Contacts of the helix formed by residues 276 - 296 (chain B) in PDB entry 3Q41
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 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASN* 3.3 34.5 + - - +
274B GLY 3.4 0.2 - - - -
275B LYS* 1.3 72.4 - - - +
277B GLU* 1.3 64.3 + - - +
278B SER 3.4 0.4 - - - -
279B ALA* 3.0 32.5 + - + +
280B HIS* 3.4 11.5 - - - -
408B NAG 1.5 76.9 + - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.2 0.2 - - - +
34B SER* 2.6 37.5 + - - -
38B HIS* 3.2 35.4 + - + +
93B SER* 2.7 30.5 + - - +
94B HIS 3.6 9.0 - - - +
95B PRO* 4.7 1.0 - - - +
96B PRO* 5.2 3.7 - - + +
121B LEU* 4.2 6.3 - - + -
122B THR* 4.5 3.3 + - + +
275B LYS 3.0 12.4 + - - +
276B ASN* 1.3 71.9 - - - +
278B SER* 1.3 62.2 + - - +
280B HIS* 3.2 7.6 + - - +
281B ILE* 3.0 28.8 + - + +
408B NAG 5.0 2.2 + - - -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 4.3 4.1 + - - -
41B MET* 3.0 39.9 - - - +
277B GLU* 1.3 78.7 - - - +
279B ALA* 1.3 62.7 + - - +
281B ILE* 3.8 5.9 + - - +
282B SER* 3.4 20.8 + - - -
408B NAG 3.3 38.3 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASN* 4.9 4.7 - - - +
276B ASN* 3.0 33.1 + - + +
277B GLU 3.1 0.2 - - - -
278B SER* 1.3 81.7 + - - +
280B HIS* 1.3 58.1 + - + +
282B SER* 3.0 7.2 + - - -
283B ASP* 2.9 24.4 + - - +
334B VAL* 3.3 27.7 - - + +
335B THR* 4.0 11.7 - - - +
408B NAG 4.5 7.0 - - - +
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Residues in contact with HIS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.7 36.6 + - + +
140B THR* 2.9 42.3 + - - +
141B VAL* 4.3 10.3 - - + -
271B LEU* 5.2 3.1 - - + +
273B ASN 2.9 32.0 + - - -
274B GLY* 4.5 7.1 + - - -
276B ASN 3.4 14.8 - - - +
277B GLU* 3.2 5.1 + - - +
279B ALA* 1.3 77.4 - - + +
281B ILE* 1.3 59.5 - - - +
283B ASP* 3.9 5.3 - - - +
284B ALA* 3.0 32.2 + - - +
335B THR* 3.8 30.3 + - + +
346B ARG* 4.6 0.6 + - - -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.9 21.3 - - + -
38B HIS* 3.6 50.3 - - + +
41B MET* 4.3 9.9 - - + +
42B PHE* 3.7 41.1 - - + +
45B ALA* 4.6 2.0 - - + +
91B LEU* 4.5 2.2 - - + +
121B LEU* 4.3 8.7 - - + -
277B GLU* 3.0 23.9 + - + +
278B SER* 4.0 7.2 - - - +
280B HIS* 1.3 77.2 - - - +
282B SER* 1.3 61.9 + - - +
284B ALA* 4.3 0.3 - - - +
285B VAL* 3.2 27.2 + - + +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 4.3 18.4 - - - +
278B SER 3.4 11.7 + - - -
279B ALA* 3.0 10.6 + - - -
281B ILE* 1.3 81.1 - - - +
283B ASP* 1.3 58.7 + - - +
285B VAL* 4.0 2.6 - - - +
286B GLY* 3.1 21.3 + - - -
330B TYR* 5.0 2.1 + - - -
334B VAL* 3.9 20.1 - - - +
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 5.1 5.6 - - + -
279B ALA 2.9 10.7 + - - +
280B HIS* 4.4 5.2 - - - +
282B SER* 1.3 75.1 + - - +
284B ALA* 1.3 59.9 - - - +
286B GLY* 3.1 3.4 + - - +
287B VAL* 3.1 30.2 + - - +
330B TYR* 4.4 7.3 + - - -
333B GLY* 3.4 13.1 - - - -
334B VAL* 2.8 34.2 + - - +
335B THR* 2.8 34.9 + - - +
336B GLY 4.0 0.3 + - - -
338B VAL* 4.0 13.4 - - + +
346B ARG* 4.0 8.4 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.8 25.6 - - + -
119B LEU* 4.2 8.5 - - + -
121B LEU* 4.1 7.2 - - + -
140B THR* 4.2 15.9 - - + +
280B HIS 3.0 21.0 + - - +
283B ASP* 1.3 74.4 - - - +
285B VAL* 1.3 63.5 + - - +
287B VAL* 3.4 9.0 - - - +
288B VAL* 3.1 31.9 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 5.6 4.9 - - + -
42B PHE* 3.7 36.1 - - + -
45B ALA* 3.5 27.6 - - + +
46B VAL* 3.6 24.2 - - + +
49B ALA* 4.2 8.2 - - + +
60B LEU* 5.9 0.2 - - + -
91B LEU* 4.1 6.3 - - + -
281B ILE* 3.2 21.7 + - + +
282B SER 4.1 4.0 - - - +
284B ALA* 1.3 74.2 - - - +
286B GLY* 1.3 64.2 + - - +
288B VAL* 4.6 4.7 - - - -
289B ALA* 3.0 26.3 + - + +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 5.5 4.9 - - - -
53B HIS* 4.9 1.4 + - - -
282B SER 3.1 12.0 + - - -
283B ASP 3.1 8.2 + - - -
284B ALA 3.1 1.0 - - - -
285B VAL* 1.3 78.6 - - - +
287B VAL* 1.3 61.0 + - - +
289B ALA* 3.9 2.8 - - - +
290B GLN* 3.1 24.1 + - - +
330B TYR* 3.7 30.1 - - - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 4.4 10.5 - - + -
140B THR* 5.2 0.7 - - + -
283B ASP 3.1 11.4 + - - +
284B ALA* 3.4 16.2 - - - +
286B GLY* 1.3 71.6 - - - +
288B VAL* 1.3 57.4 + - + +
290B GLN* 3.4 8.3 + - - +
291B ALA* 2.7 37.7 + - - +
325B LEU* 4.6 4.7 - - + -
328B SER* 4.7 10.2 + - - -
330B TYR* 3.6 33.4 - - + -
338B VAL* 4.2 13.0 - - + +
340B PHE* 4.0 36.1 - - + -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.5 36.6 - - + -
89B ALA* 4.5 14.6 - - + -
91B LEU* 4.3 12.3 - - + -
119B LEU* 3.6 28.0 - - + -
284B ALA 3.1 21.1 + - - +
285B VAL* 4.3 4.3 - - - +
287B VAL* 1.3 73.6 - - - +
289B ALA* 1.3 56.5 + - - +
291B ALA* 3.2 1.3 + - - +
292B VAL* 2.8 45.7 + - + +
321B PHE* 4.5 3.3 - - + -
325B LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.8 0.6 - - - +
49B ALA* 4.5 11.7 - - + -
53B HIS* 4.2 17.0 - - + -
60B LEU* 3.4 32.7 - - + +
285B VAL* 3.0 20.7 + - + +
286B GLY* 3.9 2.7 - - - +
288B VAL* 1.3 76.1 - - - +
290B GLN* 1.3 62.7 + - - +
292B VAL* 3.1 11.5 + - - +
293B HIS* 3.0 23.3 + - - -
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS* 3.7 25.6 + - + +
286B GLY 3.1 17.3 + - - +
287B VAL* 3.6 6.2 - - - +
289B ALA* 1.3 79.4 - - - +
291B ALA* 1.3 60.7 + - - +
293B HIS* 3.9 3.5 + - - +
294B GLU* 3.5 26.5 + - - +
328B SER* 3.6 19.1 + - - -
329B LYS 2.8 33.1 + - - +
330B TYR* 4.1 18.8 - - + +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL 2.7 21.7 + - - +
288B VAL 4.0 2.5 - - - +
290B GLN* 1.3 73.2 - - - +
292B VAL* 1.3 60.7 + - - +
293B HIS 3.4 0.2 - - - -
294B GLU* 3.5 9.1 - - - +
295B LEU* 2.9 27.9 + - - +
321B PHE* 3.7 14.6 - - + -
324B VAL* 3.8 13.3 - - + +
325B LEU* 4.3 12.6 - - + -
328B SER* 3.5 20.4 - - - +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.9 26.7 - - + -
29B ILE* 4.4 9.9 - - + -
58B ILE* 3.8 18.8 - - + -
60B LEU* 3.9 8.1 - - + -
88B TYR* 5.0 6.1 - - + -
288B VAL* 2.8 31.8 + - + +
289B ALA 3.1 5.4 + - - +
291B ALA* 1.3 75.4 - - - +
293B HIS* 1.3 59.4 + - - +
295B LEU* 3.1 2.3 + - - -
296B LEU* 2.9 41.5 + - + +
321B PHE* 3.5 25.8 - - + -
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Residues in contact with HIS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASN* 5.8 1.8 - - - -
53B HIS* 3.6 44.9 + + + +
54B GLY 4.2 11.2 + - - -
57B LYS* 5.8 4.7 - - + -
58B ILE* 3.4 41.2 + - + +
60B LEU* 4.7 15.9 - - + -
289B ALA 3.0 23.5 + - - +
290B GLN 4.0 4.7 - - - +
292B VAL* 1.3 75.1 - - - +
294B GLU* 1.3 64.8 + - - +
295B LEU 3.3 0.3 + - - -
296B LEU* 3.5 2.9 + - - +
297B GLU* 3.4 27.2 + - - +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN* 3.5 22.5 + - - +
291B ALA* 3.5 13.5 - - - +
293B HIS* 1.3 80.0 - - - +
295B LEU* 1.3 59.9 + - - +
297B GLU* 3.5 16.8 - - - +
298B LYS* 3.8 24.9 + - - -
324B VAL* 4.0 15.8 - - + +
328B SER* 5.7 1.1 - - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 5.2 8.1 - - + -
291B ALA 2.9 18.8 + - - +
292B VAL* 3.1 6.0 + - - +
294B GLU* 1.3 72.6 - - - +
296B LEU* 1.3 70.0 + - + +
297B GLU 2.8 15.9 + - - -
298B LYS* 3.0 30.4 + - + +
301B ILE* 3.9 24.8 - - + +
315B TRP* 5.4 3.4 - - + -
317B THR* 5.1 5.8 - - - +
320B LEU* 4.5 24.2 - - + -
321B PHE* 3.7 46.4 - - + +
324B VAL* 4.6 6.7 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.6 15.9 - - + +
27B VAL* 4.1 12.8 - - + -
57B LYS* 6.0 2.1 - - - +
58B ILE* 3.8 32.5 - - + -
88B TYR* 4.3 18.4 - - + +
292B VAL* 2.9 37.6 + - + +
293B HIS 3.5 5.1 + - - +
295B LEU* 1.3 89.7 - - + +
297B GLU* 1.3 57.5 + - - +
298B LYS 3.6 0.4 - - - -
299B GLU* 3.6 20.1 - - - +
301B ILE* 4.5 20.5 - - + +
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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