Contacts of the helix formed by residues 337 - 349 (chain 3) in PDB entry 1MVW
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 TYR 337 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183 LYS* 3.8 21.1 - - + -
263 ALA* 4.5 10.8 - - + -
273 PRO* 3.6 42.4 - - + -
303 VAL* 4.1 18.1 - - + +
3343 GLU* 2.8 15.9 + - + +
3363 LYS* 1.3 123.1 + - + +
3383 SER* 1.4 62.3 + - - -
3393 VAL* 3.3 3.1 - - - -
3403 TRP* 3.0 9.1 + - + +
3413 ILE* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1403 LEU 3.8 0.2 - - - +
1413 SER* 3.2 27.1 + - - -
1443 ALA* 3.5 12.0 - - - +
2983 VAL* 5.9 1.4 - - - +
2993 MET 4.4 2.4 + - - -
3003 SER* 3.7 16.0 - - - -
3323 PRO* 5.2 6.4 - - - +
3343 GLU* 3.8 9.1 + - - -
3353 ARG* 3.3 25.0 + - - +
3373 TYR* 1.4 72.0 - - - +
3393 VAL* 1.3 54.3 - - - +
3413 ILE* 3.1 7.7 + - - +
3423 GLY* 2.8 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 ASP* 3.4 35.0 - - + +
1063 THR* 4.2 2.2 - - + -
1373 GLN* 4.0 25.1 - - + +
1403 LEU* 3.3 27.1 - - + +
1413 SER* 3.1 24.4 + - - +
1543 ASP* 4.2 16.8 - - - +
3003 SER* 4.5 4.5 - - - +
3373 TYR 5.0 1.3 - - - -
3383 SER* 1.3 80.5 - - - +
3403 TRP* 1.3 61.7 + - - +
3433 GLY 3.2 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 VAL* 2.8 43.2 + - + +
113 ASP* 4.0 9.9 - - + +
183 LYS* 3.4 38.8 + - + -
193 ALA* 3.6 5.9 - - - +
203 GLY* 3.6 27.8 - - - -
213 PHE 3.5 23.3 - - - -
243 ASP* 3.8 17.5 - - + -
253 ASP 4.3 0.7 - - - -
263 ALA* 3.5 28.5 - - - -
273 PRO* 3.7 16.8 - - + -
1063 THR* 6.2 0.2 - - - -
3373 TYR* 3.0 17.9 + - + +
3393 VAL* 1.3 78.3 - - - +
3413 ILE* 1.3 66.4 + - + +
3433 GLY* 3.0 4.7 + - - +
3443 SER* 2.9 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253 ASP* 3.5 28.3 - - - +
263 ALA* 4.9 0.2 - - - -
1443 ALA* 4.5 6.5 - - + +
3343 GLU* 3.7 42.2 - - + +
3373 TYR* 2.9 36.4 + - + +
3383 SER* 3.6 4.7 - - - +
3403 TRP* 1.3 83.9 - - + +
3423 GLY* 1.3 57.9 + - - +
3443 SER* 3.0 7.1 + - - -
3453 ILE* 3.0 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1403 LEU* 3.4 31.4 - - - +
1433 TYR* 3.7 7.6 - - - -
1443 ALA* 3.5 14.9 - - - +
3383 SER 2.8 10.9 + - - -
3393 VAL 3.8 0.4 - - - -
3413 ILE* 1.3 75.3 - - - +
3433 GLY* 1.3 55.1 + - - +
3453 ILE* 3.8 2.9 - - - +
3463 LEU* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 VAL* 3.8 14.9 - - - +
1043 LEU* 4.3 7.3 - - - +
1403 LEU* 3.8 18.8 - - - +
3393 VAL 3.2 8.4 + - - -
3403 TRP 3.0 8.2 + - - -
3423 GLY* 1.3 75.2 - - - +
3443 SER* 1.3 53.6 + - - +
3463 LEU* 3.8 1.9 - - - +
3473 ALA* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 344 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 VAL* 3.9 10.2 - - - +
213 PHE 3.7 1.9 + - - -
223 ALA* 3.4 4.9 - - - +
233 GLY* 2.8 28.2 + - - -
243 ASP 3.0 15.4 + - - -
3403 TRP* 2.9 29.7 + - - -
3413 ILE* 3.3 11.4 - - - -
3433 GLY* 1.3 72.1 - - - +
3453 ILE* 1.3 59.5 + - - +
3483 SER* 2.7 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 TYR* 3.5 28.9 - - + +
1443 ALA* 4.4 20.4 - - - +
3413 ILE* 3.0 39.6 + - + +
3423 GLY 3.8 3.4 - - - +
3443 SER* 1.3 73.6 - - - +
3463 LEU* 1.3 66.9 + - - +
3483 SER* 2.7 21.1 + - - -
3493 LEU* 2.9 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043 LEU* 4.2 12.3 - - + -
1333 TYR* 4.5 7.9 - - + -
1353 ALA* 4.7 1.3 - - + -
1403 LEU* 3.7 24.9 - - + -
1433 TYR* 3.8 22.9 - - + +
3423 GLY 3.1 14.0 + - - +
3433 GLY 3.8 1.3 - - - +
3453 ILE* 1.3 80.7 - - - +
3473 ALA* 1.3 61.0 + - - +
3493 LEU* 3.1 24.5 - - + +
3523 PHE* 3.2 48.5 - - + +
3553 MET* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 ASP 5.7 0.5 - - - +
73 ALA* 4.3 8.4 - - + +
93 VAL* 4.5 2.0 - - + -
223 ALA* 3.9 16.2 - - + -
1043 LEU* 4.2 17.0 - - + -
3433 GLY 2.8 22.8 + - - +
3463 LEU* 1.3 75.5 - - - +
3483 SER* 1.3 59.6 + - - +
3493 LEU 3.3 4.2 - - - +
3523 PHE* 3.9 12.3 - - - -
3563 TRP* 4.1 29.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43 GLU* 5.0 19.0 - - - +
73 ALA* 5.7 0.2 - - - -
223 ALA* 3.9 6.9 - - - +
233 GLY* 4.0 20.7 + - - -
3443 SER 2.7 23.7 + - - -
3453 ILE* 2.7 14.9 + - - -
3473 ALA* 1.3 76.3 - - - +
3493 LEU* 1.3 65.0 + - - +
3503 SER* 3.6 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 TYR* 4.2 19.1 - - - +
3453 ILE* 2.9 24.2 + - + +
3463 LEU* 3.1 19.7 + - + +
3473 ALA 4.3 2.3 - - - +
3483 SER* 1.3 80.4 + - - +
3503 SER* 1.3 80.1 - - - +
3513 THR* 3.2 28.7 - - - +
3523 PHE* 3.3 18.7 + - + +
3533 GLN* 4.2 4.0 + - - +
----------------------------------------------------------
Back to top of page
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