Contacts of the strand formed by residues 266 - 275 (chain D) in PDB entry 4CKG
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 LEU 266 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259D LEU* 3.6 44.0 - - + +
260D ARG* 3.6 2.7 - - - -
261D GLU* 3.6 34.3 - - + +
265D GLY* 1.3 73.4 - - - +
267D VAL* 1.4 60.6 + - - +
290D ILE* 4.0 12.6 - - - +
291D GLN* 4.6 5.7 - - - -
292D SER 5.1 1.9 + - - -
357D SER* 4.6 20.4 - - - +
358D SER* 5.6 4.1 + - - +
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D SER 3.0 14.4 - - - +
259D LEU* 3.6 4.4 - - - -
260D ARG* 3.0 50.2 + - - +
262D GLY* 4.6 10.8 - - - -
263D PRO* 5.2 5.8 - - + -
264D GLY 6.2 0.4 - - - +
265D GLY 3.8 9.9 - - - +
266D LEU* 1.4 74.9 - - - +
268D MET* 1.4 67.1 - - - +
269D GLU* 4.1 7.6 - - - +
289D THR* 4.9 8.3 - - + -
290D ILE 3.5 12.3 - - - +
291D GLN* 4.6 12.3 - - + -
292D SER 5.9 0.2 - - - +
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Residues in contact with MET 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D PRO* 3.5 15.0 - - + -
258D SER 3.4 22.9 - - - +
259D LEU* 4.0 17.0 - - + -
260D ARG* 3.7 2.5 - - - +
267D VAL* 1.4 75.6 - - - +
269D GLU* 1.3 65.8 + - - +
288D PHE 4.1 0.2 - - - +
289D THR* 3.5 1.7 - - - +
290D ILE* 2.8 49.5 + - + +
350D LEU* 3.7 32.3 - - + +
351D TRP* 3.4 48.2 - - + +
354D ALA* 3.8 15.3 - - + -
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Residues in contact with GLU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PRO* 3.8 16.5 - - - +
258D SER 4.8 2.6 + - - +
260D ARG* 2.8 43.2 + - - -
267D VAL* 4.1 6.2 - - - +
268D MET* 1.3 77.0 - - - +
270D GLY* 1.3 59.5 + - - +
287D TRP* 3.5 30.3 - - + +
288D PHE 3.2 4.7 - - - -
289D THR* 3.4 28.0 - - + +
351D TRP* 4.2 3.6 - - - -
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Residues in contact with GLY 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D PRO* 4.4 8.3 - - - -
269D GLU* 1.3 77.8 - - - +
271D HIS* 1.4 66.5 - - - -
272D LEU 3.7 0.2 + - - -
287D TRP* 3.8 23.1 - - - -
288D PHE* 2.8 34.4 + - - +
351D TRP* 3.9 11.8 - - - -
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Residues in contact with HIS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LYS 5.2 2.4 + - - -
13C ASP* 3.2 26.4 + - - +
14C SER 5.0 0.2 - - - -
15C PRO* 3.7 18.4 - - + -
163C ARG* 6.0 3.1 - - - -
255D PRO* 5.8 7.9 - - + -
257D PRO* 5.4 1.5 - - - +
270D GLY* 1.4 73.4 - - - -
272D LEU* 1.4 71.6 + - - +
285D ARG* 3.5 39.9 + - + +
286D ARG 3.7 7.0 + - - +
287D TRP* 3.5 34.2 - + - +
342D ALA* 5.5 1.9 - - - +
343D ASP* 4.6 7.2 - - - +
347D LEU* 6.2 0.5 - - - +
351D TRP* 4.4 4.9 + - - -
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D GLY 3.7 2.4 + - - +
271D HIS* 1.4 83.4 - - - +
273D PHE* 1.3 62.9 + - - +
285D ARG* 3.4 9.4 - - - +
286D ARG 2.9 34.1 + - - +
288D PHE* 3.5 42.2 - - + -
295D LEU* 5.5 0.7 - - + -
329D PHE* 4.1 15.3 - - + -
340D LEU* 3.8 27.6 - - + -
341D GLN 4.0 10.8 - - - +
342D ALA* 4.3 6.3 - - + +
343D ASP* 5.9 0.2 - - - -
351D TRP* 3.9 44.9 - - + -
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Residues in contact with PHE 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 4.3 21.8 - - + -
139C THR* 5.0 4.9 - - - -
142C ALA* 3.9 28.0 - - + -
272D LEU* 1.3 74.3 - - - +
274D LYS* 1.4 59.8 + - - +
283D TRP* 4.1 13.2 - + + -
284D SER* 3.5 16.6 - - - -
285D ARG* 3.0 60.1 - - + +
325D ARG* 5.9 0.7 - - - -
340D LEU* 3.2 10.0 - - - +
341D GLN* 2.9 55.9 + - + +
342D ALA 5.5 2.2 - - - -
343D ASP* 4.2 6.5 - - - -
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Residues in contact with LYS 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D LEU 4.8 0.2 - - - +
273D PHE* 1.4 73.9 - - - +
275D ARG* 1.3 78.4 + - - +
276D ALA* 4.5 6.9 - - - +
277D SER* 5.6 3.2 + - - -
283D TRP* 3.2 14.3 - - - -
284D SER* 2.8 50.5 + - - +
286D ARG* 4.4 17.2 - - + +
288D PHE* 4.3 20.0 - - + -
297D TYR* 4.6 23.5 + - + -
338D CYS* 4.8 8.7 - - - -
339D LEU 4.0 15.3 - - - +
340D LEU* 4.3 10.5 - - + -
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Residues in contact with ARG 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D LYS* 1.3 88.8 + - - +
276D ALA* 1.4 65.6 + - - +
277D SER* 5.2 0.7 + - - -
280D PHE 4.2 4.9 + - - -
281D LYS* 2.9 42.9 + - + +
282D THR* 3.9 4.2 - - - +
283D TRP* 3.4 54.3 - - + +
284D SER 5.2 0.2 - - - -
339D LEU* 4.0 23.1 + - + +
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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