Contacts of the strand formed by residues 250 - 262 (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 ASP 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A LYS* 5.5 1.9 - - - +
244A THR* 3.8 3.7 - - - +
245A LYS* 4.7 18.3 + - - +
249A TYR* 1.3 74.7 - - - +
251A VAL* 1.3 77.8 + - - +
275A VAL* 3.3 6.2 - - - +
276A PHE* 2.7 49.9 + - + +
277A LYS 4.9 3.8 - - - +
278A SER 4.4 3.8 + - - +
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Residues in contact with VAL 251 (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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237A PHE* 4.0 21.9 - - + -
240A PHE* 3.9 14.1 - - + -
241A LYS* 3.8 41.2 - - + +
244A THR* 3.9 15.9 - - + -
245A LYS* 5.9 0.2 - - + -
250A ASP* 1.3 90.6 + - - +
252A GLU* 1.3 63.8 + - - +
273A LEU* 3.8 26.0 - - + -
274A ARG 3.2 11.4 - - - +
275A VAL* 4.0 4.7 - - + -
276A PHE* 4.7 2.0 - - - -
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Residues in contact with GLU 252 (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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237A PHE* 5.0 0.2 - - - -
251A VAL* 1.3 75.9 - - - +
253A LYS* 1.3 64.9 + - - +
254A LEU* 3.7 20.7 + - + +
273A LEU* 3.4 2.6 - - - -
274A ARG* 2.6 42.7 + - + +
276A PHE* 4.0 24.1 - - + -
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Residues in contact with LYS 253 (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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233A PRO* 4.9 6.3 + - - +
237A PHE* 3.9 44.6 - - + +
252A GLU* 1.3 77.4 - - - +
254A LEU* 1.3 64.2 + - - +
255A ASN 3.9 19.7 - - - +
256A GLU* 2.8 31.3 + - + +
271A LEU* 4.1 14.8 - - + -
273A LEU* 3.7 15.3 - - + -
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Residues in contact with LEU 254 (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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220A ILE* 4.4 21.5 - - + -
252A GLU* 4.2 29.2 - - + +
253A LYS* 1.3 79.2 - - - +
255A ASN* 1.3 60.6 + - + +
272A ASP* 2.8 29.3 + - + +
273A LEU 4.7 0.2 - - - -
274A ARG* 4.3 35.7 - - + +
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Residues in contact with ASN 255 (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* 4.0 6.3 - - - +
253A LYS* 3.7 9.9 - - - +
254A LEU* 1.3 81.7 - - + +
256A GLU* 1.3 73.5 + - - +
257A LEU* 3.9 27.7 - - - +
271A LEU* 3.4 2.6 - - - -
272A ASP* 2.9 49.8 + - + +
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Residues in contact with GLU 256 (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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232A MSE 4.7 8.2 - - - +
233A PRO* 4.7 11.0 - - - +
235A GLU 4.7 1.6 - - - +
236A PRO* 3.8 14.7 - - - +
237A PHE* 5.1 0.7 - - - +
253A LYS* 2.8 36.9 + - - +
255A ASN* 1.3 81.8 + - - +
257A LEU* 1.3 79.9 + - - +
258A LYS* 6.1 1.1 - - + -
269A VAL* 3.9 13.0 - - + +
270A VAL 3.5 11.7 - - - +
271A LEU* 3.5 26.7 - - + +
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Residues in contact with LEU 257 (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* 4.3 5.2 - - - +
118A ARG* 3.5 43.5 - - - +
255A ASN* 3.9 19.7 - - - +
256A GLU* 1.3 85.0 - - - +
258A LYS* 1.3 67.4 + - - +
259A ILE* 5.3 1.6 - - + -
269A VAL* 3.3 5.0 - - - +
270A VAL* 2.8 42.4 + - + +
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Residues in contact with LYS 258 (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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232A MSE 4.2 23.3 - - + -
256A GLU* 6.1 1.3 - - + -
257A LEU* 1.3 78.0 - - - +
259A ILE* 1.3 63.6 + - - +
267A TRP* 3.7 50.0 - - + -
268A HIS 4.0 4.0 - - - -
269A VAL* 4.1 5.4 - - + -
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Residues in contact with ILE 259 (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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111A ALA 5.7 1.5 - - - +
112A ASN* 3.4 39.2 - - + +
115A GLU* 3.9 19.7 - - + +
224A HIS* 3.8 14.6 - - + -
257A LEU* 4.9 2.0 - - + -
258A LYS* 1.3 78.1 - - - +
260A LYS* 1.3 61.2 + - + +
267A TRP* 5.0 1.8 - - - -
268A HIS* 2.7 45.6 + - + +
270A VAL* 3.8 32.5 - - + +
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Residues in contact with LYS 260 (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 SER* 5.7 5.2 - - - -
111A ALA* 4.9 16.6 - - + -
112A ASN* 4.7 13.2 - - - +
258A LYS 3.9 0.2 - - - -
259A ILE* 1.3 85.0 - - + +
261A ARG* 1.3 69.9 + - - +
262A TYR* 3.1 53.5 + - + +
267A TRP* 3.5 11.5 - - - -
268A HIS* 2.8 35.8 + - + +
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Residues in contact with ARG 261 (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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229A GLU* 2.3 40.6 + - - +
260A LYS* 1.3 84.4 + - - +
262A TYR* 1.3 72.6 + - - +
263A ALA* 5.1 0.8 - - - +
264A PRO 3.3 26.5 + - - -
265A GLY* 3.8 1.5 - - - -
266A VAL 3.4 8.7 - - - +
267A TRP* 3.5 42.0 - - + +
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Residues in contact with TYR 262 (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* 5.3 3.3 + - - -
226A THR* 6.1 1.3 - - + -
260A LYS* 3.1 63.4 - - + +
261A ARG* 1.3 80.3 - - - +
263A ALA* 1.3 69.1 + - - +
264A PRO 3.4 1.6 - - - -
265A GLY* 3.1 4.2 + - - -
266A VAL* 2.8 50.5 + - + +
267A TRP 5.3 0.2 - - - -
268A HIS* 4.1 20.9 + - + -
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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