Contacts of the helix formed by residues 275 - 289 (chain D) in PDB entry 5FHK
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 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D MET* 3.6 37.0 - - + -
139D ASP* 4.9 6.1 - - - +
271D LYS* 5.2 4.9 - - + -
273D HIS 3.7 3.6 - - - +
274D LEU* 1.3 94.9 - - + +
276D GLU* 1.3 67.1 + - - +
277D LYS* 3.3 11.7 - - - -
278D VAL* 3.1 32.6 + - + -
279D ARG* 3.2 8.8 + - - +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D MET* 2.5 44.6 - - + +
88D GLY* 3.0 27.2 - - - +
89D ALA* 4.0 2.7 - - - +
274D LEU 3.5 1.6 + - - -
275D PRO* 1.3 71.0 - - - +
277D LYS* 1.3 57.7 + - - +
279D ARG* 3.1 30.8 + - - +
280D LEU* 2.9 46.7 + - + +
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D MET* 3.8 24.3 - - + +
88D GLY 3.5 7.3 + - - +
90D SER 3.0 26.0 - - - +
91D GLY* 3.9 9.0 - - - -
92D LYS* 2.8 39.6 + - - +
93D ILE* 3.3 21.4 - - + +
120D ILE* 3.8 25.4 - - + +
139D ASP* 5.6 1.1 - - - -
275D PRO* 4.2 14.4 - - + -
276D GLU* 1.3 74.2 - - - +
278D VAL* 1.3 68.9 + - + +
280D LEU* 3.6 5.4 + - - +
281D PHE* 3.1 16.1 + - - +
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Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 4.2 11.0 - - + -
139D ASP* 3.9 34.3 - - + +
140D VAL* 4.0 19.3 - - + -
274D LEU* 4.5 11.0 - - + -
275D PRO* 3.1 32.4 + - + +
277D LYS* 1.3 82.7 - - + +
279D ARG* 1.3 60.9 + - - +
281D PHE* 3.1 3.6 + - + +
282D ILE* 2.9 46.8 + - + +
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Residues in contact with ARG 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D MET* 5.4 1.6 - - - +
273D HIS* 5.8 2.6 - - - +
274D LEU* 3.3 41.1 + - + +
275D PRO 3.2 6.8 + - - +
276D GLU* 3.1 41.6 + - - +
278D VAL* 1.3 77.4 - - - +
280D LEU* 1.3 65.0 + - + +
282D ILE* 3.3 9.2 + - + +
283D ASP* 3.0 40.0 + - - +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ALA* 3.5 37.9 - - + -
113D PHE* 3.9 3.2 - - + -
117D TYR* 4.0 37.8 + - + +
120D ILE* 4.4 8.5 - - + -
276D GLU* 2.9 34.7 + - + +
277D LYS 3.7 4.5 - - - +
279D ARG* 1.3 76.8 - - + +
281D PHE* 1.3 56.8 + - - +
283D ASP* 3.5 6.7 + - + +
284D TYR* 3.0 29.3 + - - +
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Residues in contact with PHE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 3.9 14.1 - - + -
95D ILE* 4.2 12.8 - - + -
109D MET* 4.4 1.3 - - - -
110D LEU* 3.6 29.6 - - + -
113D PHE* 3.4 43.5 - + + -
122D ILE* 4.6 3.1 - - + -
140D VAL* 3.7 33.9 - - + -
142D PHE* 3.8 33.0 - + - -
266D MET* 4.9 0.7 - - - -
277D LYS 3.1 13.3 + - - +
278D VAL 3.1 8.3 + - - +
280D LEU* 1.3 74.6 - - - +
282D ILE* 1.3 67.5 + - - +
284D TYR* 3.1 3.5 + - - +
285D VAL* 3.0 35.6 + - + +
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Residues in contact with ILE 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.6 7.9 - - + -
266D MET* 4.5 14.1 - - + +
268D TYR* 3.5 53.2 - - + +
274D LEU* 3.6 21.8 - - + -
278D VAL* 2.9 36.7 + - + +
279D ARG* 3.9 5.4 - - + +
281D PHE* 1.3 73.2 - - - +
283D ASP* 1.3 67.2 + - - +
285D VAL* 3.3 6.7 + - - +
286D ILE* 3.0 40.9 + - + +
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Residues in contact with ASP 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ARG* 3.0 32.1 + - - +
280D LEU* 4.0 7.5 + - + +
282D ILE* 1.3 83.3 - - - +
284D TYR* 1.3 58.0 + - - +
286D ILE* 3.4 11.3 + - - +
287D ALA* 2.8 31.2 + - - +
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Residues in contact with TYR 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D MET* 3.4 29.4 - - + -
112D GLY* 3.1 23.9 - - - -
113D PHE* 3.4 37.0 - + + -
116D GLN* 3.3 39.3 - - - -
117D TYR* 4.5 2.7 - + + +
280D LEU 3.0 18.9 + - - +
281D PHE 3.1 5.4 + - - +
283D ASP* 1.3 73.9 - - - +
285D VAL* 1.3 60.7 + - - +
287D ALA* 3.1 6.0 + - + +
288D TYR* 2.8 61.4 + + + +
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D MET* 3.6 37.9 - - + -
142D PHE* 4.2 5.4 - - + -
157D ILE* 4.4 15.0 - - + -
266D MET* 3.8 29.2 - - + -
281D PHE* 3.0 33.6 + - + +
282D ILE 3.3 5.8 + - - +
284D TYR* 1.3 75.3 - - + +
286D ILE* 1.3 64.7 + - - +
288D TYR* 3.1 16.5 + - - +
289D ASN* 3.1 12.8 + - - -
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ARG* 3.6 53.9 + - - +
266D MET* 4.4 4.3 - - + -
268D TYR* 5.8 2.5 - - + +
282D ILE* 3.0 37.3 + - + +
283D ASP* 3.8 12.1 - - - +
285D VAL* 1.3 76.2 - - - +
287D ALA* 1.3 63.2 + - - +
288D TYR 3.3 0.5 + - - -
289D ASN* 3.6 16.7 + - - +
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Residues in contact with ALA 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D ASP 2.8 21.5 + - - +
284D TYR* 3.1 6.7 + - + +
286D ILE* 1.3 75.8 - - + +
288D TYR* 1.3 61.2 + - - +
289D ASN* 4.6 2.8 + - - +
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Residues in contact with TYR 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PRO* 3.7 26.2 + - + +
109D MET* 3.7 38.6 - - + -
112D GLY* 5.3 0.4 - - - -
284D TYR* 2.8 47.8 + + - +
285D VAL 3.1 5.8 + - - +
287D ALA* 1.3 78.9 - - - +
289D ASN* 1.3 82.9 + - - +
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Residues in contact with ASN 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ARG* 5.1 7.7 + - - -
157D ILE* 5.2 9.0 - - - -
285D VAL 3.1 12.7 + - - -
286D ILE 3.6 10.0 + - - +
287D ALA 3.4 3.2 + - - +
288D TYR* 1.3 97.4 - - - +
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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