Contacts of the helix formed by residues 280 - 291 (chain C) in PDB entry 5CYP
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 ILE 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C PHE* 3.7 42.6 - - + -
276C ILE* 3.0 23.1 + - + +
279C SER* 1.3 98.1 - - - +
281C HIS* 1.3 78.7 + - + +
282C PHE 3.4 0.7 - - - -
283C GLU* 3.6 1.0 + - - +
284C ALA* 3.2 22.9 + - - +
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Residues in contact with HIS 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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112C TYR* 3.5 24.2 - - - +
159C SER 3.5 24.1 + - - -
160C LYS 4.2 4.7 + - - -
161C VAL* 3.8 11.6 - - - +
162C VAL* 3.6 18.7 + - - -
163C ASN* 2.6 42.1 + - - -
200C GLN* 3.8 9.7 + - - -
203C PHE* 5.8 1.3 - + - -
276C ILE* 3.2 24.6 + - + +
277C THR* 3.5 7.4 - - - +
280C ILE* 1.3 88.2 - - + +
282C PHE* 1.3 62.4 + - - +
284C ALA* 3.4 18.7 - - - +
285C TYR* 3.4 7.4 + - - +
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Residues in contact with PHE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C TYR* 3.3 53.8 + + + -
115C TYR* 3.8 28.0 - + + -
116C LEU* 4.1 13.5 - - + -
119C GLU* 4.0 12.8 - - - -
132C ARG* 3.4 24.7 - - - +
277C THR 2.8 21.3 + - - +
278C SER* 3.3 7.9 - - - +
280C ILE 3.4 0.2 - - - -
281C HIS* 1.3 71.1 - - - +
283C GLU* 1.3 73.4 + - - +
285C TYR* 3.0 10.1 + + + +
286C ARG* 2.9 50.4 + - + +
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Residues in contact with GLU 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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278C SER 3.3 9.4 + - - +
279C SER* 3.3 29.3 - - - +
280C ILE 3.6 2.6 + - - +
281C HIS 3.4 0.4 - - - -
282C PHE* 1.3 84.4 - - - +
284C ALA* 1.3 59.2 + - - +
286C ARG* 3.2 34.6 + - - +
287C VAL* 3.0 39.7 + - + +
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Residues in contact with ALA 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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160C LYS 5.2 8.5 - - - +
280C ILE 3.2 15.2 + - - +
281C HIS* 3.4 13.2 - - - +
283C GLU* 1.3 77.4 - - - +
285C TYR* 1.3 60.6 + - - +
287C VAL* 3.2 21.6 - - - +
288C LYS* 3.4 11.4 + - - +
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Residues in contact with TYR 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 ASN* 3.4 43.0 + - + +
112C TYR* 3.3 49.1 - + + -
113C GLU* 2.3 40.6 + - - +
116C LEU* 4.1 11.0 - - + -
281C HIS 3.4 3.1 + - - +
282C PHE* 3.0 14.6 + + - +
284C ALA* 1.3 77.8 - - - +
286C ARG* 1.3 66.2 + - - +
288C LYS* 3.4 5.8 + - + +
289C ARG* 3.2 45.8 + - + +
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Residues in contact with ARG 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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116C LEU* 3.6 31.4 - - + +
119C GLU* 2.3 36.5 + - - +
120C VAL* 5.7 4.4 - - - +
282C PHE* 2.9 32.0 + - + +
283C GLU* 3.2 40.7 + - - +
285C TYR* 1.3 80.3 - - - +
287C VAL* 1.3 64.9 + - + +
289C ARG* 3.4 1.7 + - - -
290C LEU* 3.1 48.3 + - + +
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Residues in contact with VAL 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 GLU* 3.0 19.4 + - + +
284C ALA* 3.2 23.3 - - - +
286C ARG* 1.3 75.5 - - + +
288C LYS* 1.3 60.6 + - + +
290C LEU* 5.0 1.3 - - - -
291C ASN* 2.6 41.3 + - - +
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Residues in contact with LYS 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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284C ALA 3.6 13.2 - - - +
285C TYR* 3.4 8.7 + - + +
286C ARG 3.3 0.6 - - - -
287C VAL* 1.3 85.2 - - + +
289C ARG* 1.3 62.6 + - + +
290C LEU 3.4 0.7 + - - -
291C ASN* 4.3 4.7 + - - +
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Residues in contact with ARG 289 (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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113C GLU* 2.6 35.9 + - - -
116C LEU* 4.2 16.0 - - + +
285C TYR* 3.2 49.3 + - + +
286C ARG 4.0 3.1 - - - +
287C VAL 3.4 0.2 - - - -
288C LYS* 1.3 79.2 - - + +
290C LEU* 1.3 66.8 + - + +
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Residues in contact with LEU 290 (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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116C LEU* 4.6 18.4 - - + -
120C VAL* 5.7 4.7 - - + -
286C ARG* 3.1 43.4 + - - +
287C VAL* 4.9 0.9 - - - -
289C ARG* 1.3 93.9 - - + +
291C ASN* 1.3 72.4 + - - +
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Residues in contact with ASN 291 (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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287C VAL* 2.6 30.8 + - - +
288C LYS 4.3 4.0 + - - +
290C LEU* 1.3 82.0 - - - +
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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