Contacts of the strand formed by residues 266 - 276 (chain A) in PDB entry 3K6R
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 VAL 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A THR* 3.9 25.1 - - + -
227A VAL 3.3 8.1 - - - +
228A PRO* 4.1 17.5 - - + -
260A LYS 4.0 0.3 - - - +
261A ARG* 3.4 3.1 - - - +
262A TYR* 2.8 58.8 + - + +
263A ALA 4.3 4.7 - - - +
264A PRO* 4.4 9.9 - - + -
265A GLY* 1.3 84.2 - - - +
267A TRP* 1.3 62.8 + - - +
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Residues in contact with TRP 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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225A ASN 3.4 1.4 - - - +
226A THR* 3.2 6.5 - - - -
227A VAL* 2.7 38.8 + - + +
229A GLU* 3.1 41.3 + - + +
232A MSE 3.5 28.0 - - + -
258A LYS* 3.7 51.8 - - + +
259A ILE 5.0 1.1 - - - -
260A LYS* 3.5 23.6 - - - -
261A ARG* 3.5 36.8 - - + +
262A TYR* 5.3 0.2 - - - -
266A VAL* 1.3 77.2 - - - +
268A HIS* 1.3 60.1 + - - +
269A VAL* 3.5 11.0 + - + -
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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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112A ASN* 4.0 22.9 + - - -
201A VAL* 3.6 30.2 - - + +
224A HIS* 3.0 30.1 + + + -
225A ASN 3.4 6.5 - - - -
226A THR* 4.5 4.5 - - - +
258A LYS* 4.0 0.3 - - - -
259A ILE* 2.7 49.3 + - + +
260A LYS* 2.8 21.3 + - - +
262A TYR* 4.1 21.0 + - + -
266A VAL 4.2 0.2 + - - -
267A TRP* 1.3 72.8 - - - +
269A VAL* 1.3 68.5 + - - +
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Residues in contact with VAL 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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223A TYR 3.9 0.2 - - - +
224A HIS* 3.3 4.0 - - - -
225A ASN 3.0 40.1 + - - +
227A VAL* 4.1 7.9 - - + -
232A MSE 4.0 19.3 - - + -
236A PRO* 3.9 16.4 - - + -
256A GLU* 3.9 13.2 - - - +
257A LEU 3.3 13.0 - - - +
258A LYS* 4.1 8.3 - - + -
259A ILE* 4.2 1.6 - - - +
267A TRP* 3.9 20.4 - - + -
268A HIS* 1.3 83.5 - - - +
270A VAL* 1.3 59.8 + - - +
271A LEU* 3.7 21.1 - - + -
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Residues in contact with VAL 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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115A GLU* 3.7 23.6 - - - +
118A ARG* 3.8 21.8 - - - +
222A HIS* 4.2 3.8 - - + -
223A TYR 3.5 6.7 - - - +
224A HIS* 3.5 34.1 - - + +
256A GLU* 3.5 3.3 - - - +
257A LEU* 2.8 51.7 + - + +
259A ILE* 3.8 13.4 - - + +
269A VAL* 1.3 74.2 - - - +
271A LEU* 1.3 73.2 + - - +
272A ASP* 4.1 2.9 - - - +
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Residues in contact with LEU 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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221A ILE 3.4 2.9 - - - +
222A HIS* 3.5 2.1 - - - -
223A TYR* 2.8 44.1 + - + +
236A PRO* 3.6 20.6 - - + -
237A PHE* 3.8 39.7 - - + +
240A PHE* 5.6 0.2 - - + -
253A LYS* 4.1 7.4 - - + -
255A ASN 3.4 5.8 - - - +
256A GLU* 3.5 37.9 - - + +
269A VAL* 3.7 8.5 - - + -
270A VAL* 1.3 78.1 - - - +
272A ASP* 1.3 62.2 + - - +
273A LEU* 3.8 25.0 + - + -
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Residues in contact with ASP 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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118A ARG* 2.8 36.0 + - - -
122A VAL* 5.7 0.2 - - - +
220A ILE* 4.8 2.5 - - + -
221A ILE 3.5 4.0 - - - -
222A HIS* 2.6 36.3 + - + +
253A LYS 3.7 0.9 - - - -
254A LEU* 2.8 44.9 + - + +
255A ASN* 2.9 32.6 + - + +
270A VAL* 4.1 1.4 - - - +
271A LEU* 1.3 74.2 - - - +
273A LEU* 1.3 56.4 + - - +
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Residues in contact with LEU 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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219A ALA 3.6 0.7 - - - +
220A ILE* 3.2 5.2 - - - +
221A ILE* 2.8 44.6 + - + +
223A TYR* 3.8 19.1 - - + -
237A PHE* 3.6 32.8 - - + -
240A PHE* 3.7 44.4 - - + -
251A VAL* 3.8 10.3 - - + -
252A GLU 3.4 2.2 - - - +
253A LYS* 3.7 21.1 - - + -
254A LEU* 4.7 3.4 - - - -
271A LEU* 4.0 18.8 - - + +
272A ASP* 1.3 77.7 - - - +
274A ARG* 1.3 61.5 + - - +
275A VAL* 4.2 1.3 + - + -
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Residues in contact with ARG 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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218A GLY* 3.0 37.7 + - - +
219A ALA 3.3 5.6 - - - +
220A ILE* 3.6 27.8 - - + +
251A VAL* 3.2 3.5 - - - -
252A GLU* 2.6 46.3 + - + +
254A LEU* 4.3 28.6 - - + +
273A LEU* 1.3 74.1 - - - +
275A VAL* 1.3 61.1 + - - +
276A PHE* 3.4 35.1 - - + -
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Residues in contact with VAL 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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212A LEU* 3.9 26.9 - - + -
215A ALA* 4.0 27.1 - - + -
216A LYS 4.4 2.2 - - - +
217A ASP* 4.3 0.4 - - - -
218A GLY* 2.8 35.5 + - - -
219A ALA* 3.0 15.8 + - + +
221A ILE* 3.9 20.2 - - + -
240A PHE* 4.2 7.2 - - + -
244A THR* 4.9 0.4 - - + -
249A TYR* 4.6 5.8 - - + -
250A ASP 3.3 7.0 - - - +
251A VAL* 4.0 17.3 - - + -
273A LEU 5.0 1.3 - - - +
274A ARG* 1.3 77.4 - - - +
276A PHE* 1.3 59.7 + - - +
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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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217A ASP* 3.2 18.2 - - - +
218A GLY* 4.1 10.5 - - - +
249A TYR* 3.3 9.6 - - - -
250A ASP* 2.7 52.5 + - + +
251A VAL 4.7 0.7 - - - -
252A GLU* 4.0 26.0 - - + -
274A ARG* 3.4 50.7 - - + -
275A VAL* 1.3 78.1 - - - +
277A LYS* 1.3 63.4 + - - +
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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