Contacts of the helix formed by residues 260 - 281 (chain M) in PDB entry 3HOU
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 260 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M ARG* 3.4 29.4 - - - +
248M PRO* 3.5 17.0 + - - +
259M GLU* 1.3 79.7 + - - +
261M ASP* 1.3 63.2 + - - +
262M LEU* 2.7 27.9 + - - +
263M THR* 2.7 28.5 + - - +
264M PHE* 3.1 12.3 + - - -
328M ARG* 3.3 26.0 + - - -
1114N LEU* 5.6 3.1 - - - +
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Residues in contact with ASP 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M GLU 4.3 0.8 + - - -
260M ASP* 1.3 77.3 + - - +
262M LEU* 1.3 62.3 + - + +
264M PHE* 3.0 20.0 + - - +
265M LYS* 3.0 16.9 + - - +
316M GLN* 3.0 20.3 + - - +
320M ARG* 3.2 23.0 + - - -
322M VAL* 3.5 21.8 - - + +
323M LYS* 3.1 46.5 + - + +
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Residues in contact with LEU 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M PRO* 5.1 4.3 - - + -
246M VAL* 4.2 14.8 - - + +
247M ARG* 3.9 12.6 - - + -
260M ASP* 2.7 14.7 + - - +
261M ASP* 1.3 71.7 - - + +
263M THR* 1.3 64.8 + - - +
265M LYS* 3.2 6.9 + - + +
266M LEU* 3.1 27.8 + - + +
303M TYR* 3.9 23.7 - - + +
323M LYS 3.8 20.9 - - - +
324M SER* 5.0 0.2 - - - -
325M ILE* 3.9 33.7 - - + +
328M ARG* 3.1 38.8 - - - +
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Residues in contact with THR 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M THR* 5.1 4.7 - - - +
53M LEU* 4.3 11.6 - - + +
54M ASN* 4.3 6.7 - - - +
247M ARG* 3.3 53.7 + - - +
259M GLU* 3.5 32.0 + - + +
260M ASP* 2.7 19.3 + - - +
262M LEU* 1.3 74.5 - - - +
264M PHE* 1.3 60.7 + - + -
266M LEU* 3.7 5.9 + - - +
267M ALA* 3.3 18.2 + - - +
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Residues in contact with PHE 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284 A 5.2 7.9 - - - -
257M ARG* 2.9 36.1 - - - -
259M GLU* 3.4 32.8 - - + -
260M ASP 3.1 8.5 + - - -
261M ASP* 3.0 12.1 + - - +
263M THR* 1.3 79.2 - - + +
265M LYS* 1.3 72.0 + - - +
266M LEU 3.0 4.0 - - - -
267M ALA* 2.8 25.4 + - + +
268M ASP* 2.8 18.4 + - - +
316M GLN* 3.3 28.7 - - - -
317M LYS* 3.4 26.5 - - - -
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Residues in contact with LYS 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261M ASP 3.0 10.6 + - - +
262M LEU* 3.2 8.9 + - + +
264M PHE* 1.3 94.3 - - - +
266M LEU* 1.3 59.4 + - - +
268M ASP* 3.0 30.1 + - + +
269M ILE* 3.1 30.0 + - - +
299M HIS* 4.9 1.8 - - + +
302M THR* 3.5 32.8 - - + +
303M TYR* 4.2 23.6 - - + -
314M ALA* 5.6 2.2 - - + +
316M GLN* 3.7 17.0 + - - +
322M VAL* 3.4 40.4 - - + +
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Residues in contact with LEU 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M LEU* 4.2 12.1 - - + -
84M ILE* 4.7 17.9 - - + +
239M LEU* 4.7 5.4 - - + -
241M VAL* 4.2 20.4 - - + -
242M PRO* 4.3 11.7 - - + -
247M ARG* 3.8 31.2 - - - +
262M LEU 3.1 18.1 + - - +
263M THR* 3.9 4.9 - - - +
264M PHE 3.0 1.0 - - - -
265M LYS* 1.3 74.4 - - - +
267M ALA* 1.3 57.7 + - - +
269M ILE* 2.9 15.1 + - + +
270M LEU* 2.6 38.5 + - + +
303M TYR* 3.8 30.1 - - + +
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Residues in contact with ALA 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M PRO* 3.9 26.7 - - + +
53M LEU* 4.2 3.9 - - + +
263M THR 3.3 11.1 + - - +
264M PHE* 2.8 18.3 + - + +
266M LEU* 1.3 78.4 - - - +
268M ASP* 1.3 55.9 + - - +
270M LEU* 3.4 7.1 - - - +
271M LYS* 2.8 50.5 + - - +
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Residues in contact with ASP 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264M PHE* 2.8 21.0 + - - +
265M LYS* 3.0 35.0 + - - +
266M LEU 3.0 0.2 - - - -
267M ALA* 1.3 80.1 - - - +
269M ILE* 1.3 53.2 + - - +
271M LYS* 3.5 12.3 + - - +
272M ALA* 2.6 37.1 + - - +
299M HIS* 3.2 36.8 + - + +
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Residues in contact with ILE 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M ILE* 4.6 11.2 - - + -
86M LEU* 4.6 7.0 - - + -
239M LEU* 4.1 17.0 - - + -
265M LYS 3.1 16.2 - - - +
266M LEU* 2.9 12.5 + - + +
268M ASP* 1.3 78.0 - - - +
270M LEU* 1.3 56.3 + - - +
272M ALA* 3.6 7.5 - - - +
273M ASN* 2.7 37.0 + - + +
296M LEU* 3.7 6.1 - - + +
299M HIS* 3.5 20.2 - - + -
300M VAL* 3.6 39.7 - - + -
303M TYR* 3.8 26.9 - - + -
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Residues in contact with LEU 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ILE* 4.1 15.0 - - + +
36M ARG* 3.8 16.6 - - - +
37M PHE 3.1 35.9 - - - +
38M PRO* 3.4 11.4 - - + -
53M LEU* 4.1 14.8 - - + -
84M ILE* 3.2 44.9 - - + -
266M LEU 2.6 17.5 + - - +
267M ALA 3.4 4.3 - - - +
269M ILE* 1.3 71.5 - - - +
271M LYS* 1.3 64.0 + - - +
273M ASN* 3.0 7.0 + - + +
274M ILE* 2.9 28.3 + - + +
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Residues in contact with LYS 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M PRO* 3.8 29.6 - - + +
267M ALA* 2.8 35.7 + - - +
268M ASP* 3.5 11.7 + - - +
270M LEU* 1.3 74.5 - - - +
272M ALA* 1.3 65.6 + - - +
273M ASN 2.8 1.9 + - - -
274M ILE* 3.0 9.8 + - - +
275M SER* 2.9 23.5 + - - -
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Residues in contact with ALA 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268M ASP 2.6 22.1 + - - +
269M ILE 3.7 4.7 - - - +
271M LYS* 1.3 72.9 - - - +
273M ASN* 1.3 61.4 + - - +
275M SER* 3.7 7.3 + - - -
276M LEU* 3.4 17.3 + - - +
292M ALA 4.4 6.8 - - - +
295M LEU* 3.6 27.2 - - + +
296M LEU* 4.2 16.0 - - + +
299M HIS* 3.6 19.1 - - + +
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Residues in contact with ASN 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASP* 5.6 1.2 + - - -
84M ILE* 4.6 6.7 - - + +
85M ASP 3.4 20.6 + - - -
86M LEU* 3.4 10.6 - - - +
87M ALA* 2.7 31.2 + - - +
269M ILE* 2.7 23.6 + - + +
270M LEU* 3.3 7.4 - - + +
271M LYS 2.8 0.6 + - - -
272M ALA* 1.3 69.6 - - - +
274M ILE* 1.3 71.5 + - + +
275M SER 3.0 1.1 - - - -
276M LEU* 2.8 15.8 + - - +
277M GLU* 3.0 15.8 + - - +
296M LEU* 3.2 21.9 - - + +
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Residues in contact with ILE 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M ARG 3.5 24.0 - - - +
37M PHE* 5.3 0.2 - - - -
38M PRO* 4.1 18.6 - - + -
270M LEU* 2.9 21.0 + - + +
271M LYS* 3.7 6.1 - - - +
273M ASN* 1.3 75.3 - - + +
275M SER* 1.3 63.6 + - - +
277M GLU* 3.4 15.8 + - - +
278M THR* 3.0 37.7 + - - +
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Residues in contact with SER 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M LYS 2.9 16.6 + - - -
272M ALA* 3.7 9.8 + - - -
274M ILE* 1.3 77.5 - - - +
276M LEU* 1.3 69.8 + - - +
278M THR* 3.1 11.3 + - - -
279M LEU* 3.2 19.6 + - - +
292M ALA* 4.4 14.4 + - - +
295M LEU* 5.5 3.9 - - - +
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Residues in contact with LEU 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M ALA* 3.2 24.9 - - + -
88M LYS* 4.1 13.2 - - + +
272M ALA 3.4 9.5 + - - +
273M ASN* 2.8 13.8 + - - +
275M SER* 1.3 76.8 + - - +
277M GLU* 1.3 57.4 + - - +
279M LEU* 2.8 32.6 + - + +
280M GLU* 3.4 12.3 + - - +
289M ILE* 3.6 22.4 - - + +
292M ALA* 3.6 7.9 - - + +
293M GLU* 3.4 55.9 - - + +
296M LEU* 4.3 8.7 - - + -
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Residues in contact with GLU 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASP* 3.8 29.5 - - - +
209D ARG* 3.2 28.9 + - - +
87M ALA* 4.1 10.2 - - + +
273M ASN* 3.0 12.2 + - - +
274M ILE* 3.7 19.3 - - - +
276M LEU* 1.3 78.2 - - - +
278M THR* 1.3 64.3 + - - +
279M LEU 2.9 5.5 + - - -
280M GLU* 3.0 26.3 + - + +
281M HIS* 3.2 12.3 + - + +
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Residues in contact with THR 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ARG* 4.9 4.8 + - - +
274M ILE* 3.0 26.5 + - - +
275M SER* 3.1 7.1 + - - -
277M GLU* 1.3 82.2 + - - +
279M LEU* 1.3 63.5 + - - +
280M GLU 3.5 0.2 - - - -
281M HIS* 4.2 8.1 - - + +
282M ASN* 3.1 37.5 - - - +
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Residues in contact with LEU 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275M SER* 3.2 20.4 - - - +
276M LEU* 2.8 11.3 + - - +
278M THR* 1.3 87.3 - - - +
280M GLU* 1.3 59.4 + - - +
281M HIS 3.3 1.3 - - - -
282M ASN* 3.5 11.8 - - + +
283M GLY 5.1 6.5 - - - +
284M ALA* 3.2 29.8 - - - +
285M PRO* 5.9 3.6 - - + -
288M ALA 4.5 5.2 - - - +
289M ILE* 3.2 26.9 - - + +
292M ALA* 4.2 24.9 - - + -
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Residues in contact with GLU 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M ALA* 4.0 10.9 - - - +
88M LYS* 3.1 34.6 + - - +
276M LEU* 3.8 13.9 - - - +
277M GLU* 3.0 27.2 + - + +
279M LEU* 1.3 79.0 - - - +
281M HIS* 1.3 56.0 + - - +
282M ASN 3.3 6.4 - - - +
284M ALA* 4.7 3.9 - - - +
289M ILE* 3.8 23.6 - - + +
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Residues in contact with HIS 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D GLU* 4.1 18.4 + - - +
209D ARG* 4.1 38.7 + - - +
277M GLU* 3.2 12.6 + - + +
278M THR* 4.7 4.5 - - + -
280M GLU* 1.3 79.1 - - - +
282M ASN* 1.3 77.4 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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