Contacts of the helix formed by residues 284 - 289 (chain x) 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 TYR 284 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266H THR* 3.3 17.5 + - - -
268H LYS* 5.7 11.4 + - + +
282x VAL* 3.3 9.1 - - - +
283x LYS* 1.3 110.7 - - + +
285x LEU* 1.3 69.9 + - - +
286x PHE* 2.6 10.7 + - + +
287x THR* 2.9 20.1 + - - +
346x VAL* 5.3 0.4 - - - -
347x LYS* 3.2 47.6 + - + -
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Residues in contact with LEU 285 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276x CYS* 3.4 33.4 - - + -
282x VAL* 4.8 1.3 - - - -
283x LYS 4.3 0.4 - - - -
284x TYR* 1.3 68.3 - - - +
286x PHE* 1.3 68.7 + - - +
288x GLY* 2.9 13.4 + - - +
289x LEU* 3.4 19.8 + - + -
325x ILE* 4.0 15.5 - - + -
327x MET* 4.3 7.9 - - - -
346x VAL* 4.4 8.8 - - - +
347x LYS 2.9 21.9 + - - +
348x PHE* 3.7 13.2 - - + -
349x PRO* 3.6 27.6 - - + -
352x LEU* 4.6 4.7 - - + -
477x LEU* 3.9 8.7 - - + -
479x TYR* 3.8 15.5 - - + +
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Residues in contact with PHE 286 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284x TYR* 2.6 11.0 + - + +
285x LEU* 1.3 74.7 - - - +
287x THR* 1.3 60.7 + - - +
289x LEU* 2.6 47.7 + - + +
290x LYS* 3.6 23.9 + - + -
349x PRO* 5.8 1.6 - - - +
352x LEU* 6.5 1.6 - - + -
353x ASP 4.3 17.9 - - - -
354x MET* 5.8 1.8 - - - -
356x GLU* 4.5 22.7 - - + -
357x LEU* 3.2 35.9 - - + -
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Residues in contact with THR 287 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281x GLU* 5.1 4.7 - - + +
282x VAL* 3.2 23.6 - - + +
283x LYS 5.1 0.2 + - - -
284x TYR* 2.9 17.3 + - - +
286x PHE* 1.3 74.5 - - - +
288x GLY* 1.3 54.6 + - - +
290x LYS* 2.6 52.6 + - - +
291x LEU* 2.8 30.9 - - + +
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Residues in contact with GLY 288 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275x SER 4.2 2.1 - - - +
276x CYS* 4.0 6.5 - - - -
277x PHE* 3.1 51.4 + - - +
282x VAL* 2.8 22.7 - - - +
285x LEU 2.9 7.3 + - - -
287x THR* 1.3 72.7 - - - +
289x LEU* 1.3 61.0 + - - +
290x LYS 3.2 0.9 + - - -
291x LEU* 3.9 7.8 + - - +
292x ARG* 4.5 1.0 + - - +
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Residues in contact with LEU 289 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274x LEU* 3.7 30.1 - - + -
275x SER 4.1 17.5 - - - +
276x CYS* 4.5 0.9 - - + -
285x LEU* 3.5 31.4 - - + +
286x PHE* 2.6 34.8 + - + +
288x GLY* 1.3 73.6 - - - +
290x LYS* 1.3 56.4 + - - -
292x ARG* 4.5 6.1 + - - +
293x LEU* 3.3 21.4 - - - +
325x ILE* 4.2 24.2 - - + -
352x LEU* 5.7 3.8 - - + -
354x MET* 4.6 17.3 - - + -
357x LEU* 4.2 13.6 - - + +
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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