Contacts of the helix formed by residues 264 - 279 (chain D) in PDB entry 4HHM
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 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B SER* 6.1 0.7 - - - -
263B GLY 4.4 9.8 - - - +
264B ASP* 5.5 7.4 - - - +
265B LEU 5.8 0.3 + - - -
222D GLN* 3.9 20.9 - - - +
248D GLY* 5.4 0.2 - - - -
249D GLN 3.5 8.5 + - - +
262D ALA 3.4 5.4 + - - +
263D GLY* 1.3 70.0 - - - -
265D LEU* 1.3 62.1 + - - +
266D ARG* 3.6 7.6 + - - +
267D ALA* 3.1 31.5 + - + +
268D ALA* 3.0 19.2 + - - +
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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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265B LEU* 3.6 34.3 - - + +
266B ARG* 4.0 18.1 - - + +
380B MET* 3.9 15.0 - - - -
383B LEU* 3.6 25.8 - - + -
384B LEU* 4.1 15.3 - - + -
261D GLY* 3.5 28.0 - - - +
263D GLY 3.1 7.7 + - - -
264D ASP* 1.3 70.0 + - - +
266D ARG* 1.3 58.7 + - - +
268D ALA* 3.0 7.2 + - - +
269D PHE* 2.9 24.4 + - - +
309D ASN* 6.3 0.4 - - + -
313D LEU* 4.3 19.1 - - + -
383D LEU* 4.4 5.2 - - + -
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Residues in contact with ARG 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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262B ALA* 3.9 24.8 - - - +
263B GLY 4.6 12.6 + - - +
265B LEU* 3.8 26.6 - - + +
145C SER* 5.7 0.8 - - - +
264D ASP* 3.4 6.1 + - - +
265D LEU* 1.3 76.4 - - - +
267D ALA* 1.3 61.1 + - - +
269D PHE* 3.1 10.3 + - - +
270D TRP* 3.0 60.0 + - + +
376D ASP* 2.7 52.4 + - - -
379D ALA* 4.4 1.0 - - - +
380D MET* 3.6 34.9 - - - +
383D LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 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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218D VAL* 6.2 0.9 - - + -
222D GLN* 3.9 13.0 - - - +
228D PHE* 5.5 1.8 - - + +
229D PRO* 4.2 18.4 - - + +
264D ASP* 3.1 37.2 + - + +
266D ARG* 1.3 77.9 - - - +
268D ALA* 1.3 56.8 + - - +
270D TRP* 3.6 9.0 + - - +
271D LEU* 3.1 27.5 + - - +
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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
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218D VAL* 6.4 2.5 - - + -
260D PHE* 3.8 22.5 - - + -
261D GLY* 4.4 12.6 - - - +
262D ALA 5.6 0.7 - - - +
264D ASP 3.0 11.1 + - - +
265D LEU* 3.0 13.4 + - + +
267D ALA* 1.3 76.0 - - - +
269D PHE* 1.3 64.7 + - - +
271D LEU* 3.4 4.8 + - - +
272D VAL* 3.1 28.8 + - - +
313D LEU* 3.6 16.2 - - + -
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Residues in contact with PHE 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 LEU 2.9 11.9 + - - +
266D ARG* 3.3 14.1 - - - +
268D ALA* 1.3 76.5 - - - +
270D TRP* 1.3 99.7 + + - +
272D VAL* 3.4 3.5 + - - +
273D ASP* 2.9 27.2 + - + +
313D LEU* 3.8 19.0 - - + +
316D ARG* 3.9 13.2 - - + -
317D ALA* 3.5 40.1 - - + +
320D PHE* 4.4 11.9 - + + -
379D ALA* 4.4 19.3 - - + -
383D LEU* 3.6 35.9 - - + -
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Residues in contact with TRP 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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146C GLY* 3.4 35.5 - - - +
147C ALA* 3.5 30.1 - - + -
229D PRO* 4.0 22.1 - - + +
266D ARG* 3.0 48.6 + - + +
267D ALA* 4.0 3.6 - - - +
269D PHE* 1.3 92.3 - + - +
271D LEU* 1.3 60.4 + - - +
273D ASP* 3.3 17.0 - - + +
274D LEU* 2.9 28.4 + - - +
320D PHE* 4.3 9.2 - + - -
321D ARG* 4.3 6.7 - - - -
376D ASP* 3.9 10.1 - - - -
379D ALA* 3.6 32.5 - - + -
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Residues in contact with LEU 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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218D VAL* 4.1 3.6 - - + -
228D PHE* 3.4 43.3 - - + -
229D PRO* 4.1 10.5 - - + +
232D ILE* 4.1 18.6 - - + -
244D ILE* 4.2 2.2 - - + -
246D LEU* 3.7 24.5 - - + -
260D PHE* 4.0 17.7 - - + -
267D ALA 3.1 19.2 + - - +
268D ALA* 3.5 4.9 - - - +
269D PHE 3.2 0.2 - - - -
270D TRP* 1.3 74.0 - - - +
272D VAL* 1.3 68.8 + - + +
274D LEU* 3.0 6.5 + - + +
275D LEU* 2.9 42.6 + - + +
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Residues in contact with VAL 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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260D PHE* 3.6 22.4 - - + -
268D ALA 3.1 15.1 + - - +
269D PHE 3.7 7.0 - - - +
271D LEU* 1.3 79.0 - - + +
273D ASP* 1.3 65.2 + - - +
275D LEU* 3.2 5.6 + - - +
276D GLU* 2.9 33.9 + - + +
310D TYR* 3.8 23.1 - - + +
313D LEU* 3.8 18.8 - - + +
314D LYS* 3.5 36.3 - - + +
317D ALA* 4.6 1.3 - - + -
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Residues in contact with ASP 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 PHE* 2.9 16.5 + - + +
270D TRP* 3.3 26.3 - - + +
272D VAL* 1.3 75.5 - - - +
274D LEU* 1.3 53.7 + - - +
276D GLU* 3.9 2.4 - - - +
277D SER* 2.6 44.3 + - - -
317D ALA* 4.0 22.8 - - + +
320D PHE* 4.6 3.3 - - - -
321D ARG* 2.9 52.4 + - - +
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Residues in contact with LEU 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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150C ASP* 5.3 3.6 - - - +
152C ARG* 3.7 31.6 - - - +
229D PRO* 3.3 32.3 - - + +
232D ILE* 3.5 26.7 - - + -
233D ALA* 3.6 15.9 - - + +
236D LEU* 3.9 10.5 - - + -
270D TRP 2.9 14.4 + - - +
271D LEU* 3.0 7.8 + - + +
273D ASP* 1.3 78.6 + - - +
275D LEU* 1.3 57.9 - - - +
277D SER* 3.0 5.7 + - - +
278D ALA* 2.9 33.1 + - - +
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Residues in contact with LEU 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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232D ILE* 4.4 13.0 - - + -
236D LEU* 4.9 2.9 - - + -
241D LEU* 4.0 20.0 - - + -
244D ILE* 4.4 12.3 - - + -
246D LEU* 4.6 5.8 - - + -
271D LEU* 2.9 39.6 + - + +
272D VAL 3.8 3.1 - - - +
274D LEU* 1.3 75.8 - - - +
276D GLU* 1.3 61.8 + - - +
278D ALA* 3.4 1.7 + - - -
279D GLY* 3.1 17.3 + - - -
280D TRP* 3.2 40.7 + - + +
284D ARG* 3.8 22.2 + - + +
310D TYR* 4.1 21.8 - - + +
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Residues in contact with GLU 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 VAL* 2.9 33.4 + - + +
273D ASP* 4.0 2.9 - - - +
275D LEU* 1.3 75.9 - - - +
277D SER* 1.3 63.0 + - - +
279D GLY* 3.2 13.1 + - - -
284D ARG* 3.3 13.8 + - - -
310D TYR* 2.9 26.3 + - - +
314D LYS* 3.6 38.5 + - + +
317D ALA* 5.9 2.0 - - + -
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Residues in contact with SER 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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152C ARG* 3.9 14.9 + - - -
273D ASP* 2.6 31.6 + - - -
274D LEU* 3.0 15.4 + - - +
276D GLU* 1.3 78.3 - - - +
278D ALA* 1.3 57.6 + - - +
279D GLY 3.7 0.2 + - - -
321D ARG* 5.6 9.4 - - - -
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Residues in contact with ALA 278 (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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152C ARG* 3.8 25.3 + - - +
236D LEU* 3.9 27.8 - - + -
274D LEU 2.9 19.0 + - - +
275D LEU* 3.9 4.5 - - - +
277D SER* 1.3 76.0 + - - +
279D GLY* 1.3 62.8 + - - +
280D TRP* 3.4 4.1 + - + +
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Residues in contact with GLY 279 (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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275D LEU 3.1 5.1 + - - -
276D GLU* 3.2 12.4 + - - -
277D SER 3.3 0.6 + - - -
278D ALA* 1.3 79.2 - - - +
280D TRP* 1.3 67.9 + - - +
281D GLU* 3.2 17.7 + - - +
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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