Contacts of the helix formed by residues 268 - 289 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.7 12.7 - - - +
267A ASN* 1.4 83.9 - - - +
269A CYS* 1.4 60.3 + - - +
270A SER* 3.4 17.0 + - - +
271A SER* 3.3 22.6 + - - +
272A SER* 3.1 25.3 + - - -
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A CYS* 2.0 53.6 - - + -
21A GLN 4.9 1.1 - - - -
268A ASN* 1.4 70.0 - - - +
270A SER* 1.4 65.7 + - - +
272A SER* 3.3 3.8 + - - -
273A ASN* 3.2 40.5 + - - +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 3.9 11.4 - - - +
269A CYS* 1.4 80.2 - - - +
271A SER* 1.4 60.3 + - - +
273A ASN* 3.5 10.6 + - - +
274A ARG* 3.1 35.5 + - - +
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.6 32.4 - - - +
268A ASN* 3.3 26.3 + - - -
270A SER* 1.4 78.8 + - - +
272A SER* 1.4 59.4 + - - +
274A ARG* 3.3 30.6 + - - +
275A LEU* 3.0 37.2 + - - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 5.3 8.3 - - - -
20A CYS* 5.0 10.1 - - - -
258A ASN* 4.8 2.3 - - - +
266A LEU 5.5 0.9 + - - -
267A ASN 5.1 2.4 - - - -
268A ASN 3.1 19.0 + - - -
269A CYS* 3.3 10.5 + - - -
271A SER* 1.4 74.5 - - - +
273A ASN* 1.3 60.6 + - - +
275A LEU* 4.2 4.1 - - - +
276A ASP* 3.2 27.4 + - - +
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Residues in contact with ASN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A CYS* 4.4 7.8 - - - +
21A GLN 4.4 7.5 + - - -
22A LYS* 3.7 28.9 + - + +
23A ILE* 4.9 8.8 - - + +
269A CYS* 3.2 30.4 + - - +
270A SER* 3.7 8.8 - - - +
271A SER 3.3 0.2 - - - -
272A SER* 1.3 78.8 - - - +
274A ARG* 1.3 57.3 + - - +
276A ASP* 3.3 5.9 + - - +
277A GLN* 3.0 38.0 + - + +
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A SER* 3.1 24.6 + - - +
271A SER* 3.3 31.2 + - - +
273A ASN* 1.3 75.9 - - - +
275A LEU* 1.4 68.9 + - + +
277A GLN* 4.0 5.2 - - - +
278A ALA* 3.1 27.3 + - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 3.8 10.2 - - + +
257A LEU* 3.7 29.4 - - + +
258A ASN* 3.7 42.1 - - + +
261A GLN 5.7 0.4 - - - -
262A GLU* 5.3 3.8 - - + -
266A LEU* 5.1 16.8 - - + +
271A SER* 3.0 23.7 + - - +
272A SER* 4.3 3.6 - - - +
274A ARG* 1.4 91.8 - - + +
276A ASP* 1.3 59.3 + - - +
278A ALA* 3.6 9.0 + - + +
279A MET* 3.1 25.5 + - - +
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 5.0 10.9 - - - +
25A VAL* 6.0 1.7 - - - +
258A ASN* 3.9 7.8 + - - +
272A SER 3.2 20.4 + - - +
273A ASN* 3.3 6.7 + - - +
275A LEU* 1.3 75.2 - - - +
277A GLN* 1.4 66.3 + - - +
279A MET* 3.3 9.9 + - - +
280A GLN* 3.2 27.2 + - - +
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Residues in contact with GLN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 6.4 1.8 - - + -
25A VAL* 4.7 25.6 - - + -
273A ASN* 3.0 22.0 + - + +
274A ARG* 4.0 6.1 - - - +
276A ASP* 1.4 77.4 - - - +
278A ALA* 1.4 57.7 + - - +
280A GLN* 3.3 10.1 + - - +
281A VAL* 3.1 33.9 + - + +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 3.9 20.2 - - + -
274A ARG 3.1 19.0 + - - +
275A LEU* 3.7 11.2 - - + +
277A GLN* 1.4 73.2 - - - +
279A MET* 1.3 59.6 + - - +
281A VAL* 4.0 6.0 - - - +
282A THR* 2.9 37.4 + - + +
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Residues in contact with MET 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.4 37.9 - - + +
254A VAL* 3.7 16.8 - - + +
255A LEU* 3.9 14.8 - - + +
258A ASN* 3.7 30.3 - - + -
275A LEU 3.1 12.2 + - - +
276A ASP* 3.4 14.8 - - - +
277A GLN 3.3 0.2 - - - -
278A ALA* 1.3 76.6 - - - +
280A GLN* 1.3 60.3 + - + +
282A THR* 3.3 4.9 + - - -
283A GLU* 3.1 32.9 + - - +
1101A MRV 3.9 25.1 - - + +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 5.9 7.4 - - + -
276A ASP* 3.2 19.7 + - - +
277A GLN* 3.3 11.4 + - - +
279A MET* 1.3 77.7 - - + +
281A VAL* 1.4 57.7 + - + +
283A GLU* 4.0 5.3 - - - +
284A THR* 2.9 33.3 + - - +
1101A MRV 4.9 1.7 - - - +
1107A OLC 5.4 3.4 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLN* 3.1 20.1 + - + +
278A ALA* 4.0 6.3 - - - +
280A GLN* 1.4 75.0 - - + +
282A THR* 1.4 60.4 + - + +
284A THR* 3.2 5.2 + - - -
285A LEU* 2.9 26.3 + - + +
1107A OLC 3.7 43.6 - - - +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A PHE 4.4 2.4 - - - +
250A PRO* 3.9 21.1 - - + -
251A TYR* 3.4 33.8 - - - +
254A VAL* 4.0 18.9 - - + +
278A ALA* 2.9 25.7 + - + +
279A MET* 3.3 7.4 + - - -
281A VAL* 1.4 75.0 - - + +
283A GLU* 1.3 62.7 + - - +
285A LEU* 3.5 11.9 + - + +
286A GLY* 3.0 23.4 + - - -
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 2.8 23.1 + - - +
248A TRP* 4.2 4.3 - - + -
251A TYR* 3.8 22.7 + - + -
279A MET* 3.1 24.2 + - - +
280A GLN* 4.0 5.1 - - - +
282A THR* 1.3 74.8 + - - +
284A THR* 1.4 59.9 + - - +
286A GLY* 3.4 1.0 + - - -
287A MET* 2.9 28.8 + - - +
1101A MRV 2.8 80.6 + - + +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.4 1.7 - - - +
36A LEU* 3.7 21.3 - - + -
37A TYR* 3.6 24.7 + - + -
280A GLN* 2.9 19.0 + - - +
281A VAL 3.2 9.2 + - - -
283A GLU* 1.4 73.1 - - - +
285A LEU* 1.4 62.2 + - - +
287A MET* 3.3 7.5 + - + +
288A THR* 3.1 26.0 + - - +
1101A MRV 3.7 11.0 - - - +
1107A OLC 3.2 37.0 + - + +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LEU 4.2 7.2 - - - +
247A PHE* 3.3 50.7 - - + +
250A PRO* 4.0 25.4 - - + -
281A VAL* 2.9 15.8 + - + +
282A THR* 3.6 11.4 - - + +
283A GLU 3.4 0.2 - - - -
284A THR* 1.4 74.9 - - - +
286A GLY* 1.3 61.5 + - - +
288A THR* 3.2 20.8 - - + -
1107A OLC 3.5 22.3 + - + +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 5.0 0.3 - - - -
247A PHE 3.4 17.4 + - - -
248A TRP* 3.4 33.0 + - - -
282A THR 3.0 13.3 + - - -
283A GLU 3.4 2.9 + - - -
284A THR 3.3 0.4 - - - -
285A LEU* 1.3 73.9 - - - +
287A MET* 1.3 64.3 + - - +
289A HIS* 3.0 22.9 + - - +
290A CYS 4.4 0.2 + - - -
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 5.4 0.9 - - + -
37A TYR* 4.1 28.3 - - + -
40A VAL* 4.0 18.4 - - + -
79A PHE* 3.6 28.3 - - + -
83A VAL* 3.8 32.8 - - + -
108A TYR* 4.0 6.5 - - - +
248A TRP* 3.8 1.4 - - - -
283A GLU 2.9 18.3 + - - +
284A THR* 3.3 10.3 + - + +
286A GLY* 1.3 73.8 - - - +
288A THR* 1.3 89.0 - - - +
289A HIS 3.1 1.6 + - - -
290A CYS* 3.1 27.8 + - - +
1101A MRV 3.9 21.8 - - + -
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 5.4 1.9 - - - +
40A VAL* 4.0 11.6 - - + +
247A PHE* 3.7 16.8 - - + -
284A THR* 3.1 15.3 + - - +
285A LEU* 3.2 16.4 - - + +
287A MET* 1.3 88.1 - - - +
289A HIS* 1.4 59.8 + - - +
290A CYS* 3.1 1.8 + - - -
291A CYS* 3.2 23.3 + - - +
292A ILE* 3.9 1.7 - - + +
1107A OLC 3.4 51.0 - - + +
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Residues in contact with HIS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP* 4.5 8.1 + - - +
119A ILE* 4.9 4.3 - - + -
240A ILE 4.9 0.6 + - - -
243A VAL* 4.2 5.5 - - + +
244A TYR* 3.6 41.6 + + + +
247A PHE* 3.7 41.3 - + + -
248A TRP* 4.2 10.0 + + - +
285A LEU 3.7 1.4 + - - -
286A GLY 3.0 17.9 + - - +
288A THR* 1.4 72.8 - - - +
290A CYS* 1.4 56.7 + - - +
291A CYS 3.0 11.4 + - - -
292A ILE* 3.1 26.6 + - + +
293A ASN* 3.9 30.6 + - - -
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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