Contacts of the helix formed by residues 258 - 276 (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 ARG 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D LYS* 4.5 21.0 - - - +
253D LEU* 3.4 31.2 + - + +
254D PRO 3.2 16.7 + - - +
255D ILE* 4.1 11.7 + - - +
256D ALA 3.8 0.9 - - - -
257D MET* 1.3 78.5 - - - +
259D ALA* 1.3 66.3 - - - +
260D LEU* 3.1 12.2 + - + +
261D THR* 3.2 22.2 + - - +
262D ASN* 3.4 11.5 + - - -
1232D ASP* 4.3 18.6 + - - +
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Residues in contact with ALA 259 (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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257D MET 3.6 2.2 + - - -
258D ARG* 1.3 71.5 - - - +
260D LEU* 1.3 56.8 + - - +
262D ASN* 3.8 10.5 - - - +
263D TYR* 2.9 31.9 + - - +
389D GLY 4.6 15.0 - - - +
393D THR* 4.2 4.1 - - + +
1228D LEU* 4.7 7.6 - - + -
1231D THR* 4.1 19.5 - - + +
1232D ASP* 3.2 23.7 + - - +
1235D ASN* 4.5 13.4 - - - +
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Residues in contact with LEU 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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258D ARG* 3.1 8.4 - - + +
259D ALA* 1.3 78.7 - - - +
261D THR* 1.3 59.5 + - - +
263D TYR* 3.4 17.6 + - + +
264D GLN* 2.9 34.7 + - - +
1225D GLN* 5.5 4.9 - - - +
1228D LEU* 3.8 34.3 - - + +
1232D ASP* 4.9 1.2 + - - -
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Residues in contact with THR 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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255D ILE 4.0 17.6 + - - +
256D ALA* 5.7 5.8 - - - -
258D ARG* 3.2 15.0 + - - +
260D LEU* 1.3 78.9 - - - +
262D ASN* 1.3 59.1 + - - +
264D GLN* 3.3 9.2 + - + +
265D ARG* 2.9 43.6 + - + +
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Residues in contact with ASN 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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256D ALA 5.2 3.3 + - - +
257D MET* 4.2 5.9 + - - +
258D ARG 3.4 14.8 + - - -
259D ALA* 3.8 10.2 - - - +
260D LEU 3.3 0.6 - - - -
261D THR* 1.3 77.0 - - - +
263D TYR* 1.3 60.4 + - - +
265D ARG* 3.4 13.9 + - - +
266D LEU* 2.9 30.7 + - - +
386D ASN* 2.6 52.1 + - - +
389D GLY* 5.9 0.4 - - - -
390D ALA* 3.9 20.3 - - + +
1235D ASN* 5.9 2.0 - - - +
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Residues in contact with TYR 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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259D ALA 2.9 18.8 + - - +
260D LEU* 3.7 19.5 - - + +
262D ASN* 1.3 75.0 - - - +
264D GLN* 1.3 63.8 + - - +
266D LEU* 3.7 5.9 - - + +
267D CYS* 2.9 57.8 + - + +
390D ALA* 4.1 4.5 - - - +
393D THR* 3.4 37.0 - - + +
394D LYS* 3.9 25.8 - - + -
397D ASN* 3.6 30.1 + - + -
1224D GLN* 4.7 9.2 - - - -
1228D LEU* 6.2 0.4 - - + -
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Residues in contact with GLN 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 LEU* 2.9 24.4 + - - +
261D THR* 3.4 11.9 - - + +
262D ASN 3.2 0.2 - - - -
263D TYR* 1.3 84.2 - - - +
265D ARG* 1.3 64.3 + - - +
267D CYS* 3.8 5.3 - - - +
268D VAL* 2.9 42.8 + - + +
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Residues in contact with ARG 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 THR* 2.9 31.8 + - + +
262D ASN* 3.8 13.8 + - - +
264D GLN* 1.3 74.2 - - - +
266D LEU* 1.3 57.7 + - - +
268D VAL* 3.3 6.6 + - - +
269D ALA* 2.9 29.9 + - + +
293D HIS* 6.3 1.8 - - + +
294D ALA* 3.8 33.9 + - + +
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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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262D ASN 2.9 18.2 + - - +
263D TYR* 3.7 4.5 - - + +
265D ARG* 1.3 78.9 - - - +
267D CYS* 1.3 56.9 + - - +
269D ALA* 3.3 3.7 + - - +
270D PHE* 2.8 29.3 + - - +
290D ALA* 4.8 11.4 - - + +
291D LEU* 3.8 26.5 - - + +
294D ALA* 4.7 16.6 - - + +
295D PHE* 6.4 0.2 - - + -
390D ALA* 3.8 32.8 - - + +
391D ILE* 4.3 10.5 - - + +
394D LYS* 3.6 35.4 - - + +
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Residues in contact with CYS 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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263D TYR* 2.9 51.9 + - + +
264D GLN* 3.9 6.3 - - - +
266D LEU* 1.3 74.1 - - - +
268D VAL* 1.3 61.0 + - + +
270D PHE* 3.6 9.7 - - - +
271D ASP* 2.9 30.7 + - - +
394D LYS* 4.3 20.0 - - - +
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D GLN* 2.9 39.1 + - + +
265D ARG* 3.7 7.2 - - - +
267D CYS* 1.3 76.6 - - + +
269D ALA* 1.3 59.0 + - - +
271D ASP* 3.3 7.2 + - - +
272D ALA* 3.0 29.3 + - + +
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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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265D ARG* 2.9 17.6 + - + +
266D LEU* 3.8 5.8 - - - +
268D VAL* 1.3 78.1 - - - +
270D PHE* 1.3 58.0 + - - +
272D ALA* 3.3 6.7 + - - +
273D GLN* 2.9 30.3 + - - +
290D ALA* 4.4 19.6 - - + +
293D HIS* 4.1 28.7 - - + +
294D ALA* 4.9 4.0 - - + -
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Residues in contact with PHE 270 (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 2.8 18.3 + - - +
267D CYS* 3.6 9.0 - - - +
269D ALA* 1.3 77.0 - - - +
271D ASP* 1.3 60.8 + - + +
273D GLN* 3.3 8.2 + - + +
274D ALA* 2.9 38.1 + - + +
283D GLY 6.0 2.9 - - - -
286D ALA* 5.6 5.4 - - + -
287D ILE* 3.6 34.5 - - + -
290D ALA* 4.4 8.7 - - + +
394D LYS* 3.3 28.9 - - - +
614D LEU* 4.0 25.6 - - + -
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Residues in contact with ASP 271 (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 CYS 2.9 17.8 + - - +
268D VAL* 3.6 7.0 - - - +
270D PHE* 1.3 80.7 - - + +
272D ALA* 1.3 62.4 + - - +
274D ALA* 3.1 7.4 + - - +
275D ARG* 2.9 29.7 + - - +
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Residues in contact with ALA 272 (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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268D VAL* 3.0 19.2 + - + +
269D ALA* 3.7 7.9 - - - +
271D ASP* 1.3 77.3 - - - +
273D GLN* 1.3 61.2 + - - +
275D ARG* 3.6 28.2 + - - +
276D LYS* 3.4 20.8 + - - +
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Residues in contact with GLN 273 (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 ALA 2.9 17.7 + - - +
270D PHE* 3.6 9.6 - - + +
271D ASP 3.2 0.2 - - - -
272D ALA* 1.3 75.5 - - - +
274D ALA* 1.3 63.7 + - - +
276D LYS* 3.4 25.6 + - - +
286D ALA* 3.7 37.8 - - + +
289D ARG* 3.6 26.9 - - - +
290D ALA* 4.4 6.4 + - + -
293D HIS* 6.0 1.0 - - - +
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Residues in contact with ALA 274 (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* 2.9 29.9 + - + +
271D ASP* 3.1 9.2 + - - +
273D GLN* 1.3 75.3 - - - +
275D ARG* 1.3 63.7 + - - +
276D LYS 3.3 4.7 + - - -
286D ALA* 6.2 1.6 - - - -
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Residues in contact with ARG 275 (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 ASP* 2.9 22.0 + - - +
272D ALA* 4.0 29.0 + - - +
274D ALA* 1.3 77.2 - - - +
276D LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 276 (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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272D ALA 3.4 12.2 + - - +
273D GLN* 3.7 25.4 - - - +
274D ALA 3.2 5.0 - - - +
275D ARG* 1.3 87.0 - - - +
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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