Contacts of the helix formed by residues 257 - 277 (chain D) in PDB entry 4RZR
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 ASN 257 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D SER* 2.9 12.8 + - - +
256D ARG* 1.3 75.1 - - - +
258D LEU* 1.3 68.2 + - - +
259D GLU* 3.0 22.1 + - - +
260D GLU* 3.1 23.3 + - + +
261D ILE* 3.0 25.3 + - - +
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Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ARG 3.3 5.4 + - - -
257D ASN* 1.3 74.1 + - - +
259D GLU* 1.3 75.3 + - + +
261D ILE* 3.4 2.9 + - - +
262D LYS* 3.1 43.9 + - - +
316D VAL* 4.6 9.2 - - + -
319D LEU* 3.6 34.5 - - + -
320D GLN* 3.6 42.0 - - + +
323D LEU* 4.1 13.7 - - + -
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ASN* 3.0 13.1 + - - +
258D LEU* 1.3 92.6 - - + +
260D GLU* 1.3 60.1 + - - +
262D LYS* 2.7 37.7 + - - +
263D PRO* 3.4 18.2 - - - +
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Residues in contact with GLU 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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251D MET* 5.3 0.9 - - - -
253D ARG* 3.7 33.8 + - - +
254D ASN 5.3 0.2 - - - +
255D SER* 2.8 27.1 + - - +
257D ASN* 3.1 28.2 + - + +
259D GLU* 1.3 80.4 - - - +
261D ILE* 1.3 60.5 + - - +
263D PRO* 3.3 12.1 - - - +
264D TYR* 3.5 21.7 - - + -
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Residues in contact with ILE 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D MET* 3.6 32.1 - - + -
255D SER* 3.8 25.8 - - - +
256D ARG* 4.0 7.2 - - - -
257D ASN 3.0 22.7 + - - +
258D LEU* 4.0 2.7 - - - +
260D GLU* 1.3 77.7 - - - +
262D LYS* 1.3 64.3 + - - +
264D TYR* 3.0 15.2 + - - +
265D LEU* 3.2 6.8 + - + +
319D LEU* 3.6 22.9 - - + -
323D LEU* 4.3 17.5 - - + -
330D ILE* 4.4 9.0 - - + -
333D ILE* 3.8 23.3 - - + -
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Residues in contact with LYS 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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258D LEU* 3.1 30.9 + - + +
259D GLU* 2.7 35.6 + - - +
261D ILE* 1.3 76.0 - - - +
263D PRO* 1.4 65.0 - - + +
265D LEU* 3.1 10.4 + - + +
266D PHE* 2.8 58.6 + - + -
316D VAL* 4.1 31.8 - - + +
319D LEU* 4.7 3.6 - - + +
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Residues in contact with PRO 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 GLU 3.4 11.9 - - - +
260D GLU 3.3 16.8 - - - +
261D ILE 3.4 0.7 - - - -
262D LYS* 1.4 95.4 - - + +
264D TYR* 1.3 64.9 + - + +
266D PHE* 3.4 9.2 + - + +
267D ARG* 3.0 36.1 + - - +
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Residues in contact with TYR 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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249D VAL* 3.9 24.3 - - + +
250D THR 3.9 4.5 - - - -
251D MET* 3.5 41.5 - - + -
252D LYS* 3.2 39.4 + - + +
260D GLU* 3.5 28.3 - - + -
261D ILE 3.0 6.9 + - - +
263D PRO* 1.3 80.6 - - + +
265D LEU* 1.3 62.5 + - - +
267D ARG* 3.4 27.5 + - - +
268D ALA* 3.2 20.8 + - - +
333D ILE* 3.4 18.7 - - + +
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Residues in contact with LEU 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 ILE 3.2 8.5 + - - +
262D LYS* 3.1 11.1 + - - +
264D TYR* 1.3 78.9 - - - +
266D PHE* 1.3 68.2 + - + +
268D ALA* 3.2 7.0 + - - +
269D ILE* 3.1 25.7 + - + +
286D VAL* 4.3 9.4 - - + -
315D SER* 3.7 47.6 - - - +
316D VAL* 4.4 3.8 - - + +
319D LEU* 3.9 23.6 - - + -
333D ILE* 3.9 18.7 - - + +
334D GLY* 3.9 26.7 - - - +
335D VAL* 4.5 6.1 - - + -
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Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D LYS* 2.8 44.6 + - + +
263D PRO* 3.9 8.5 - - + +
264D TYR 3.3 0.2 - - - -
265D LEU* 1.3 77.8 - - + +
267D ARG* 1.3 61.8 + - - +
269D ILE* 3.2 13.3 + - + +
270D GLU* 3.0 20.5 + - - +
312D TYR* 3.6 49.2 + + + +
315D SER* 4.0 10.1 - - - -
316D VAL* 3.6 32.5 - - + -
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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
----------------------------------------------------------
247D ARG* 5.6 1.6 - - - +
249D VAL* 4.7 17.3 - - + +
263D PRO* 3.0 20.1 + - - +
264D TYR* 3.4 42.6 + - - +
265D LEU 3.3 0.2 - - - -
266D PHE* 1.3 72.1 - - - +
268D ALA* 1.3 66.2 + - - +
269D ILE 3.2 0.2 + - - -
270D GLU* 3.3 7.0 + - + +
271D GLU* 3.0 55.0 + - + +
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Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ARG* 3.4 41.6 - - + +
249D VAL* 4.7 3.7 - - + +
264D TYR 3.2 13.5 + - - +
265D LEU* 3.2 10.1 + - - +
267D ARG* 1.3 75.9 - - - +
269D ILE* 1.3 56.0 + - - +
271D GLU 4.0 0.2 - - - -
272D SER* 2.7 36.8 + - - -
333D ILE 4.7 2.5 - - - +
334D GLY* 4.4 9.4 - - - -
335D VAL* 3.8 9.2 - - + -
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Residues in contact with ILE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D LEU* 3.1 17.4 + - + +
266D PHE* 3.5 15.9 - - + +
267D ARG 3.1 0.6 - - - -
268D ALA* 1.3 74.1 - - - +
270D GLU* 1.3 54.7 + - - +
272D SER* 3.4 2.4 + - - -
273D TYR* 2.8 51.5 + - + +
308D LYS* 4.5 1.1 - - + -
311D ALA* 3.8 16.2 - - + +
312D TYR* 3.4 34.3 - - + -
315D SER* 3.2 35.4 - - - +
335D VAL* 4.2 23.3 - - + -
337D PHE* 4.6 3.4 - - + -
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Residues in contact with GLU 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 PHE 3.0 11.3 + - - +
267D ARG* 3.7 10.8 - - + +
269D ILE* 1.3 72.9 - - - +
271D GLU* 1.3 68.4 + - + +
273D TYR* 3.1 4.7 + - - +
274D TYR* 2.9 25.0 + - - +
308D LYS* 3.3 37.5 + - - +
312D TYR* 2.4 29.8 + - - +
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Residues in contact with GLU 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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247D ARG* 2.7 47.3 + - + -
267D ARG* 3.0 43.6 + - + +
268D ALA 4.1 2.5 - - - +
270D GLU* 1.3 80.5 - - + +
272D SER* 1.3 62.9 + - - +
274D TYR* 3.4 8.3 + - - +
275D LYS* 3.1 33.8 + - - +
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Residues in contact with SER 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ILE* 3.3 21.7 - - - +
246D GLY* 3.4 10.3 - - - -
247D ARG* 3.3 18.5 + - - +
268D ALA 2.7 23.5 + - - -
269D ILE 3.7 3.4 - - - -
271D GLU* 1.3 74.3 - - - +
273D TYR* 1.3 59.3 + - - +
275D LYS* 3.4 0.8 + - - +
276D LEU* 3.0 32.1 + - - +
335D VAL* 3.7 2.8 - - - +
337D PHE* 3.9 23.3 - - - -
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Residues in contact with TYR 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ILE* 2.8 25.6 + - + +
270D GLU 3.1 3.3 + - - +
272D SER* 1.3 69.8 - - - +
274D TYR* 1.3 68.6 + - - +
276D LEU* 3.1 31.9 + - + +
277D ASP* 3.2 12.5 + - - +
279D ARG 5.5 1.8 - - - -
280D ILE* 6.1 1.6 - - + -
281D PRO* 4.0 8.4 - - + +
306D ILE* 2.7 35.9 + - - +
307D SER* 3.2 7.9 + - - -
308D LYS* 3.8 53.6 - - + +
311D ALA* 3.7 9.2 - - + -
337D PHE* 3.5 30.2 - + - -
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Residues in contact with TYR 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 GLU 2.9 13.1 + - - +
271D GLU* 3.4 12.1 - - - +
273D TYR* 1.3 78.9 - - - +
275D LYS* 1.3 75.9 + - + +
276D LEU 3.2 0.3 + - - -
277D ASP* 3.3 16.8 + - - +
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Residues in contact with LYS 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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245D ILE* 3.4 25.4 - - + +
246D GLY 3.3 23.3 + - - -
247D ARG* 4.9 6.4 - - - +
271D GLU* 3.1 23.8 + - - +
272D SER* 4.5 0.9 - - - +
274D TYR* 1.3 91.8 - - + +
276D LEU* 1.3 60.7 + - - +
277D ASP* 4.5 2.2 - - - +
279D ARG* 3.2 18.4 + - - -
7E A 4.2 19.4 + - - -
8E C 4.1 13.7 + - - +
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Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ILE* 3.6 16.6 - - + -
272D SER 3.0 23.7 + - - +
273D TYR* 3.1 39.6 + - + +
275D LYS* 1.3 74.0 - - - +
277D ASP* 1.3 68.2 + - - +
278D LYS 3.1 7.6 + - - -
279D ARG* 3.2 41.0 + - + +
281D PRO* 4.0 22.0 - - + -
337D PHE* 4.2 9.6 - - + -
340D PHE* 3.2 39.9 - - + -
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Residues in contact with ASP 277 (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 TYR* 3.2 10.0 + - - +
274D TYR 3.3 12.8 + - - +
275D LYS 4.5 2.7 - - - +
276D LEU* 1.3 78.6 - - - +
278D LYS* 1.3 93.4 + - + +
279D ARG* 4.4 3.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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