Contacts of the helix formed by residues 359 - 370 (chain R) in PDB entry 5FYW
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 359 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360R GLU* 1.3 61.4 + - - +
361R GLU* 4.3 4.5 - - + +
362R GLU* 3.5 22.8 + - + +
363R ARG 3.1 21.0 + - - -
123X HIS* 3.4 17.0 - - - +
124X ASP* 3.9 28.1 - - - +
127X LYS* 5.4 2.3 - - - +
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Residues in contact with GLU 360 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301R ASP* 6.1 0.2 - - - -
304R PHE* 5.6 8.6 - - + +
305R LYS* 5.9 5.6 - - - +
308R ASP* 6.4 2.0 - - + -
359R LYS* 1.3 71.7 - - - +
361R GLU* 1.3 59.7 + - - +
363R ARG* 3.2 7.3 + - - +
364R LYS* 2.9 28.6 + - - +
123X HIS* 4.5 15.5 - - + +
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Residues in contact with GLU 361 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359R LYS* 3.4 4.5 - - + +
360R GLU* 1.3 77.6 - - - +
362R GLU* 1.3 57.6 + - - +
364R LYS* 3.2 7.0 + - - +
365R ALA* 2.9 29.3 + - - +
152X SER 4.9 2.6 - - - +
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Residues in contact with GLU 362 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359R LYS* 3.5 23.6 + - + +
360R GLU 3.3 0.6 - - - -
361R GLU* 1.3 77.4 - - - +
363R ARG* 1.3 58.9 + - - +
365R ALA* 3.4 4.8 + - - +
366R THR* 2.9 28.8 + - - -
127X LYS* 4.4 14.3 - - + +
151X LEU* 4.2 3.3 - - + +
153X MET* 4.0 28.0 - - + +
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Residues in contact with ARG 363 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301R ASP* 6.0 0.4 - - - -
304R PHE* 6.1 4.7 - - + -
359R LYS 3.1 17.7 + - - +
360R GLU* 3.2 7.4 + - - +
362R GLU* 1.3 75.4 - - - +
364R LYS* 1.3 58.2 + - - +
366R THR* 3.3 7.9 + - - -
367R LEU* 2.9 28.4 + - - +
123X HIS* 3.9 15.5 - - + +
126X SER* 4.1 22.1 - - - -
127X LYS* 4.4 8.6 - - + +
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Residues in contact with LYS 364 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297R LYS 5.1 0.7 - - - +
301R ASP* 3.6 32.7 - - + +
360R GLU 2.9 15.6 + - - +
361R GLU* 3.2 8.5 + - - +
363R ARG* 1.3 77.5 - - - +
365R ALA* 1.3 57.0 + - - +
367R LEU* 3.2 4.8 + - - +
368R GLY* 2.9 24.1 + - - -
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Residues in contact with ALA 365 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361R GLU 2.9 16.5 + - - +
362R GLU 3.9 1.1 - - - +
364R LYS* 1.3 76.1 - - - +
366R THR* 1.3 57.7 + - - +
368R GLY* 3.2 2.4 + - - +
369R GLU* 2.9 28.4 + - - +
150X TYR 4.7 1.0 - - - +
151X LEU* 2.8 28.4 - - - +
152X SER* 3.6 24.0 - - - +
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Residues in contact with THR 366 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362R GLU 2.9 17.8 + - - -
363R ARG 3.5 5.6 - - - -
365R ALA* 1.3 77.4 - - - +
367R LEU* 1.3 56.8 + - - +
369R GLU* 3.3 7.1 + - - +
370R LEU* 3.0 23.4 + - - +
126X SER 4.9 0.4 - - - -
127X LYS* 4.1 20.2 - - - -
130X TRP* 3.4 33.5 - - - +
131X ALA* 4.9 0.9 - - - -
151X LEU* 4.2 12.5 + - - -
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Residues in contact with LEU 367 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296R LYS 5.0 1.3 - - - +
297R LYS* 3.2 41.6 - - - +
300R LEU* 5.2 7.4 - - + -
301R ASP* 5.2 0.9 - - + +
363R ARG 2.9 13.8 + - - +
364R LYS* 3.2 10.9 + - - +
366R THR* 1.3 75.1 - - - +
368R GLY* 1.3 62.2 + - - +
370R LEU* 3.3 21.3 - - - +
130X TRP* 4.5 2.6 - - - +
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Residues in contact with GLY 368 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297R LYS* 3.9 11.7 - - - +
364R LYS 2.9 14.8 + - - -
365R ALA* 3.2 4.2 + - - -
367R LEU* 1.3 79.4 - - - +
369R GLU* 1.3 60.7 + - - +
370R LEU 4.4 2.4 - - - +
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Residues in contact with GLU 369 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365R ALA 2.9 16.7 + - - +
366R THR* 3.6 8.3 - - - +
368R GLY* 1.3 78.8 - - - +
370R LEU* 1.3 60.3 + - + +
130X TRP 6.0 1.6 - - - +
150X TYR* 4.2 20.2 - - + +
151X LEU* 5.0 2.5 - - + -
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Residues in contact with LEU 370 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297R LYS* 5.6 1.1 - - - -
366R THR 3.0 15.0 + - - +
367R LEU* 3.3 17.7 + - - +
368R GLY 4.4 2.7 - - - +
369R GLU* 1.3 80.1 - - - +
130X TRP* 4.4 21.1 - - + +
133X GLU* 6.2 2.9 - - + -
134X TYR* 6.0 2.9 - - + +
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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