Contacts of the helix formed by residues 269 - 280 (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 HIS 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TYR* 2.9 37.1 + + + +
199A PRO* 4.5 1.6 - - + -
212A VAL* 3.8 20.8 + - + +
213A ASN* 3.5 24.5 + - - -
216A PHE* 3.3 42.7 - + + +
264A LEU* 2.5 30.4 + - + +
265A LEU* 4.2 2.0 - - - -
268A THR* 1.3 86.2 - - + +
270A MET* 1.3 62.7 + - - +
271A GLN 3.5 2.0 - - - -
272A ASN* 3.4 7.3 + - - +
273A ILE* 3.1 29.3 + - + +
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Residues in contact with MET 270 (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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22A PHE* 4.9 20.2 - - + +
23A GLU 4.7 2.0 - - - +
24A PHE* 3.7 31.4 - - + -
265A LEU 3.3 15.4 + - - +
266A ILE* 3.2 28.5 - - + +
267A ARG 4.1 5.6 - - - +
268A THR 3.4 2.2 - - - -
269A HIS* 1.3 80.0 - - - +
271A GLN* 1.3 82.8 + - + +
273A ILE* 3.4 3.3 + - - +
274A LYS* 3.3 45.6 + - - +
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Residues in contact with GLN 271 (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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22A PHE* 5.1 10.9 - - - +
267A ARG 5.2 0.6 + - - -
268A THR 5.1 1.4 + - - -
269A HIS 3.5 0.2 - - - -
270A MET* 1.3 95.7 - - + +
272A ASN* 1.3 60.1 + - - +
274A LYS* 3.4 18.7 + - - +
275A ASP* 3.0 64.5 + - - +
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Residues in contact with ASN 272 (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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198A TYR* 3.0 29.5 + - - +
199A PRO* 5.2 0.4 - - - +
203A PHE 5.8 1.8 + - - -
209A ASP* 5.0 5.8 + - - -
213A ASN* 4.7 17.0 + - - +
268A THR 5.5 1.3 + - - +
269A HIS* 3.4 8.3 + - - +
270A MET 3.3 0.8 - - - -
271A GLN* 1.3 76.0 - - - +
273A ILE* 1.3 65.7 + - - +
275A ASP* 3.4 9.2 + - - +
276A ILE* 3.1 37.4 + - - +
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Residues in contact with ILE 273 (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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24A PHE* 4.0 16.6 - - + -
134A HIS* 3.3 38.8 - - + +
135A CYS* 4.1 10.5 - - + -
163A ASN* 3.4 10.0 + - + +
198A TYR* 3.4 34.8 - - + -
265A LEU* 3.6 30.3 - - + +
269A HIS 3.1 24.6 + - - +
270A MET 3.6 4.9 - - - +
272A ASN* 1.3 77.2 - - - +
274A LYS* 1.3 53.3 + - - +
276A ILE* 3.2 1.6 + - - -
277A THR* 2.7 35.9 + - - -
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Residues in contact with LYS 274 (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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22A PHE* 4.9 6.6 - - + +
23A GLU* 2.9 42.1 + - - +
24A PHE* 3.9 5.4 - - + -
130A ASP* 4.2 10.3 + - - +
132A ARG* 5.8 0.7 - - - +
134A HIS* 3.7 33.1 - - + +
270A MET* 3.3 28.1 + - - +
271A GLN* 3.8 22.5 + - - +
272A ASN 3.4 0.4 - - - -
273A ILE* 1.3 76.4 - - - +
275A ASP* 1.3 58.0 + - - +
277A THR* 3.3 7.9 + - - -
278A SER* 3.0 36.4 + - - +
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Residues in contact with ASP 275 (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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271A GLN* 3.0 48.7 + - - +
272A ASN* 3.7 11.7 - - - +
274A LYS* 1.3 75.9 - - - +
276A ILE* 1.3 53.9 + - + +
278A SER* 4.0 3.0 - - - +
279A SER* 2.6 41.4 + - - +
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Residues in contact with ILE 276 (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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163A ASN* 3.8 19.7 - - - +
198A TYR* 3.8 22.9 - - + -
199A PRO* 5.9 0.9 - - + -
200A GLN* 4.1 4.7 - - - +
203A PHE* 3.8 48.0 - - + -
272A ASN* 3.1 32.3 + - - +
273A ILE 3.2 3.3 + - - +
275A ASP* 1.3 74.7 - - + +
277A THR* 1.3 66.0 + - - +
279A SER* 4.0 4.7 - - - -
280A ILE* 3.1 28.8 + - + +
281A HIS* 3.2 9.6 + - + +
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Residues in contact with THR 277 (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* 4.0 17.3 - - + +
132A ARG* 4.8 7.0 - - + +
133A VAL 3.6 21.8 - - - +
134A HIS* 3.0 39.3 + - + +
162A VAL* 5.6 0.7 - - + -
163A ASN* 3.2 4.0 + - - -
273A ILE 2.7 22.8 + - - -
274A LYS* 3.3 8.5 + - - -
276A ILE* 1.3 77.8 - - - +
278A SER* 1.3 53.1 + - - +
281A HIS* 3.5 10.3 - - + +
282A PHE* 2.8 33.3 + - - +
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Residues in contact with SER 278 (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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132A ARG* 2.9 29.8 + - - +
274A LYS* 3.0 19.4 + - - +
275A ASP* 4.0 3.4 - - - -
277A THR* 1.3 76.9 - - - +
279A SER* 1.3 64.9 + - - +
280A ILE 3.4 0.5 + - - -
282A PHE* 3.3 24.4 - - - +
283A GLU* 3.5 13.7 + - - +
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Residues in contact with SER 279 (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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275A ASP 2.6 24.5 + - - -
276A ILE* 4.0 0.5 - - - -
278A SER* 1.3 78.8 - - - +
280A ILE* 1.3 76.7 + - - +
283A GLU* 3.3 22.5 - - - +
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Residues in contact with ILE 280 (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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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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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