Contacts of the helix formed by residues 275 - 289 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F ASP* 5.2 5.6 - - - +
273F HIS 4.0 5.2 - - - +
274F LEU* 1.3 91.1 - - + +
276F GLU* 1.3 65.8 - - - +
277F LYS* 3.4 19.1 - - + -
278F VAL* 3.1 27.9 + - + -
279F ARG* 3.0 18.7 + - - +
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Residues in contact with GLU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ALA* 3.5 26.1 - - + +
274F LEU 4.6 0.2 - - - -
275F PRO* 1.3 74.2 - - - +
277F LYS* 1.3 58.7 + - - +
279F ARG* 3.1 15.7 + - - +
280F LEU* 2.8 50.9 + - + +
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Residues in contact with LYS 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.9 3.6 + - - -
136A THR* 5.1 1.8 + - - -
137A GLU* 3.4 22.2 + - - +
89F ALA 4.3 2.3 - - - +
90F SER 3.5 27.6 + - - +
91F GLY* 4.1 7.2 - - - -
92F LYS 2.6 37.7 + - - +
93F ILE* 3.1 23.3 - - + +
113F PHE* 4.5 2.6 - - - -
120F ILE* 4.3 13.0 - - + -
139F ASP* 5.3 2.9 + - - -
275F PRO* 4.4 19.3 - - + -
276F GLU* 1.3 79.5 - - - +
278F VAL* 1.3 75.4 + - + +
280F LEU* 3.6 14.2 + - - +
281F PHE* 3.2 12.8 + - - +
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Residues in contact with VAL 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ILE* 4.0 10.1 - - + -
139F ASP* 4.1 31.2 - - + +
140F VAL* 4.0 25.8 - - + -
268F TYR* 5.4 0.2 - - + -
274F LEU* 4.0 19.5 - - + -
275F PRO* 3.1 30.7 + - + +
277F LYS* 1.3 89.6 - - + +
279F ARG* 1.3 61.2 + - - +
281F PHE* 3.0 4.6 + - + +
282F ILE* 2.8 35.4 + - + +
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Residues in contact with ARG 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ILE* 5.6 0.2 - - - +
268F TYR* 4.5 14.3 + - - -
271F LYS* 3.7 27.7 - - - +
274F LEU* 3.4 38.4 - - + +
275F PRO 3.0 13.1 + - - +
276F GLU* 3.6 17.0 - - - +
278F VAL* 1.3 74.4 - - - +
280F LEU* 1.3 66.7 + - + +
282F ILE* 4.3 14.5 - - - +
283F ASP* 2.9 54.4 + - - +
286F ILE* 5.1 4.0 - - - +
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Residues in contact with LEU 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ALA* 4.1 18.4 - - + +
113F PHE* 4.0 7.3 - - + -
117F TYR* 3.9 43.4 + - + +
120F ILE* 4.3 7.0 - - + -
276F GLU* 2.8 46.9 + - + +
277F LYS* 3.7 10.1 - - - +
279F ARG* 1.3 78.2 - - + +
281F PHE* 1.3 57.2 + - - +
283F ASP* 3.6 6.7 + - + +
284F TYR* 3.1 28.8 + - - +
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Residues in contact with PHE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ILE* 3.8 15.5 - - + -
95F ILE* 4.4 9.0 - - + -
109F MET* 6.1 0.4 - - + -
110F LEU* 3.6 30.5 - - + -
113F PHE* 3.4 41.0 - + + -
122F ILE* 4.4 6.1 - - + -
140F VAL* 3.8 27.1 - - + -
142F PHE* 3.7 33.9 - + - -
277F LYS 3.2 11.4 + - - +
278F VAL 3.0 7.9 + - - +
280F LEU* 1.3 77.3 - - - +
282F ILE* 1.3 72.4 + - + +
284F TYR* 3.2 4.0 + - - +
285F VAL* 3.0 40.1 + - + +
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Residues in contact with ILE 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 3.8 28.9 - - + -
266F MET* 3.9 13.7 - - + -
268F TYR* 3.8 53.2 - - + +
274F LEU* 4.9 4.0 - - + -
278F VAL* 2.8 28.8 + - + +
279F ARG* 3.8 19.1 - - - +
281F PHE* 1.3 75.0 - - + +
283F ASP* 1.3 63.8 + - - +
285F VAL* 3.0 7.1 + - - +
286F ILE* 3.0 39.9 + - + +
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Residues in contact with ASP 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F ARG* 2.9 59.9 + - - +
280F LEU* 3.8 7.7 - - - +
282F ILE* 1.3 76.7 - - - +
284F TYR* 1.3 57.4 + - - +
286F ILE* 3.2 12.8 + - - +
287F ALA* 2.9 31.2 + - - +
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Residues in contact with TYR 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F MET* 3.3 28.7 - - + -
112F GLY* 3.1 24.0 - - - -
113F PHE* 3.4 37.7 - + + -
116F GLN* 3.6 35.2 - - - -
117F TYR* 4.6 2.7 - + + +
280F LEU 3.1 15.3 + - - +
281F PHE 3.5 7.9 - - - +
283F ASP* 1.3 74.9 - - - +
285F VAL* 1.3 60.9 + - + +
287F ALA* 3.7 6.4 - - + +
288F TYR* 2.8 60.4 + + - +
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Residues in contact with VAL 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F MET* 3.7 39.7 - - + +
142F PHE* 4.4 2.0 - - + -
155F ARG* 5.7 0.4 - - - -
157F ILE* 4.4 14.4 - - + -
266F MET* 3.6 28.0 - - + -
281F PHE* 3.0 46.8 + - + +
282F ILE 3.0 7.4 + - - +
284F TYR* 1.3 78.1 - - + +
286F ILE* 1.3 64.2 + - - +
288F TYR* 3.2 3.1 + - - +
289F ASN* 3.1 20.6 + - - -
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Residues in contact with ILE 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ARG* 3.6 53.2 + - - +
266F MET* 4.6 1.8 - - + -
268F TYR* 4.7 6.1 - - - +
279F ARG* 5.1 3.4 - - - +
282F ILE* 3.0 33.4 + - + +
283F ASP* 3.6 15.0 - - - +
285F VAL* 1.3 76.2 - - - +
287F ALA* 1.3 61.5 - - - +
289F ASN* 3.2 21.9 + - - +
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Residues in contact with ALA 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F ASP 2.9 17.0 + - - +
284F TYR* 3.9 8.1 - - + +
286F ILE* 1.3 77.6 - - - +
288F TYR* 1.3 62.6 + - - +
289F ASN* 3.5 10.3 + - - +
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Residues in contact with TYR 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PRO* 3.5 26.2 + - + +
109F MET* 3.7 42.6 - - + -
112F GLY* 5.3 0.4 - - - -
284F TYR* 2.8 50.9 + + - +
285F VAL 3.4 6.1 - - - +
286F ILE 3.2 0.2 - - - -
287F ALA* 1.3 79.1 - - - +
289F ASN* 1.3 80.5 + - - +
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Residues in contact with ASN 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F MET* 5.6 2.5 - - - +
157F ILE* 4.8 9.5 - - - +
285F VAL 3.1 13.0 + - - -
286F ILE* 3.2 12.7 + - - +
287F ALA* 3.5 14.6 + - - +
288F TYR* 1.3 93.5 + - - +
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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