Contacts of the helix formed by residues 261 - 275 (chain D) in PDB entry 5MR5
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 ASP 261 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257D VAL 4.7 1.8 - - - +
258D CYS* 3.0 12.0 + - - +
260D THR* 1.3 81.4 + - - +
262D HIS* 1.3 65.2 + - - +
263D LEU* 2.9 22.9 + - - +
264D CYS* 2.9 17.5 + - + -
265D ARG* 2.9 26.1 + - - +
303D PHE* 4.1 9.7 - - - -
304D ASP* 5.7 4.3 - - - +
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Residues in contact with HIS 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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260D THR 3.7 4.6 + - - -
261D ASP* 1.3 72.2 + - - +
263D LEU* 1.3 74.1 + - + +
265D ARG* 3.6 29.3 + - - +
266D SER* 3.3 27.8 + - - -
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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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205D ARG* 5.8 1.6 - - - +
209D ASP* 5.7 3.6 - - - +
261D ASP* 2.9 8.7 + - - +
262D HIS* 1.3 86.6 - - + +
264D CYS* 1.3 61.7 + - - +
266D SER* 3.3 6.6 + - - -
267D ARG* 2.8 69.4 + - + +
303D PHE* 3.6 21.8 - - + -
403D SO4 3.9 17.5 - - - +
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Residues in contact with CYS 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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258D CYS* 2.1 58.3 - - - +
261D ASP* 2.9 15.4 + - + +
263D LEU* 1.3 75.9 - - - +
265D ARG* 1.3 54.3 + - - +
267D ARG* 3.8 3.7 - - - +
268D LEU* 2.8 37.4 + - - +
300D MET* 6.0 2.0 - - - -
303D PHE* 3.6 39.1 - - + -
304D ASP* 4.0 4.7 - - + +
305D MET* 4.0 11.0 - - - -
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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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258D CYS* 3.7 7.3 + - - -
259D ARG* 2.6 63.6 + - + +
260D THR* 4.1 5.1 + - - +
261D ASP 2.9 17.4 + - - +
262D HIS* 3.7 40.7 + - - +
264D CYS* 1.3 77.1 - - - +
266D SER* 1.3 56.9 + - - +
268D LEU* 3.9 3.4 - - - +
269D ALA* 3.1 27.4 + - + +
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Residues in contact with SER 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 HIS* 3.3 22.1 + - - -
263D LEU* 3.6 9.2 - - - -
265D ARG* 1.3 78.8 - - - +
267D ARG* 1.3 60.2 + - - +
269D ALA* 3.3 6.4 + - - +
270D ASP* 2.9 38.8 + - - +
403D SO4 4.5 13.2 + - - -
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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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209D ASP* 3.6 27.0 + - - -
263D LEU* 2.8 44.5 + - + +
264D CYS* 3.8 5.2 - - - +
266D SER* 1.3 69.6 - - - +
268D LEU* 1.3 66.5 - - - +
270D ASP* 3.3 10.7 + - - +
271D PHE* 3.0 22.2 + - - +
296D SER* 4.5 3.8 - - - +
299D GLY* 2.8 54.0 + - - +
300D MET* 4.1 12.6 - - + +
303D PHE* 3.5 17.4 - - + -
403D SO4 2.4 44.4 + - - -
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Residues in contact with LEU 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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255D ARG* 3.9 27.8 - - + -
258D CYS* 4.0 20.2 - - - -
259D ARG* 4.5 18.4 - - + +
264D CYS 2.8 21.0 + - - +
265D ARG 3.9 3.8 - - - +
267D ARG* 1.3 73.2 - - - +
269D ALA* 1.3 57.0 + - - +
271D PHE* 3.2 8.0 + - + +
272D HIS* 2.9 31.4 + - + +
300D MET* 3.9 25.6 - - + +
305D MET* 4.2 8.3 - - + -
338D PHE* 4.2 15.9 - - + -
342D PHE* 4.1 17.5 - - + -
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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 3.1 20.2 + - - +
266D SER* 3.6 7.2 - - - +
267D ARG 3.3 0.2 - - - -
268D LEU* 1.3 76.5 - - - +
270D ASP* 1.3 64.4 + - - +
272D HIS* 3.4 7.4 + - - +
273D ALA* 3.0 24.3 + - - +
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Residues in contact with ASP 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 SER* 2.9 24.7 + - - +
267D ARG* 3.5 14.3 - - - +
268D LEU 3.2 0.2 - - - -
269D ALA* 1.3 75.4 - - - +
271D PHE* 1.3 53.4 + - - +
273D ALA* 3.3 3.7 + - - -
274D ASN* 2.8 47.1 + - - +
296D SER* 3.7 17.3 - - - +
403D SO4 4.1 16.3 + - - -
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Residues in contact with PHE 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 ARG 3.0 12.5 + - - +
268D LEU* 3.4 13.5 - - + +
270D ASP* 1.3 77.6 - - - +
272D HIS* 1.3 61.9 + - + +
275D CYS* 2.9 59.2 + - + +
296D SER* 3.5 13.1 - - - +
297D TYR* 4.2 14.1 - + - -
300D MET* 3.4 29.6 - - + -
341D ASP* 3.4 33.4 - - + -
342D PHE* 3.5 40.4 - + - -
348D LEU* 4.1 17.3 - - + -
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Residues in contact with HIS 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 LEU* 2.9 22.8 + - + +
269D ALA* 3.8 7.4 - - - +
271D PHE* 1.3 80.5 - - + +
273D ALA* 1.3 63.3 + - + +
275D CYS 4.3 0.2 - - - -
276D ARG* 3.4 47.3 + - + +
337D LYS* 6.0 6.5 - - - -
338D PHE* 6.0 1.6 - - - -
341D ASP* 2.8 35.8 + - - -
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Residues in contact with ALA 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 3.0 17.5 + - - +
270D ASP* 3.8 4.3 - - - +
272D HIS* 1.3 83.0 - - + +
274D ASN* 1.3 70.1 + - - +
276D ARG* 3.6 15.5 - - - +
286D PRO* 3.7 10.2 - - - +
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Residues in contact with ASN 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 ASP* 2.8 28.7 + - - +
273D ALA* 1.3 81.9 - - - +
275D CYS* 1.3 59.7 + - - +
276D ARG 3.4 0.2 - - - -
286D PRO* 3.6 20.8 - - - +
289D ASN 4.6 3.6 - - - +
292D ALA* 3.6 31.8 + - + +
293D CYS* 3.5 13.8 + - - +
296D SER* 2.9 25.6 + - - +
347D CYS* 4.2 0.5 - - - -
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Residues in contact with CYS 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 PHE* 2.9 45.8 + - + +
272D HIS* 4.3 0.4 - - - -
274D ASN* 1.3 75.0 - - - +
276D ARG* 1.3 63.2 + - - +
293D CYS* 2.0 62.8 - - - -
296D SER* 4.7 2.0 - - - -
345D ASN* 2.7 38.4 + - - +
347D CYS* 3.5 7.3 - - - +
348D LEU* 4.4 2.9 - - + -
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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