR* 5.4 4.9 - - - +
295T THR* 1.3 73.8 - - - +
297T LYS* 1.3 64.8 - - + +
299T MET* 2.1 43.2 - - + +
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Residues in contact with LYS 297 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295T THR* 3.4 14.6 + - - +
296T PRO* 1.3 84.6 - - + +
298T LYS* 1.3 72.5 + - + +
299T MET* 2.9 4.7 + - - -
300T THR* 3.2 9.0 + - - +
301T ASP* 3.0 31.2 + - - -
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Residues in contact with LYS 298 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293T PHE* 3.6 26.5 - - + -
295T THR* 3.4 26.5 - - - +
297T LYS* 1.3 81.5 - - + +
299T MET* 1.3 64.2 + - - +
301T ASP* 3.2 12.0 - - - +
302T TYR* 2.9 21.0 + - - +
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Residues in contact with MET 299 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284T PHE* 3.6 28.0 - - + +
287T ALA* 5.0 13.7 - - + -
288T THR* 5.3 2.2 - - - +
291T LEU* 6.1 0.4 - - - -
293T PHE* 3.5 22.2 - - + -
295T THR 5.0 0.4 - - - +
296T PRO* 2.1 34.6 + - + +
297T LYS* 4.0 1.6 - - - +
298T LYS* 1.3 76.2 - - - +
300T THR* 1.3 72.2 + - - +
302T TYR* 2.6 28.1 + - - +
303T ALA* 2.8 12.6 + - - +
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Residues in contact with THR 300 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297T LYS* 3.2 10.8 + - - +
299T MET* 1.3 84.1 - - - +
301T ASP* 1.3 67.6 + - - +
303T ALA* 3.8 10.1 - - - -
304T LYS* 2.9 35.0 + - - +
310T LEU* 5.0 14.1 - - - -
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Residues in contact with ASP 301 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297T LYS* 3.0 33.8 + - - -
298T LYS* 3.2 15.0 - - - +
300T THR* 1.3 77.7 + - - +
302T TYR* 1.3 63.7 + - - +
304T LYS* 3.7 3.8 - - - +
305T LYS* 3.0 31.0 + - + +
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Residues in contact with TYR 302 (chain T).
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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268T ARG* 6.1 4.5 - - + -
291T LEU* 4.6 13.0 - - + -
293T PHE* 4.0 20.9 - + + -
298T LYS 2.9 12.0 + - - +
299T MET 2.6 16.6 + - - +
301T ASP* 1.3 72.6 - - - +
303T ALA* 1.3 48.3 + - - +
305T LYS* 3.1 11.1 + - + +
306T ARG* 2.6 52.4 + - + +
308T TRP* 6.1 2.5 - + - -
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Residues in contact with ALA 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299T MET 2.8 16.1 + - - +
300T THR* 4.1 9.4 - - - -
302T TYR* 1.3 70.3 - - - +
304T LYS* 1.3 54.5 + - - +
306T ARG* 2.9 9.5 + - - -
307T GLY 2.6 30.3 + - - -
308T TRP* 2.6 46.0 + - + -
310T LEU* 4.1 15.5 - - + -
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Residues in contact with LYS 304 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300T THR* 2.9 30.1 + - - +
301T ASP* 3.7 4.0 - - - +
303T ALA* 1.3 71.2 - - - +
305T LYS* 1.3 60.7 + - + +
307T GLY* 2.6 25.9 + - - +
308T TRP 4.5 6.5 + - - +
310T LEU* 6.2 1.3 - - + -
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Residues in contact with LYS 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301T ASP* 3.0 28.2 + - + +
302T TYR* 3.2 14.1 - - + +
304T LYS* 1.3 75.9 - - + +
306T ARG* 1.3 61.5 + - + +
307T GLY 3.3 0.2 - - - -
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Residues in contact with ARG 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269T ASP* 4.3 19.6 - - - +
272T ALA* 3.8 17.4 - - + +
273T GLY* 3.9 14.1 - - - +
276T GLU* 2.4 39.5 + - - +
302T TYR* 2.6 35.4 + - + +
303T ALA* 2.9 9.1 + - - +
305T LYS* 1.3 76.4 - - - +
307T GLY* 1.3 57.6 + - - +
308T TRP* 2.9 43.0 + - + +
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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