Contacts of the helix formed by residues 275 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C ASP* 5.6 2.5 - - - +
273C HIS* 3.6 11.6 - - + +
274C LEU* 1.3 92.7 - - + +
276C GLU* 1.3 66.5 + - - +
277C LYS* 4.2 22.2 - - + -
278C VAL* 3.0 25.1 + - + -
279C ARG* 3.0 18.4 + - - +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLY* 3.7 31.2 - - - +
89C ALA* 4.6 0.4 - - + +
273C HIS* 5.2 7.9 + - - -
274C LEU 3.5 4.1 + - - +
275C PRO* 1.3 71.7 - - - +
277C LYS* 1.3 64.4 + - - +
279C ARG* 2.5 51.2 + - - +
280C LEU* 2.9 44.4 + - + +
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Residues in contact with LYS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLY 4.4 3.9 + - - -
90C SER 3.6 26.9 + - - +
91C GLY* 3.9 8.9 - - - -
92C LYS* 2.7 38.9 + - - +
93C ILE* 3.4 19.9 - - + +
113C PHE* 3.9 1.9 - - - -
120C ILE* 3.8 23.8 - - + -
139C ASP* 5.0 6.2 + - - -
275C PRO* 4.2 22.0 - - + -
276C GLU* 1.3 77.3 - - - +
278C VAL* 1.3 69.6 + - + +
280C LEU* 3.6 4.0 + - - +
281C PHE* 3.1 21.0 + - - +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 4.6 6.3 - - + -
139C ASP* 4.2 33.4 - - + +
140C VAL* 4.3 13.0 - - + -
268C TYR* 5.3 2.0 - - + -
274C LEU* 4.1 15.5 - - + -
275C PRO* 3.0 30.0 + - + +
277C LYS* 1.3 83.3 - - + +
279C ARG* 1.3 65.4 + - - +
281C PHE* 3.1 6.4 + - - +
282C ILE* 2.8 44.8 + - + +
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Residues in contact with ARG 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C HIS* 6.3 2.9 - - - -
274C LEU* 4.6 18.0 - - + +
275C PRO 3.0 12.4 + - - +
276C GLU* 2.5 40.8 + - - +
278C VAL* 1.3 76.9 - - - +
280C LEU* 1.3 82.3 + - - +
282C ILE* 3.6 9.0 + - - +
283C ASP* 3.0 56.0 + - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.6 32.8 - - + -
113C PHE* 3.7 11.6 - - + -
117C TYR* 3.7 29.6 + - + +
120C ILE* 5.1 0.9 - - + -
276C GLU* 2.9 31.8 + - + +
277C LYS* 3.9 4.0 - - - +
279C ARG* 1.3 102.3 - - - +
281C PHE* 1.3 58.8 + - - +
283C ASP* 3.4 5.6 + - + +
284C TYR* 2.8 30.3 + - - +
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Residues in contact with PHE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 4.0 11.4 - - + -
95C ILE* 3.7 15.3 - - + -
109C MET 5.8 0.4 - - - -
110C LEU* 3.6 33.7 - - + -
113C PHE* 3.3 41.9 - + + -
122C ILE* 5.1 0.9 - - + -
140C VAL* 3.9 31.2 - - + -
142C PHE* 3.9 23.3 - + - -
266C MET* 4.7 0.9 - - - -
277C LYS 3.1 18.5 + - - +
278C VAL* 3.1 4.9 + - - +
280C LEU* 1.3 76.9 - - - +
282C ILE* 1.3 67.4 + - - +
284C TYR* 3.0 4.7 + + - +
285C VAL* 3.0 42.6 + - + +
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Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 4.8 6.7 - - + -
155C ARG* 4.8 4.5 - - - +
266C MET* 3.9 22.7 - - + -
268C TYR* 3.9 47.6 - - + +
274C LEU* 3.7 22.7 - - + -
278C VAL* 2.8 45.1 + - + +
279C ARG* 3.9 4.5 - - - +
281C PHE* 1.3 72.7 - - - +
283C ASP* 1.3 70.4 + - - +
285C VAL* 3.2 3.1 + - - +
286C ILE* 3.1 31.7 + - + +
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Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C ARG* 3.0 49.1 + - - +
280C LEU* 3.8 7.7 - - + +
282C ILE* 1.3 81.9 - - - +
284C TYR* 1.3 63.0 + - - +
286C ILE* 3.2 10.0 + - - +
287C ALA* 3.0 24.8 + - - +
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Residues in contact with TYR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C MET* 3.4 22.7 - - + -
112C GLY* 3.1 24.6 - - - -
113C PHE* 3.4 36.6 - + + -
116C GLN* 3.5 27.4 - - - -
117C TYR* 5.0 2.5 - + + -
280C LEU 2.8 19.1 + - - +
281C PHE* 3.0 5.6 + + - +
283C ASP* 1.3 75.5 - - - +
285C VAL* 1.3 71.4 + - + +
287C ALA* 3.3 6.8 + - + +
288C TYR* 3.1 48.9 + + - -
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C MET* 4.1 32.2 - - + +
142C PHE* 4.3 6.5 - - + -
157C ILE* 3.7 30.2 - - + +
266C MET* 3.7 17.9 - - + -
281C PHE* 3.0 44.6 + - + +
282C ILE 3.2 6.9 + - - +
284C TYR* 1.3 79.5 - - + +
286C ILE* 1.3 65.3 + - - +
288C TYR* 3.2 16.6 + - - +
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Residues in contact with ILE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ARG* 3.3 54.3 - - + +
157C ILE* 5.5 1.8 - - + -
266C MET* 3.9 10.3 - - + -
282C ILE* 3.1 22.1 + - + +
283C ASP* 3.5 10.5 - - - +
285C VAL* 1.3 78.9 - - + +
287C ALA* 1.3 60.2 - - - +
288C TYR 3.3 2.1 + - - +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C ASP 3.0 15.8 + - - +
284C TYR* 3.3 5.4 + - - +
286C ILE* 1.3 76.5 - - + +
288C TYR* 1.3 64.5 + - - +
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Residues in contact with TYR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PRO* 3.6 27.6 + - + +
109C MET* 3.6 42.0 - - + -
112C GLY* 5.5 0.4 - - - -
284C TYR* 3.1 43.7 + + - +
285C VAL 3.2 16.6 + - - +
286C ILE 3.2 2.2 - - - +
287C ALA* 1.3 82.8 - - - +
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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