Contacts of the helix formed by residues 268 - 289 (chain B) in PDB entry 4MBS
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 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LEU* 3.7 12.9 - - - +
267B ASN* 1.4 84.8 - - - +
269B CYS* 1.4 59.4 + - - +
270B SER* 3.4 17.2 + - - +
271B SER* 3.3 22.6 + - - +
272B SER* 3.1 25.3 + - - -
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Residues in contact with CYS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS* 2.0 54.6 - - + +
21B GLN 4.9 4.0 - - - -
268B ASN* 1.4 70.9 - - - +
270B SER* 1.4 64.6 + - - +
272B SER* 3.3 4.6 + - - -
273B ASN* 3.2 22.8 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 3.9 12.3 - - - +
269B CYS* 1.4 79.8 - - - +
271B SER* 1.3 61.1 + - - +
273B ASN* 3.4 7.1 + - - +
274B ARG* 3.1 42.5 + - - +
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.6 31.2 - - - +
268B ASN* 3.3 26.5 + - - -
270B SER* 1.3 79.9 + - - +
272B SER* 1.4 59.6 + - - +
274B ARG* 3.6 17.3 + - - +
275B LEU* 3.0 38.3 + - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PRO* 5.0 13.7 - - - -
20B CYS* 4.9 9.2 - - - -
258B ASN* 4.8 2.3 - - - +
262B GLU* 4.7 21.7 - - - +
266B LEU 5.5 0.6 + - - -
267B ASN 5.1 2.7 - - - -
268B ASN 3.1 20.0 + - - -
269B CYS* 3.3 9.8 + - - -
271B SER* 1.4 76.0 - - - +
273B ASN* 1.4 56.1 + - - +
275B LEU* 4.2 2.6 - - - +
276B ASP* 3.2 27.0 + - - +
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Residues in contact with ASN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 5.1 18.2 - - + -
23B ILE* 5.3 7.0 - - + +
269B CYS* 3.2 13.4 + - - +
270B SER* 3.7 9.2 - - - +
271B SER 3.3 0.2 - - - -
272B SER* 1.4 74.9 - - - +
274B ARG* 1.4 57.2 + - - +
276B ASP* 3.3 5.4 + - - +
277B GLN* 3.0 38.9 + - + +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER* 3.1 33.9 + - - +
271B SER* 3.6 16.6 + - - +
273B ASN* 1.4 75.9 - - - +
275B LEU* 1.3 62.3 + - + +
277B GLN* 4.0 5.2 - - - +
278B ALA* 3.1 26.9 + - - +
1105B OLC 4.3 18.8 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 3.8 9.9 - - + +
257B LEU* 3.7 26.2 - - + +
258B ASN* 3.7 42.5 - - + +
261B GLN 5.7 0.4 - - - -
262B GLU* 4.8 11.7 - - + +
266B LEU* 5.1 12.8 - - + +
271B SER* 3.0 23.3 + - - +
272B SER* 4.3 3.6 - - - +
274B ARG* 1.3 78.8 - - + +
276B ASP* 1.3 59.7 + - - +
277B GLN 3.4 0.2 - - - -
278B ALA* 3.6 6.8 + - + +
279B MET* 3.1 25.1 + - - +
1103B OLC 4.4 17.9 - - - +
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Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 6.0 0.3 - - - +
258B ASN* 3.9 7.9 + - - +
272B SER 3.2 20.2 + - - +
273B ASN* 3.3 6.7 + - - +
275B LEU* 1.3 75.4 - - - +
277B GLN* 1.4 66.5 + - - +
279B MET* 3.3 10.8 + - - +
280B GLN* 3.2 33.9 + - - +
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 6.2 3.4 - - + -
25B VAL* 4.6 20.4 - - + -
273B ASN* 3.0 22.7 + - + +
274B ARG* 4.0 6.1 - - - +
276B ASP* 1.4 76.7 - - - +
278B ALA* 1.4 58.6 + - - +
280B GLN* 3.3 18.6 + - - +
281B VAL* 3.1 34.3 + - + +
1105B OLC 5.5 5.8 - - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 3.9 20.2 - - + -
274B ARG 3.1 19.1 + - - +
275B LEU* 3.7 9.2 - - + +
277B GLN* 1.4 73.2 - - - +
279B MET* 1.4 59.4 + - - +
281B VAL* 4.6 5.6 - - - -
282B THR* 2.8 36.4 + - + +
1103B OLC 4.7 6.3 - - - +
1105B OLC 3.6 26.4 - - - +
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Residues in contact with MET 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B TYR* 3.4 37.7 - - + +
254B VAL* 3.7 16.8 - - + +
255B LEU* 4.0 20.6 - - + -
258B ASN* 3.7 31.4 - - + -
275B LEU 3.1 12.0 + - - +
276B ASP* 3.4 14.6 - - - +
277B GLN 3.3 0.4 - - - -
278B ALA* 1.4 77.0 - - - +
280B GLN* 1.4 55.6 + - + +
282B THR* 3.3 5.0 + - - -
283B GLU* 3.1 37.9 + - - +
1101B MRV 4.0 17.0 - - + +
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.4 29.4 - - - +
29B ALA* 5.6 7.1 - - - +
276B ASP* 3.2 23.4 + - - +
277B GLN* 3.3 16.4 + - - +
279B MET* 1.4 77.9 - - + +
281B VAL* 1.4 57.6 + - + +
283B GLU* 3.5 5.0 + - - +
284B THR* 2.8 34.0 + - - +
1101B MRV 4.7 2.3 - - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLN* 3.1 20.1 + - + +
278B ALA* 4.0 7.0 - - - +
280B GLN* 1.4 75.6 - - + +
282B THR* 1.4 56.9 + - - +
284B THR* 3.2 8.7 + - - -
285B LEU* 3.0 26.3 + - + +
1105B OLC 4.5 42.6 - - + +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE 4.3 2.6 - - - +
250B PRO* 3.9 21.8 - - + -
251B TYR* 3.4 35.0 - - - +
254B VAL* 4.0 13.4 - - + +
278B ALA* 2.8 24.6 + - - +
279B MET* 3.3 7.4 + - - -
281B VAL* 1.4 72.0 - - - +
283B GLU* 1.3 62.0 + - - +
285B LEU* 3.5 10.2 + - + +
286B GLY* 3.0 23.6 + - - -
1105B OLC 3.9 27.6 - - + -
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B TYR* 2.9 23.8 + - - +
248B TRP* 4.2 3.7 - - + -
251B TYR* 3.8 18.0 + - + -
279B MET* 3.1 24.4 + - - +
280B GLN* 4.0 3.8 - - - +
282B THR* 1.3 74.7 + - - +
284B THR* 1.4 60.4 + - - +
286B GLY* 3.4 0.7 + - - -
287B MET* 2.9 28.4 + - - +
1101B MRV 2.9 87.8 + - + +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.3 11.2 - - + +
36B LEU* 3.8 29.8 - - + -
37B TYR* 3.6 26.2 + - + -
280B GLN* 2.8 19.6 + - - +
281B VAL* 3.4 11.7 - - - -
283B GLU* 1.4 73.5 - - - +
285B LEU* 1.4 64.2 + - - +
287B MET* 3.3 7.4 + - + +
288B THR* 3.2 25.4 + - - +
1101B MRV 3.8 9.6 - - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B LEU 4.1 6.5 - - - +
247B PHE* 3.3 51.6 - - + +
250B PRO* 4.1 21.1 - - + -
281B VAL* 3.0 14.4 + - + +
282B THR* 3.6 10.3 - - - +
283B GLU 3.4 0.2 - - - -
284B THR* 1.4 74.5 - - - +
286B GLY* 1.3 63.4 + - - +
288B THR* 3.2 22.5 - - + -
1103B OLC 4.3 5.8 - - + -
1105B OLC 3.8 36.1 - - + -
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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
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79B PHE* 5.0 0.5 - - - -
247B PHE 3.4 17.4 + - - -
248B TRP* 3.4 31.9 + - - -
282B THR 3.0 13.3 + - - -
283B GLU 3.4 2.9 + - - -
284B THR 3.3 0.4 - - - -
285B LEU* 1.3 73.7 - - - +
287B MET* 1.3 64.8 + - - +
289B HIS* 3.0 22.5 + - - +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.2 1.1 - - + -
37B TYR* 4.1 35.7 - - + -
40B VAL* 4.1 17.5 - - + -
79B PHE* 3.6 27.3 - - + -
83B VAL* 3.8 29.4 - - + -
108B TYR* 4.0 1.1 - - + +
248B TRP* 3.8 1.4 - - - -
283B GLU 2.9 17.2 + - - +
284B THR* 3.3 9.4 + - + +
286B GLY* 1.3 74.3 - - - +
288B THR* 1.3 86.0 + - - +
289B HIS 3.0 6.2 + - - -
290B CYS* 3.1 27.8 + - - +
1101B MRV 3.9 25.4 - - + -
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.9 9.7 - - + +
40B VAL* 4.0 18.8 - - + +
247B PHE* 3.7 22.0 - - + -
284B THR 3.2 14.2 + - - -
285B LEU* 3.2 17.7 - - + -
287B MET* 1.3 87.3 - - - +
289B HIS* 1.3 59.8 + - - +
290B CYS 3.1 2.0 + - - -
291B CYS* 3.3 24.5 + - - -
292B ILE* 3.7 8.2 - - + +
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Residues in contact with HIS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASP* 4.4 6.8 + - - +
119B ILE* 4.7 4.3 - - + -
240B ILE 4.7 0.6 + - - -
243B VAL* 4.2 5.7 - - + +
244B TYR* 3.6 44.1 + + + +
247B PHE* 3.8 40.6 - + + -
248B TRP* 4.1 9.7 + + - +
285B LEU 3.7 2.0 + - - -
286B GLY 3.0 18.3 + - - +
288B THR* 1.3 77.4 - - - +
290B CYS* 1.3 60.0 + - - +
291B CYS 3.2 1.1 + - - -
292B ILE* 3.3 24.6 + - + +
293B ASN* 3.9 29.7 + - - -
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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
------------------------------------------------------------
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