Contacts of the helix formed by residues 275 - 288 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ASP* 5.0 5.8 - - - +
273E HIS* 3.5 18.1 - - + +
274E LEU* 1.3 92.0 - - + +
276E GLU* 1.3 66.2 + - - +
277E LYS* 3.3 22.2 - - + -
278E VAL* 3.0 33.2 + - + +
279E ARG* 3.0 9.9 + - - +
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Residues in contact with GLU 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ALA* 3.5 24.5 - - + -
273E HIS* 5.2 1.4 - - - -
274E LEU 3.6 2.4 + - - +
275E PRO* 1.3 73.4 - - - +
277E LYS* 1.3 63.8 + - - +
278E VAL 3.2 0.2 + - - -
279E ARG* 3.0 45.7 + - - +
280E LEU* 2.9 28.5 + - + +
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Residues in contact with LYS 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ALA* 4.1 3.3 - - + +
90E SER 3.3 32.7 + - - +
91E GLY* 4.4 0.8 - - - -
92E LYS* 2.5 39.2 + - - +
93E ILE* 3.3 26.1 - - + +
120E ILE* 3.9 15.2 - - + +
139E ASP* 5.3 1.9 + - - -
275E PRO* 4.3 24.5 - - + -
276E GLU* 1.3 74.5 - - - +
278E VAL* 1.3 61.4 + - - +
280E LEU* 3.3 13.2 + - - +
281E PHE* 3.0 22.5 + - - +
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Residues in contact with VAL 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ILE* 4.0 15.7 - - + -
139E ASP* 4.0 31.6 - - + +
140E VAL* 3.9 17.5 - - + -
274E LEU* 4.6 11.7 - - + -
275E PRO* 3.0 33.6 + - + +
277E LYS* 1.3 80.2 - - + +
279E ARG* 1.3 61.3 + - - +
281E PHE* 3.0 3.6 + - + +
282E ILE* 2.8 48.7 + - + +
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Residues in contact with ARG 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E LEU* 4.9 18.9 - - + +
275E PRO 3.0 11.6 + - - +
276E GLU* 3.0 41.5 + - - +
278E VAL* 1.3 76.5 - - - +
280E LEU* 1.3 74.3 + - - +
282E ILE* 3.2 5.4 + - + +
283E ASP* 2.1 69.3 + - - +
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Residues in contact with LEU 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ALA* 3.7 31.9 - - + +
113E PHE* 3.6 11.3 - - + -
117E TYR* 3.8 35.3 + - + +
120E ILE* 5.3 2.2 - - + -
276E GLU* 2.9 28.3 + - + +
277E LYS* 3.6 7.9 - - - +
279E ARG* 1.3 99.0 - - - +
281E PHE* 1.3 62.6 + - - +
283E ASP* 3.7 4.0 + - - +
284E TYR* 3.2 23.2 + - - +
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Residues in contact with PHE 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ILE* 4.0 14.6 - - + -
95E ILE* 4.1 10.3 - - + -
109E MET* 4.5 2.0 - - - -
110E LEU* 3.7 31.6 - - + -
113E PHE* 3.4 41.2 - + + -
122E ILE* 4.4 8.5 - - + -
140E VAL* 3.9 27.1 - - + -
142E PHE* 3.7 33.4 - + - -
277E LYS 3.0 13.5 + - - +
278E VAL* 3.0 8.4 + - - +
280E LEU* 1.3 74.6 - - - +
282E ILE* 1.3 68.4 + - + +
284E TYR* 3.2 4.0 + - - +
285E VAL* 3.0 41.3 + - + +
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Residues in contact with ILE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 3.8 16.4 - - + -
266E MET* 4.2 13.5 - - + -
268E TYR* 3.4 61.5 - - + +
274E LEU* 3.9 9.6 - - + -
278E VAL* 2.8 39.1 + - + +
279E ARG* 4.0 4.3 - - - +
281E PHE* 1.3 74.3 - - + +
283E ASP* 1.3 67.0 + - - +
285E VAL* 3.4 6.8 + - - +
286E ILE* 3.2 35.4 + - + +
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Residues in contact with ASP 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E ARG* 2.1 56.0 + - - +
280E LEU* 4.2 3.8 - - - +
282E ILE* 1.3 80.0 - - - +
284E TYR* 1.3 61.9 + - - +
286E ILE* 3.1 16.5 + - - +
287E ALA* 2.9 25.4 + - - +
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Residues in contact with TYR 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E MET* 3.3 29.6 - - + -
112E GLY* 3.1 23.1 + - - -
113E PHE* 3.5 36.3 - + + -
116E GLN* 3.8 32.2 + - - -
117E TYR* 4.7 2.7 - + + +
280E LEU 3.2 19.3 + - - +
281E PHE 3.2 5.1 + - - +
283E ASP* 1.3 78.2 - - - +
285E VAL* 1.3 62.4 + - - +
287E ALA* 3.3 7.7 + - + +
288E TYR* 3.0 52.4 + + - +
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Residues in contact with VAL 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E MET* 3.5 41.6 - - + +
142E PHE* 4.2 9.2 - - + -
157E ILE* 4.2 16.6 - - + +
266E MET* 3.7 26.2 - - + -
281E PHE* 3.0 41.8 + - + +
282E ILE 3.7 7.2 - - - +
284E TYR* 1.3 74.8 - - + +
286E ILE* 1.3 63.6 + - - +
288E TYR* 3.3 14.8 + - - +
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Residues in contact with ILE 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ARG* 3.7 54.7 - - - +
157E ILE* 6.1 2.0 - - + -
266E MET* 4.3 6.5 - - + -
268E TYR* 6.0 1.6 - - + +
282E ILE* 3.2 32.0 + - + +
283E ASP* 3.1 16.2 + - - +
285E VAL* 1.3 78.5 - - - +
287E ALA* 1.3 63.1 + - + +
288E TYR* 3.2 4.5 + - - -
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Residues in contact with ALA 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E ASP 2.9 15.7 + - - +
284E TYR* 3.7 8.3 - - + +
286E ILE* 1.3 78.2 - - + +
288E TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PRO* 3.5 26.5 + - + +
109E MET* 3.6 45.3 - - + -
112E GLY* 5.3 1.3 - - - -
284E TYR* 3.0 40.2 + + + +
285E VAL 3.7 10.3 - - - +
286E ILE 3.1 6.1 - - - -
287E ALA* 1.3 81.9 - - - +
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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