Contacts of the helix formed by residues 280 - 289 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A PHE* 3.9 35.0 - - + -
276A ILE* 3.1 26.5 + - + +
279A SER* 1.3 99.5 - - - +
281A HIS* 1.3 78.0 + - + +
282A PHE 3.4 0.9 - - - -
283A GLU* 4.0 1.6 - - - +
284A ALA* 3.1 23.9 + - - +
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 3.6 22.1 - - - +
159A SER 3.7 21.7 + - - -
160A LYS 4.4 4.5 + - - -
161A VAL* 3.8 13.1 + - - +
162A VAL* 3.7 16.4 + - - -
163A ASN* 2.6 41.9 + - - -
200A GLN* 4.0 7.9 + - - -
203A PHE* 5.8 1.6 - + - -
276A ILE* 3.2 27.7 + - + +
277A THR* 3.5 10.5 - - + +
280A ILE* 1.3 88.5 - - + +
282A PHE* 1.3 63.0 + - - +
284A ALA* 3.4 8.3 + - - +
285A TYR* 3.4 17.7 + - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 3.3 52.2 - + + -
115A TYR* 3.9 24.5 - + + -
116A LEU* 4.1 18.8 - - + -
119A GLU* 3.6 27.8 - - - -
132A ARG* 3.4 25.6 - - - +
277A THR 2.8 20.5 + - - +
278A SER* 3.3 8.1 - - - +
280A ILE 3.4 0.2 - - - -
281A HIS* 1.3 72.0 - - - +
283A GLU* 1.3 80.6 + - - +
285A TYR* 3.1 8.7 + + - +
286A ARG* 2.9 30.2 + - + +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 5.4 0.7 - - - +
278A SER 3.5 9.3 + - - +
279A SER* 3.3 28.9 - - - +
280A ILE 3.6 2.4 + - - +
281A HIS 3.4 0.2 - - - -
282A PHE* 1.3 88.9 - - - +
284A ALA* 1.3 63.5 + - - +
286A ARG* 2.8 50.4 + - - +
287A VAL* 3.1 35.5 + - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 5.3 16.4 - - - +
280A ILE 3.1 17.9 + - - +
281A HIS* 3.5 9.9 - - - +
282A PHE 3.2 0.2 - - - -
283A GLU* 1.3 79.1 - - - +
285A TYR* 1.3 58.1 + - - +
287A VAL* 3.8 5.5 + - - +
288A LYS* 3.4 20.4 + - - +
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.5 43.1 + - + +
112A TYR* 3.4 48.5 - - + -
113A GLU* 2.5 37.2 + - - +
116A LEU* 4.2 11.2 - - + -
281A HIS 3.4 4.9 + - - +
282A PHE* 3.1 12.9 + + - +
284A ALA* 1.3 78.2 - - - +
286A ARG* 1.3 68.6 + - - +
288A LYS* 3.3 9.5 + - + +
289A ARG* 3.2 27.0 + - + +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.5 34.7 - - + +
119A GLU* 2.8 34.5 + - - +
282A PHE* 2.9 19.5 + - + +
283A GLU* 2.8 47.5 + - - +
285A TYR* 1.3 82.7 - - - +
287A VAL* 1.3 65.0 + - + +
289A ARG* 3.5 17.2 + - - +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLU* 3.1 21.9 + - + +
284A ALA* 4.1 5.4 - - - +
285A TYR 3.3 0.2 - - - -
286A ARG* 1.3 76.3 - - + +
288A LYS* 1.3 67.1 + - - +
289A ARG 3.6 2.9 + - - -
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ALA 3.4 11.8 + - - +
285A TYR* 3.3 14.2 + - + +
287A VAL* 1.3 82.6 - - - +
289A ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 5.2 3.1 - - - +
116A LEU* 4.5 19.1 - - + +
285A TYR* 3.2 25.2 + - + +
286A ARG 3.5 12.6 + - - +
287A VAL 3.4 3.1 - - - -
288A LYS* 1.3 85.1 - - - +
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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