Contacts of the helix formed by residues 257 - 267 (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 GLU 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C LYS* 2.5 35.1 + - - -
219C MET* 3.2 28.5 - - + +
222C PHE* 3.6 10.2 - - + -
223C ALA* 2.7 47.0 + - + +
224C VAL* 5.0 0.9 - - - -
253C THR* 5.1 5.8 - - - +
256C CYS* 1.3 77.7 - - - +
258C PHE* 1.3 60.8 + - - +
259C ALA 3.4 2.5 - - - -
260C TYR* 3.6 9.9 + - + +
261C LEU* 3.2 22.0 + - - +
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Residues in contact with PHE 258 (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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39C LEU* 3.6 38.8 - - + -
42C THR* 3.7 19.3 - - + -
43C LEU* 3.5 44.6 - - + -
46C SER* 5.0 5.6 - - - -
137C LEU* 5.8 0.7 - - + -
223C ALA 3.9 1.6 + - - -
224C VAL* 4.3 17.3 - - + -
225C VAL 4.5 0.9 - - - +
250C VAL* 3.8 20.0 - - + -
251C GLU* 6.0 0.7 - - - -
256C CYS* 3.6 17.1 - - - -
257C GLU* 1.3 75.2 - - - +
259C ALA* 1.3 63.9 + - - +
261C LEU* 3.2 11.6 + - + +
262C ARG* 2.8 40.9 + - + +
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Residues in contact with ALA 259 (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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250C VAL 4.0 3.2 + - - +
251C GLU* 3.6 36.1 - - + +
252C ASN 5.0 2.0 - - - +
253C THR* 5.0 11.7 - - + -
257C GLU 3.4 0.4 - - - -
258C PHE* 1.3 84.0 - - - +
260C TYR* 1.3 63.1 + - - +
262C ARG* 3.5 4.8 + - - +
263C ASP* 3.2 31.4 + - - +
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Residues in contact with TYR 260 (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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219C MET* 4.6 21.5 - - + -
253C THR* 5.6 10.1 - - + +
257C GLU* 3.6 12.8 + - - +
258C PHE 3.3 0.4 - - - -
259C ALA* 1.3 75.7 - - - +
261C LEU* 1.3 67.3 + - - +
263C ASP* 3.3 6.9 + - - +
264C LEU* 2.9 34.3 + - + +
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Residues in contact with LEU 261 (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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137C LEU* 4.3 16.8 - - + -
165C VAL* 3.9 9.4 - - + -
167C VAL* 3.7 28.0 - - + -
216C PHE* 4.3 3.1 - - + -
222C PHE* 3.5 41.6 - - + -
224C VAL* 3.9 15.3 - - + -
257C GLU 3.2 16.2 + - - +
258C PHE* 3.2 11.4 + - + +
260C TYR* 1.3 79.7 - - - +
262C ARG* 1.3 62.3 + - - +
264C LEU* 3.4 2.0 + - - +
265C LEU* 3.0 51.0 + - + +
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Residues in contact with ARG 262 (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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43C LEU* 5.3 7.4 - - + -
258C PHE* 2.8 36.7 + - + +
259C ALA* 3.7 7.4 - - - +
260C TYR 3.3 0.2 - - - -
261C LEU* 1.3 77.3 - - - +
263C ASP* 1.3 61.1 + - - +
265C LEU* 3.3 5.0 + - - -
266C ILE* 2.9 48.1 + - + +
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Residues in contact with ASP 263 (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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259C ALA* 3.2 20.0 + - - +
260C TYR* 3.8 5.8 - - - +
262C ARG* 1.3 82.5 - - - +
264C LEU* 1.3 59.6 + - + +
266C ILE* 4.9 2.0 - - - +
267C ARG* 2.8 35.2 + - + +
268C THR* 3.2 9.7 + - - +
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Residues in contact with LEU 264 (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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215C LYS 5.4 1.8 - - - +
216C PHE* 3.5 39.0 - - + -
219C MET* 5.2 5.4 - - - -
222C PHE* 3.8 20.6 - - + -
260C TYR* 2.9 29.1 + - + +
261C LEU 3.7 2.9 - - - +
263C ASP* 1.3 77.9 - - + +
265C LEU* 1.3 58.4 + - - +
268C THR* 4.0 15.7 - - + +
269C HIS* 2.6 55.8 + - + +
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Residues in contact with LEU 265 (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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24C PHE* 3.4 18.3 - - + -
26C ILE* 4.5 14.6 - - + -
135C CYS* 3.7 17.7 - - - -
137C LEU* 3.8 29.6 - - + -
165C VAL* 4.4 4.0 - - + -
216C PHE* 4.2 22.2 - - + -
261C LEU* 3.0 32.9 + - + +
262C ARG* 3.9 4.7 - - - +
264C LEU* 1.3 76.3 - - - +
266C ILE* 1.3 62.6 + - + +
269C HIS 4.2 0.2 - - - -
270C MET* 3.3 24.1 - - - +
273C ILE* 3.7 25.8 - - + -
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Residues in contact with ILE 266 (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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24C PHE* 4.9 2.0 - - + -
26C ILE* 5.2 7.6 - - + -
43C LEU* 5.2 12.1 - - + +
74C ILE* 4.7 9.9 - - + -
76C GLU* 4.7 18.8 - - + -
81C MET* 3.6 32.6 - - + +
83C LEU* 4.5 20.2 - - + -
262C ARG* 2.9 31.1 + - + +
263C ASP* 4.5 2.0 - - - +
265C LEU* 1.3 84.4 - - + +
267C ARG* 1.3 61.4 + - + +
270C MET* 3.2 22.0 - - - +
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Residues in contact with ARG 267 (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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76C GLU* 6.2 2.9 - - + -
263C ASP* 2.8 24.1 + - + +
266C ILE* 1.3 77.7 - - + +
268C THR* 1.3 69.0 + - - +
269C HIS 3.6 0.6 + - - -
270C MET* 3.9 8.2 + - - +
271C GLN 5.2 0.7 + - - -
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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