Contacts of the strand formed by residues 283 - 291 (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 TRP 283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C GLU* 4.2 12.1 - - - +
273D PHE* 4.1 15.7 - - + -
274D LYS* 3.2 30.7 - - - -
275D ARG* 3.4 53.7 - - + +
282D THR* 1.4 80.0 + - - +
284D SER* 1.4 59.2 + - - +
325D ARG* 3.2 60.2 - - + +
328D CYS* 5.5 0.2 - - + -
339D LEU* 3.7 25.6 - - + -
340D LEU* 4.7 2.0 - - - -
341D GLN* 3.4 34.1 - - + -
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Residues in contact with SER 284 (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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273D PHE* 3.8 8.8 - - - -
274D LYS* 2.8 49.8 + - - +
276D ALA* 5.1 8.3 - - - -
282D THR 3.8 4.5 + - - -
283D TRP* 1.4 77.2 - - - +
285D ARG* 1.4 60.8 + - - +
286D ARG* 3.5 26.3 + - - +
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Residues in contact with ARG 285 (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* 3.8 26.1 - - - +
163C ARG* 5.1 3.2 - - - +
254D GLU* 4.7 3.4 + - - -
271D HIS* 3.5 44.2 + - + +
272D LEU* 3.4 10.4 - - - +
273D PHE* 3.0 49.9 - - + +
284D SER* 1.4 73.7 + - - +
286D ARG* 1.3 90.5 + - - +
341D GLN 5.3 0.6 + - - -
342D ALA* 5.7 0.2 - - - +
343D ASP* 2.5 46.0 + - - -
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Residues in contact with ARG 286 (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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271D HIS* 3.7 5.1 - - - +
272D LEU 2.9 32.4 + - - +
274D LYS* 4.4 14.8 - - + +
284D SER* 3.5 19.7 + - - +
285D ARG* 1.3 99.6 + - - +
287D TRP* 1.4 60.8 + - - +
288D PHE* 3.3 15.6 - - + -
297D TYR* 3.8 30.7 - - + -
298D GLN 3.8 16.0 + - - -
299D LYS* 4.8 10.8 + - - +
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Residues in contact with TRP 287 (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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12C LYS* 5.5 11.0 - - + -
14C SER* 4.3 17.0 - - - -
15C PRO* 3.4 34.5 - - + -
269D GLU* 3.5 39.7 - - + +
270D GLY* 3.8 20.9 - - - -
271D HIS* 3.5 39.5 - + - +
286D ARG* 1.4 75.3 - - - +
288D PHE* 1.3 60.1 + - - +
289D THR* 4.0 11.9 + - - -
297D TYR* 3.6 0.9 - - - -
298D GLN* 2.9 60.4 + - + +
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Residues in contact with PHE 288 (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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269D GLU* 3.2 3.1 - - - -
270D GLY 2.8 36.0 + - - +
272D LEU* 3.5 46.9 - - + -
274D LYS* 4.3 20.4 - - + -
286D ARG* 3.3 25.8 - - + -
287D TRP* 1.3 72.8 - - - +
289D THR* 1.4 62.0 + - - +
295D LEU* 3.9 23.3 - - + -
296D VAL 3.5 8.3 - - - -
297D TYR* 3.5 26.2 - - + -
308D VAL* 3.7 15.9 - - + -
338D CYS* 5.1 1.3 - - - -
340D LEU* 3.4 22.2 - - + -
351D TRP* 3.6 9.1 - - + -
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Residues in contact with THR 289 (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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267D VAL* 4.9 6.5 - - + -
268D MET 3.5 6.7 - - - +
269D GLU* 3.4 18.3 - - + +
287D TRP* 4.0 9.8 + - - -
288D PHE* 1.4 73.0 - - - +
290D ILE* 1.4 67.5 + - - +
291D GLN* 3.3 35.2 + - + +
294D GLN 3.9 0.7 - - - +
295D LEU* 3.6 4.4 - - - -
296D VAL* 3.0 45.0 + - - +
298D GLN* 6.1 0.2 - - - +
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Residues in contact with ILE 290 (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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259D LEU* 5.2 2.2 - - + -
266D LEU 4.7 7.6 - - - +
267D VAL* 3.5 9.9 - - - +
268D MET* 2.8 42.4 + - + +
289D THR* 1.4 72.1 - - - +
291D GLN* 1.3 65.2 + - - +
293D ASN 5.8 0.7 - - - +
294D GLN 3.4 4.7 - - - -
295D LEU* 3.8 9.2 - - + -
312D LEU* 3.7 27.6 - - + -
351D TRP* 3.7 34.1 - - + -
354D ALA* 3.6 34.3 - - + +
355D VAL* 4.7 6.3 - - + +
358D SER* 3.8 13.2 - - - +
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Residues in contact with GLN 291 (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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266D LEU 4.6 6.5 - - - -
267D VAL* 4.6 13.5 - - + -
289D THR* 3.3 27.4 - - + +
290D ILE* 1.3 75.6 - - - +
292D SER* 1.3 69.9 + - - +
293D ASN 3.3 2.9 - - - -
294D GLN* 3.1 23.2 + - + +
296D VAL* 4.6 16.7 - - + +
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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