Contacts of the helix formed by residues 290 - 302 (chain D) in PDB entry 4UX9
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 LYS 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D HIS* 3.8 5.6 - - - -
283D ASP* 3.5 16.6 - - + +
287D ASN 4.7 5.4 - - - +
288D LYS* 3.3 30.2 + - - +
289D LEU* 1.3 75.6 - - - +
291D ALA* 1.3 65.1 + - - +
292D SER* 3.8 21.6 + - - +
293D GLN* 3.2 42.5 + - + +
294D ALA 3.2 9.4 + - - -
320D TYR* 3.7 7.5 - - - -
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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
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125D HIS* 3.8 6.4 + - - -
277D ASP* 3.5 26.5 - - + +
280D PHE* 3.8 36.3 - - + -
281D PRO 5.0 0.7 - - - +
283D ASP* 3.0 25.5 + - - +
290D LYS* 1.3 70.1 - - - +
292D SER* 1.4 57.1 + - - +
294D ALA* 3.5 3.5 + - - +
295D ARG* 2.9 31.2 + - - +
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Residues in contact with SER 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ASP* 4.8 0.6 + - - -
283D ASP* 5.3 0.4 + - - -
290D LYS* 3.8 23.5 + - - +
291D ALA* 1.4 77.2 - - - +
293D GLN* 1.4 62.9 + - - +
295D ARG* 3.7 21.3 - - - +
296D ASP* 3.1 26.9 + - - +
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Residues in contact with GLN 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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288D LYS* 3.0 26.1 + - - +
289D LEU* 3.6 5.4 - - - -
290D LYS* 3.2 45.8 + - + +
292D SER* 1.4 75.0 + - - +
294D ALA* 1.4 61.4 + - - +
296D ASP* 3.4 5.5 + - - -
297D LEU* 3.0 23.9 + - - +
318D HIS* 3.1 20.0 - - + -
319D PRO* 3.9 32.5 + - + +
320D TYR* 4.1 14.6 - - + +
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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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125D HIS* 4.9 0.4 - - + -
128D MET* 5.8 0.7 - - - -
215D MET* 3.3 22.0 - - + +
280D PHE* 3.5 28.0 - - + -
290D LYS 3.2 5.5 + - - +
291D ALA* 3.6 4.9 - - - +
293D GLN* 1.4 77.4 - - - +
295D ARG* 1.4 55.7 + - - +
297D LEU* 3.3 2.0 + - - +
298D LEU* 3.1 25.1 + - - +
320D TYR* 3.7 36.9 - - + +
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Residues in contact with ARG 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D PHE* 3.6 29.5 - - + +
272D GLU* 3.7 37.2 + - - +
275D PHE* 2.9 31.9 + - + +
276D PRO* 3.6 2.4 - - - +
277D ASP* 2.7 42.4 + - - +
280D PHE* 3.9 16.9 - - + -
291D ALA* 2.9 17.2 + - - +
292D SER* 3.7 24.0 - - - +
294D ALA* 1.4 71.0 - - - +
296D ASP* 1.3 60.4 + - - +
298D LEU* 3.3 7.6 + - - +
299D SER* 2.9 28.9 + - - -
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Residues in contact with ASP 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 SER 3.1 20.5 + - - +
293D GLN* 3.5 8.1 - - - +
294D ALA 3.4 0.2 - - - -
295D ARG* 1.3 76.6 - - - +
297D LEU* 1.3 58.8 + - - +
299D SER* 2.6 25.6 + - - -
300D LYS* 2.8 42.4 + - - +
318D HIS* 2.8 17.6 + - - +
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Residues in contact with LEU 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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132D LEU* 5.2 0.9 - - + -
136D LEU* 5.4 0.9 - - + -
215D MET* 4.2 21.5 - - + -
293D GLN 3.0 15.9 + - - +
294D ALA* 3.7 4.7 - - - +
295D ARG 3.3 0.2 - - - -
296D ASP* 1.3 71.7 - - - +
298D LEU* 1.3 66.4 + - - +
300D LYS* 3.1 14.6 + - - +
301D MET* 3.1 39.7 + - + +
310D ILE* 4.2 8.7 - - + -
315D ALA* 4.1 14.1 - - + -
318D HIS* 3.7 34.0 + - + +
320D TYR* 4.5 7.9 - - + -
321D ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 298 (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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212D GLY* 3.4 28.0 - - - +
215D MET* 3.8 21.7 - - + -
216D GLY* 3.7 15.7 - - - +
219D VAL* 4.7 1.8 - - + -
271D PHE* 4.0 2.2 - - + -
275D PHE* 3.8 40.2 - - + -
280D PHE* 4.0 18.8 - - + -
294D ALA 3.1 17.0 + - - +
295D ARG* 3.4 8.7 - - - +
297D LEU* 1.3 76.1 - - - +
299D SER* 1.3 52.4 + - - +
301D MET* 3.1 5.0 + - - -
302D LEU* 2.8 51.7 + - + +
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Residues in contact with SER 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D PHE* 3.6 42.7 - - - -
295D ARG 2.9 13.6 + - - -
296D ASP* 2.6 29.4 + - - -
298D LEU* 1.3 75.7 - - - +
300D LYS* 1.4 60.6 + - - +
301D MET 3.5 0.2 - - - -
302D LEU 4.3 0.2 - - - -
303D VAL* 3.2 19.7 - - - +
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Residues in contact with LYS 300 (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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296D ASP* 2.8 41.0 + - - +
297D LEU 3.1 8.8 + - - +
299D SER* 1.4 81.4 + - - +
301D MET* 1.3 58.7 + - - +
303D VAL* 3.9 5.9 - - - +
308D LYS 4.9 0.6 - - - +
309D ARG* 3.6 7.8 - - - +
310D ILE* 3.0 60.7 + - + +
318D HIS* 4.2 11.6 + - + -
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Residues in contact with MET 301 (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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132D LEU* 6.1 0.2 - - + -
136D LEU* 4.2 10.8 - - + -
208D LEU* 3.7 28.7 - - + +
209D TRP* 3.7 9.5 - - - -
211D VAL* 3.6 28.5 - - + -
212D GLY* 3.8 26.0 - - - -
215D MET* 4.4 11.7 - - - +
297D LEU* 3.1 41.7 + - + +
298D LEU* 3.1 8.3 + - - +
300D LYS* 1.3 77.6 - - - +
302D LEU* 1.3 57.2 + - - +
303D VAL 3.1 10.4 + - - -
309D ARG* 3.3 24.4 + - - -
310D ILE* 3.9 14.6 - - + -
315D ALA* 4.4 1.6 - - + -
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Residues in contact with LEU 302 (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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209D TRP* 3.8 18.4 - - + +
212D GLY* 3.8 25.8 - - - -
213D CYS* 3.9 8.5 - - - +
224D LEU* 3.7 20.4 - - + -
225D PHE* 3.9 26.9 - - + -
241D LEU* 3.5 21.5 - - + +
271D PHE* 3.6 35.4 - - + -
274D LEU* 6.3 0.2 - - + -
275D PHE* 3.9 6.7 - - + -
298D LEU* 2.8 32.9 + - + +
301D MET* 1.3 71.2 - - - +
303D VAL* 1.3 62.5 + - - +
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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