Contacts of the helix formed by residues 284 - 296 (chain D) in PDB entry 5YWB
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 ALA 284 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D GLY* 1.3 72.1 - - - -
285D ARG* 1.3 65.8 + - + +
287D ILE* 3.3 18.9 - - - +
288D TRP* 3.6 7.3 + - - +
607D VAL* 4.2 6.7 - - + +
608D GLN* 4.9 17.5 - - + -
611D SER* 3.3 27.5 + - - +
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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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283D GLY* 3.4 0.8 - - - -
284D ALA* 1.3 78.8 - - + +
286D ALA* 1.3 65.8 + - - +
288D TRP* 3.2 8.1 + - - +
289D ARG* 3.0 23.3 + - - +
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Residues in contact with ALA 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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270D PHE* 5.6 5.8 - - + -
273D GLN* 3.7 27.9 - - + +
274D ALA* 6.2 1.3 - - - -
283D GLY* 3.4 20.0 + - - +
284D ALA 3.3 0.8 - - - -
285D ARG* 1.3 79.2 - - - +
287D ILE* 1.3 60.1 + - + +
289D ARG* 3.2 7.1 + - - +
290D ALA* 2.9 27.8 + - - +
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Residues in contact with ILE 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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270D PHE* 3.6 31.0 - - + -
283D GLY 3.6 13.4 + - - +
284D ALA 3.3 12.3 - - - +
286D ALA* 1.3 75.8 - - + +
288D TRP* 1.3 60.9 + - - +
290D ALA* 3.2 8.9 + - - +
291D LEU* 2.9 49.6 + - + +
394D LYS* 5.3 4.0 - - - +
607D VAL* 3.5 26.5 - - + +
610D LEU* 5.2 13.2 - - + -
611D SER* 3.4 17.3 - - - +
614D LEU* 5.2 9.9 - - + -
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Residues in contact with TRP 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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284D ALA 3.6 6.5 + - - +
285D ARG* 3.2 11.8 + - - +
286D ALA 3.2 0.6 - - - -
287D ILE* 1.3 82.2 - - - +
289D ARG* 1.3 66.3 + - - +
291D LEU* 3.2 12.0 + - + +
292D CYS* 3.0 36.0 + - - +
428D LEU* 5.8 1.6 - - + -
431D PHE* 4.3 29.4 - + - -
432D PHE* 6.1 2.2 - - - -
600D THR 5.3 0.9 - - - -
603D ALA* 4.0 7.6 - - + -
604D LEU* 3.8 42.6 - - + -
607D VAL* 3.3 44.0 - - + -
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Residues in contact with ARG 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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273D GLN* 3.6 22.2 - - - +
285D ARG 3.0 12.7 + - - +
286D ALA* 3.2 8.7 + - - +
288D TRP* 1.3 77.1 - - - +
290D ALA* 1.3 57.7 + - - +
292D CYS* 3.4 6.1 + - - +
293D HIS* 2.9 30.2 + - - +
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Residues in contact with ALA 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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266D LEU* 4.9 8.7 - - + -
269D ALA* 4.4 11.2 - - + +
270D PHE* 4.4 29.8 - - + +
273D GLN* 4.4 7.3 + - + -
286D ALA 2.9 13.8 + - - +
287D ILE* 3.5 12.6 - - - +
288D TRP 3.2 0.2 - - - -
289D ARG* 1.3 77.0 - - - +
291D LEU* 1.3 58.1 + - - +
293D HIS* 3.5 6.5 - - - +
294D ALA* 2.8 32.2 + - - +
394D LYS* 6.0 0.2 - - - +
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Residues in contact with LEU 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* 3.8 24.2 - - + -
287D ILE* 2.9 37.5 + - + +
288D TRP* 3.2 14.3 + - + +
290D ALA* 1.3 75.7 - - - +
292D CYS* 1.3 63.5 + - - +
294D ALA* 3.1 13.4 + - - +
295D PHE* 2.9 34.8 + - + -
387D LEU* 3.9 27.4 - - + -
391D ILE* 4.1 14.1 - - + -
428D LEU* 5.2 7.9 - - + -
432D PHE* 5.3 5.2 - - + -
607D VAL* 4.8 11.9 - - + -
610D LEU* 6.4 0.7 - - + -
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Residues in contact with CYS 292 (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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288D TRP* 3.0 30.2 + - + +
289D ARG* 3.8 5.8 - - - +
291D LEU* 1.3 76.1 - - - +
293D HIS* 1.3 61.6 + - - +
295D PHE* 4.5 5.1 - - - +
296D GLY* 3.3 18.9 + - - -
299D LEU* 5.2 15.0 - - - +
432D PHE* 5.3 8.5 - - - -
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Residues in contact with HIS 293 (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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265D ARG* 6.4 1.8 - - + -
269D ALA* 4.1 19.7 - - + +
273D GLN* 6.0 1.1 - - - +
289D ARG 2.9 17.8 + - - +
290D ALA* 3.5 8.1 - - - +
292D CYS* 1.3 78.8 - - - +
294D ALA* 1.3 68.1 + - - +
296D GLY* 3.4 11.8 + - - -
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Residues in contact with ALA 294 (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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265D ARG* 3.8 35.9 + - + +
266D LEU* 4.7 16.4 - - + -
269D ALA* 4.9 5.6 - - + -
290D ALA 2.8 17.8 + - - +
291D LEU* 3.1 6.0 + - - +
293D HIS* 1.3 82.1 - - - +
295D PHE* 1.3 74.3 + - + +
296D GLY* 4.3 0.2 - - - -
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Residues in contact with PHE 295 (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* 6.4 0.2 - - + -
291D LEU* 2.9 35.9 + - + +
292D CYS* 4.5 2.2 - - - +
294D ALA* 1.3 82.3 - - + +
296D GLY* 1.3 66.3 + - - +
297D ARG 3.3 2.6 + - - -
298D ARG* 3.5 17.9 + - - +
299D LEU* 4.4 7.6 - - + -
383D THR* 3.3 32.3 - - + +
386D ASN* 4.4 6.3 - - + -
387D LEU* 2.9 64.6 - - + -
390D ALA* 6.0 0.9 - - + -
432D PHE* 3.2 35.2 - + + -
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Residues in contact with GLY 296 (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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292D CYS 3.3 13.1 + - - -
293D HIS 3.6 12.8 - - - -
294D ALA 3.3 1.4 - - - -
295D PHE* 1.3 78.8 - - - +
297D ARG* 1.3 59.5 + - - -
299D LEU* 3.0 8.8 + - - +
300D ILE* 2.9 36.2 + - - +
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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