Contacts of the helix formed by residues 288 - 297 (chain D) in PDB entry 4DVQ
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 GLY 288 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D MET* 4.2 4.2 - - - +
202D LEU 4.4 1.6 - - - -
203D ALA 3.2 14.4 - - - -
204D LEU 4.1 2.7 - - - -
286D TYR* 3.4 33.7 - - - -
287D THR* 1.3 78.8 + - - +
289D ILE* 1.3 67.0 + - - +
290D VAL 3.5 2.0 - - - -
291D ALA* 3.6 4.4 + - - +
292D GLU* 3.5 14.6 + - - +
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Residues in contact with ILE 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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147D ASP* 3.6 24.6 - - + +
148D VAL* 3.8 29.6 - - + +
157D PHE* 3.9 22.4 - - + -
203D ALA* 2.8 22.5 + - + +
204D LEU* 3.5 26.7 + - + +
286D TYR* 3.5 15.9 - - - +
288D GLY* 1.3 68.9 - - - -
290D VAL* 1.3 70.6 + - - +
292D GLU* 3.2 17.8 + - - +
293D LEU* 3.3 14.7 + - + +
311D LEU* 4.6 3.8 - - + -
455D LEU* 4.2 16.4 - - + -
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 2.8 40.9 + - + +
205D PHE* 3.6 31.9 - - + -
271D ILE* 4.2 7.6 - - + -
274D ILE* 4.4 2.7 - - + -
289D ILE* 1.3 73.0 - - + +
291D ALA* 1.3 63.0 + - - +
293D LEU* 3.0 21.1 + - + +
294D LEU* 3.1 30.1 + - + +
304D ILE* 4.3 4.3 - - + -
308D SER* 3.6 28.5 - - - +
311D LEU* 5.2 1.3 - - + -
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Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ILE* 3.7 22.4 - - + +
278D LEU* 4.0 17.3 - - + -
287D THR* 3.5 28.0 - - - +
288D GLY 3.6 9.1 + - - +
289D ILE 3.1 0.8 - - - -
290D VAL* 1.3 76.6 - - - +
292D GLU* 1.3 54.3 + - + +
294D LEU* 2.9 2.6 + - - +
295D LEU* 2.7 46.3 + - + +
181F ARG* 4.4 0.2 - - - +
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Residues in contact with GLU 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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147D ASP* 3.6 29.0 - - + +
156D ARG* 4.2 11.4 + - - -
285D HIS 5.3 1.9 - - - +
286D TYR* 3.9 31.0 - - + -
287D THR 5.5 0.5 + - - -
288D GLY 3.5 11.3 + - - +
289D ILE* 3.2 8.6 + - - +
291D ALA* 1.3 78.1 - - - +
293D LEU* 1.3 62.7 + - - +
295D LEU* 4.0 15.1 - - - +
296D LYS* 3.1 47.7 + - - +
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Residues in contact with LEU 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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143D ARG 3.6 23.1 - - - +
144D LEU* 4.0 27.8 - - + +
147D ASP* 4.0 19.1 - - + +
148D VAL* 5.0 2.7 - - + -
289D ILE* 3.3 21.7 + - + +
290D VAL* 3.0 16.5 + - - +
292D GLU* 1.3 76.0 - - - +
294D LEU* 1.3 63.5 + - - +
296D LYS* 3.6 4.0 + - + +
297D ALA* 3.1 18.0 + - - -
298D GLU 4.6 1.4 + - - -
299D LEU* 4.9 7.4 + - + -
304D ILE* 3.3 36.5 - - + +
307D ASN* 5.5 1.8 - - + -
308D SER* 4.9 5.8 - - - +
311D LEU* 5.1 6.5 - - + -
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Residues in contact with LEU 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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271D ILE* 5.3 4.5 - - + -
274D ILE* 4.0 26.7 - - + -
275D TYR* 4.4 19.5 - - + -
278D LEU* 3.7 25.8 - - + -
282D ARG* 4.4 3.3 + - - -
290D VAL* 3.1 22.3 + - + +
291D ALA 2.9 5.5 + - - +
293D LEU* 1.3 74.6 - - - +
295D LEU* 1.3 69.7 + - - +
297D ALA* 3.3 16.5 + - - +
301D LEU* 4.2 19.3 - - + -
304D ILE* 3.5 32.0 - - + +
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Residues in contact with LEU 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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278D LEU* 4.1 22.4 - - + -
282D ARG* 3.2 67.9 + - + +
283D PRO* 4.4 23.1 - - + +
285D HIS 6.0 0.9 - - - +
291D ALA* 2.7 30.3 + - + +
292D GLU* 4.0 17.5 - - - +
294D LEU* 1.3 77.5 - - - +
296D LYS* 1.3 61.2 + - + +
297D ALA* 3.6 2.4 + - - +
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Residues in contact with LYS 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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146D PRO* 4.4 13.3 - - - +
147D ASP* 2.9 40.0 + - - +
292D GLU* 3.1 27.3 + - - +
293D LEU* 4.1 4.5 - - + +
295D LEU* 1.3 76.1 - - + +
297D ALA* 1.3 71.0 + - - +
298D GLU* 2.8 39.1 + - + +
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Residues in contact with ALA 297 (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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282D ARG* 5.8 1.3 - - - +
293D LEU 3.1 15.6 + - - -
294D LEU 3.3 12.6 + - - +
295D LEU 4.4 2.5 - - - +
296D LYS* 1.3 76.4 - - - +
298D GLU* 1.3 61.7 + - - +
299D LEU 3.3 14.0 + - - +
304D ILE* 5.0 2.5 - - + -
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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