Contacts of the helix formed by residues 263 - 276 (chain A) in PDB entry 1K27
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 TRP 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.9 17.3 - - + -
88A HIS* 3.1 24.0 - + + -
145A CYS* 3.9 10.5 - - - -
147A LYS* 3.5 35.2 - - + -
148A THR* 3.4 27.4 - - - -
151A VAL* 5.2 5.6 - - + -
211A CYS* 4.2 2.7 - - - -
258A ILE* 2.9 36.4 + - + +
261A THR* 2.7 45.3 + - - -
262A GLU* 1.3 78.1 + - - +
264A SER* 1.3 61.3 + - - +
265A GLU 3.3 2.7 - - - -
266A THR* 3.8 23.1 - - + -
267A LEU* 2.8 50.5 + - + +
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Residues in contact with SER 264 (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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262A GLU* 2.8 27.7 + - - +
263A TRP* 1.3 76.3 - - - +
265A GLU* 1.3 68.2 + - - +
267A LEU* 4.2 4.6 - - - +
268A HIS* 3.0 28.4 + - - +
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Residues in contact with GLU 265 (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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262A GLU* 5.3 2.8 - - + +
263A TRP 3.3 0.6 - - - -
264A SER* 1.3 80.0 + - - +
266A THR* 1.3 67.1 + - - +
268A HIS* 3.3 7.0 + - + +
269A ASN* 3.0 46.5 + - - +
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Residues in contact with THR 266 (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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145A CYS* 4.6 3.1 - - - -
146A PRO* 6.3 0.2 - - + -
147A LYS* 3.7 37.3 - - - +
211A CYS* 4.1 13.2 - - - -
262A GLU 4.6 3.1 + - - -
263A TRP* 3.2 37.6 + - + -
265A GLU* 1.3 81.3 - - - +
267A LEU* 1.3 60.8 + - - +
269A ASN* 3.4 6.9 + - - +
270A LEU* 3.3 26.5 + - + +
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Residues in contact with LEU 267 (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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9A ALA 5.5 2.0 - - - +
10A VAL* 5.2 3.1 - - + -
87A THR* 3.7 42.2 - - + +
88A HIS* 4.3 4.0 - - + -
209A GLY 4.8 11.0 - - - +
211A CYS* 3.4 29.2 - - - -
263A TRP* 2.8 37.7 + - + +
264A SER* 4.2 3.8 - - - +
266A THR* 1.3 72.0 - - - +
268A HIS* 1.3 61.7 + - - +
270A LEU* 3.4 5.2 + - - +
271A LYS* 3.0 29.0 + - - +
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Residues in contact with HIS 268 (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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264A SER 3.0 20.9 + - - +
265A GLU* 3.5 9.2 - - + +
266A THR 3.2 0.2 - - - -
267A LEU* 1.3 78.2 - - - +
269A ASN* 1.3 74.7 + - - +
271A LYS* 3.2 16.1 + - + +
272A ASN* 3.0 51.1 + - - -
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Residues in contact with ASN 269 (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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265A GLU* 3.0 33.1 + - - +
266A THR* 3.8 7.0 - - - +
267A LEU 3.3 0.2 - - - -
268A HIS* 1.3 92.3 - - - +
270A LEU* 1.3 58.0 + - + +
272A ASN* 3.4 7.2 + - - +
273A MET* 3.0 30.0 + - - +
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Residues in contact with LEU 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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145A CYS* 5.3 4.3 - - + -
206A LYS* 3.7 37.4 - - + +
209A GLY* 4.1 19.2 - - - +
210A ILE 4.0 6.7 - - - +
211A CYS* 3.4 49.1 - - - +
266A THR* 3.3 15.5 + - + +
267A LEU* 3.8 8.3 - - - +
268A HIS 3.3 0.2 - - - -
269A ASN* 1.3 75.6 - - + +
271A LYS* 1.3 65.2 + - - +
273A MET* 3.9 6.4 - - + +
274A ALA* 3.1 25.8 + - - +
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Residues in contact with LYS 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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209A GLY* 4.8 6.0 - - - +
267A LEU 3.0 14.3 + - - +
268A HIS* 3.3 20.4 - - + +
269A ASN 3.2 0.2 - - - -
270A LEU* 1.3 78.6 - - - +
272A ASN* 1.3 66.5 + - - +
274A ALA* 3.7 4.4 - - - +
275A GLN* 2.9 46.1 + - + +
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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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268A HIS* 3.0 48.4 + - - +
269A ASN* 3.8 7.3 + - - +
271A LYS* 1.3 84.3 - - - +
273A MET* 1.3 60.8 + - - +
275A GLN* 3.2 9.3 + - - -
276A PHE* 2.8 66.0 + - + -
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Residues in contact with MET 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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138A ILE* 4.5 2.5 - - + -
139A PRO* 3.8 40.2 - - + +
206A LYS* 3.5 30.5 - - - +
269A ASN 3.0 18.2 + - - +
270A LEU* 3.9 8.5 - - + +
272A ASN* 1.3 76.3 - - - +
274A ALA* 1.3 57.5 + - - +
276A PHE* 4.0 3.3 - - - +
277A SER* 2.6 34.0 + - - -
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TYR* 5.1 2.1 + - - -
136A CYS* 4.5 2.6 - - - -
138A ILE* 3.7 11.9 - - + +
206A LYS 3.9 11.7 - - - +
207A GLU 3.6 25.5 - - - +
208A ALA 5.1 0.4 - - - -
209A GLY* 4.3 6.1 - - - +
270A LEU 3.1 18.4 + - - +
271A LYS* 3.7 3.8 - - - +
273A MET* 1.3 78.2 - - - +
275A GLN* 1.3 62.5 + - - +
277A SER* 3.3 14.9 + - - -
278A VAL* 3.6 11.4 - - - +
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Residues in contact with GLN 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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125A TYR* 6.0 0.4 - - - -
271A LYS* 2.9 36.9 + - + +
272A ASN* 3.6 10.3 + - - +
274A ALA* 1.3 77.3 - - - +
276A PHE* 1.3 86.1 + - + +
277A SER 3.2 3.8 + - - -
278A VAL* 3.3 22.7 + - - +
280A LEU* 5.6 1.6 - - - +
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Residues in contact with PHE 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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272A ASN* 2.8 57.3 + - + +
273A MET* 4.0 3.8 - - - +
275A GLN* 1.3 96.6 - - + +
277A SER* 1.3 57.4 + - - +
278A VAL 3.2 8.7 + - - +
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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