Contacts of the helix formed by residues 259 - 269 (chain D) in PDB entry 3SWD
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 259 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D ARG* 3.4 32.8 - - + +
233D ILE* 6.2 0.4 - - + -
235D THR* 3.6 35.0 - - + -
236D GLY* 4.6 3.8 - - - +
239D LEU* 4.7 5.4 - - + -
255D GLN 5.0 5.2 - - - +
256D PRO 2.9 8.9 + - - +
258D THR* 1.3 86.0 - - + +
260D ASP* 1.3 67.9 + - - +
261D ALA 3.3 2.0 - - - -
262D VAL* 3.2 30.6 + - + +
263D LEU* 2.9 31.6 + - + +
280D ILE* 3.8 15.5 - - + -
303D PRO* 6.1 1.8 - - + -
306D MET* 5.7 1.8 - - + -
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Residues in contact with ASP 260 (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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256D PRO 4.1 9.0 - - - +
257D ASP* 3.6 20.7 + - - +
258D THR 3.8 1.8 - - - -
259D LEU* 1.3 76.8 - - - +
261D ALA* 1.3 63.2 + - - +
263D LEU* 3.4 6.4 + - - +
264D ALA* 3.0 22.3 + - - +
267D ARG* 5.4 0.3 + - - -
299D HIS* 6.1 0.6 - - - -
300D PRO* 5.5 8.4 - - + +
155F HIS* 4.5 10.7 - - + -
157F VAL* 4.5 8.7 - - + +
183F GLU* 3.1 39.5 - - + +
212F ARG* 4.4 4.6 + - - -
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Residues in contact with ALA 261 (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 3.3 0.8 - - - -
260D ASP* 1.3 76.1 - - - +
262D VAL* 1.3 63.4 + - - +
264D ALA* 3.2 4.5 + - - +
265D LYS* 3.0 27.9 + - + +
300D PRO 3.7 17.3 + - - +
301D ALA* 3.8 3.6 - - - +
302D PHE* 3.7 36.6 - - + +
303D PRO* 5.0 1.3 - - + -
157F VAL* 4.2 17.4 - - + +
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Residues in contact with VAL 262 (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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236D GLY* 4.6 14.6 - - - +
239D LEU* 5.2 0.9 - - + -
259D LEU* 3.2 30.2 + - + +
261D ALA* 1.3 75.7 - - - +
263D LEU* 1.3 67.4 + - + +
265D LYS* 3.2 4.7 + - - +
266D LEU* 3.0 38.0 + - + +
302D PHE* 4.3 15.5 - - + -
303D PRO* 4.0 25.6 - - + -
306D MET* 4.1 17.7 - - + -
310D PHE* 4.0 13.1 - - + -
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Residues in contact with LEU 263 (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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239D LEU* 3.7 29.8 - - + -
256D PRO* 4.4 11.9 - - + +
259D LEU* 2.9 32.2 + - + +
260D ASP* 4.0 4.9 - - - +
262D VAL* 1.3 71.9 - - + +
264D ALA* 1.3 65.8 + - - +
266D LEU* 3.3 6.4 + - + +
267D ARG* 3.1 42.3 + - - +
273D ILE* 3.8 18.9 - - + +
275D VAL* 4.1 25.1 - - + -
280D ILE* 4.1 19.3 - - + -
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Residues in contact with ALA 264 (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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260D ASP 3.0 13.8 + - - +
261D ALA 3.5 8.5 - - - +
263D LEU* 1.3 76.4 - - - +
265D LYS* 1.3 67.0 + - + +
267D ARG* 3.1 17.7 + - - +
268D ASP* 3.0 30.0 + - - +
157F VAL* 3.8 31.4 - - + +
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Residues in contact with LYS 265 (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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261D ALA* 3.0 17.7 + - + +
262D VAL 3.7 5.2 - - - +
264D ALA* 1.3 79.1 - - + +
266D LEU* 1.3 61.3 + - - +
268D ASP* 3.1 23.7 + - - +
269D ALA* 3.0 20.6 + - - +
292D VAL* 3.9 12.1 - - + +
293D ASN 2.8 30.8 + - - +
294D VAL* 3.9 25.1 - - + +
295D ARG 5.7 0.7 - - - +
302D PHE* 4.5 13.2 - - + -
310D PHE* 3.7 21.3 - - + -
157F VAL* 6.5 0.9 - - + -
159F ASP* 2.8 29.4 + - - +
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Residues in contact with LEU 266 (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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239D LEU* 3.7 31.9 - - + -
240D VAL* 4.4 9.2 - - + +
243D ALA* 4.2 16.6 - - + -
262D VAL* 3.0 29.8 + - + +
263D LEU* 3.6 3.6 - - + +
264D ALA 3.2 0.2 - - - -
265D LYS* 1.3 72.9 - - - +
267D ARG* 1.3 65.2 + - - +
269D ALA* 2.9 16.3 + - + +
270D GLY 3.2 0.5 + - - -
271D ALA* 3.1 21.3 + - + +
273D ILE* 3.6 20.9 - - + -
282D LEU* 3.7 9.9 - - + -
310D PHE* 3.7 22.4 - - + -
313D LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 267 (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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260D ASP 5.4 0.4 + - - -
263D LEU* 3.1 35.6 + - - +
264D ALA* 3.6 14.6 - - - +
266D LEU* 1.3 73.9 - - - +
268D ASP* 1.3 57.9 + - - +
270D GLY* 2.6 27.5 + - - -
271D ALA 3.6 20.2 + - - +
273D ILE* 4.1 42.2 + - + +
275D VAL* 5.1 6.3 - - - +
155F HIS* 5.5 8.8 + - - -
157F VAL* 6.2 0.8 - - - +
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Residues in contact with ASP 268 (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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264D ALA* 3.0 24.0 + - - +
265D LYS* 3.1 26.9 + - - +
267D ARG* 1.3 77.2 - - - +
269D ALA* 1.3 59.0 + - - +
270D GLY 3.0 1.1 + - - -
290D LYS* 4.2 8.7 - - - +
291D ALA 4.7 1.4 - - - +
292D VAL* 3.8 17.4 - - + +
159F ASP* 5.6 1.0 - - - +
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Residues in contact with ALA 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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243D ALA* 6.1 1.1 - - + -
265D LYS 3.0 10.5 + - - +
266D LEU* 2.9 14.3 + - + +
268D ASP* 1.3 75.0 - - - +
270D GLY* 1.3 58.4 + - - +
271D ALA* 3.7 0.7 - - + -
284D MET* 4.3 3.7 - - + +
288D ARG 4.6 0.5 - - - +
289D PRO* 3.5 9.8 - - + +
290D LYS* 2.7 50.0 + - - +
292D VAL* 3.7 5.6 - - + +
310D PHE* 5.8 0.2 - - + -
313D LEU* 4.1 26.0 - - + -
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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