Contacts of the helix formed by residues 337 - 349 (chain 8) 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 8).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188 LYS* 3.8 20.9 - - + -
268 ALA* 4.5 11.7 - - + -
278 PRO* 3.6 41.7 - - + -
308 VAL* 4.1 18.8 - - + +
3348 GLU* 2.8 12.6 + - + +
3368 LYS* 1.3 124.2 + - + +
3388 SER* 1.4 62.0 + - - -
3398 VAL* 3.3 3.6 - - - -
3408 TRP* 3.0 8.2 + - + -
3418 ILE* 2.9 39.2 + - + +
410A ASN* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1408 LEU 3.8 0.2 - - - +
1418 SER* 3.2 28.4 + - - -
1448 ALA* 3.5 10.9 - - - +
2988 VAL* 5.9 0.4 - - - +
2998 MET 4.4 2.4 + - - -
3008 SER* 3.7 15.9 - - - -
3328 PRO* 5.2 5.7 - - - +
3348 GLU* 3.8 7.2 + - - -
3358 ARG* 3.3 24.6 + - - +
3368 LYS 3.8 0.2 - - - -
3378 TYR* 1.4 72.1 - - - +
3398 VAL* 1.3 54.7 - - - +
3418 ILE* 3.1 7.8 + - - +
3428 GLY* 2.8 32.1 + - - -
636A LYS 5.2 1.3 - - - -
637A LYS* 4.9 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 ASP* 3.4 34.3 - - - +
1068 THR* 4.2 2.2 - - + -
1378 GLN* 4.0 26.2 - - + +
1408 LEU* 3.3 26.3 - - + +
1418 SER* 3.1 23.5 + - - +
1548 ASP* 4.2 17.5 - - - +
3008 SER* 4.5 4.3 - - - +
3358 ARG 6.1 0.2 - - - +
3378 TYR* 5.0 1.1 - - - -
3388 SER* 1.3 81.1 - - - +
3408 TRP* 1.3 60.2 + - - +
3438 GLY 3.2 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 VAL* 2.8 44.3 + - + +
118 ASP* 4.0 10.1 - - + +
188 LYS* 3.4 38.2 + - + -
198 ALA* 3.6 6.6 - - - +
208 GLY* 3.6 27.6 - - - -
218 PHE 3.5 10.5 - - - -
248 ASP* 3.8 3.6 - - + -
258 ASP 4.3 0.4 - - - -
268 ALA* 3.5 28.0 - - - -
278 PRO* 3.7 16.8 - - + -
1408 LEU* 5.7 0.2 - - - -
3378 TYR* 3.0 18.1 + - + +
3398 VAL* 1.3 79.0 - - - +
3418 ILE* 1.3 59.4 + - + +
3438 GLY* 3.0 4.2 + - - -
3448 SER 2.9 11.4 + - - -
642A LYS* 2.5 72.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 ASP 3.5 15.0 - - - +
268 ALA* 4.9 0.4 - - + -
3348 GLU* 3.7 16.8 - - + +
3378 TYR* 2.9 36.1 + - + +
3388 SER* 3.6 4.3 - - - +
3408 TRP* 1.3 80.1 - - + +
3428 GLY* 1.3 51.6 - - - +
3458 ILE* 3.0 2.6 + - + -
633A GLY* 5.5 2.7 - - - -
635A GLY* 2.7 64.8 - - - +
636A LYS 3.2 14.8 - - - +
637A LYS 3.4 8.3 - - - -
638A GLY* 2.0 35.5 - - - -
639A GLY 4.9 0.7 - - - +
642A LYS* 2.9 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1408 LEU* 3.4 30.9 - - - +
1438 TYR* 3.7 7.6 - - - -
1448 ALA* 3.5 13.1 - - - +
3388 SER 2.8 10.9 + - - -
3398 VAL 3.8 0.9 - - - -
3418 ILE* 1.3 75.9 - - - +
3438 GLY* 1.3 55.7 + - - +
3458 ILE* 3.7 0.3 + - - +
3468 LEU* 3.1 29.6 + - - +
637A LYS 4.0 0.7 - - - -
638A GLY* 3.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 VAL* 3.8 15.7 - - - -
1048 LEU* 4.3 6.8 - - - +
1408 LEU* 3.8 19.4 - - - +
3398 VAL 3.2 7.9 + - - -
3408 TRP 3.0 7.8 + - - -
3428 GLY* 1.3 75.7 - - - +
3448 SER* 1.3 54.8 + - - +
3468 LEU* 3.8 1.5 - - - +
3478 ALA* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 344 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 VAL* 3.9 6.0 - - - +
228 ALA* 3.7 2.0 - - - +
238 GLY 2.8 1.6 + - - -
248 ASP 3.8 0.4 - - - -
3408 TRP 2.9 1.0 + - - -
3418 ILE* 4.2 0.2 - - - -
3438 GLY* 1.3 68.9 - - - +
3458 ILE* 1.3 57.2 + - - +
3488 SER* 2.7 24.1 + - - -
639A GLY* 2.4 26.4 + - - -
642A LYS* 0.7 190.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1438 TYR* 3.5 3.8 - - + -
3418 ILE* 3.7 0.2 - - + -
3428 GLY 3.8 2.2 - - - +
3448 SER* 1.3 65.1 - - - +
3468 LEU* 1.3 54.7 - - - +
3488 SER* 2.7 12.1 + - - -
541A MET* 2.1 78.0 - - + +
637A LYS* 0.8 52.5 - - - +
638A GLY* 0.5 202.7 - - - +
639A GLY* 1.9 16.9 - - - +
640A LYS* 4.7 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048 LEU* 4.2 12.1 - - + -
1338 TYR* 4.5 7.9 - - + -
1358 ALA* 4.7 1.3 - - + -
1408 LEU* 3.7 24.9 - - + -
1438 TYR* 3.8 9.4 - - + -
3428 GLY 3.1 14.2 + - - +
3438 GLY 3.8 1.1 - - - +
3458 ILE* 1.3 71.9 - - - +
3478 ALA* 1.3 59.3 + - - +
3498 LEU* 3.1 3.6 + - - +
3528 PHE* 3.2 42.9 - - + +
3558 MET* 5.5 0.2 - - + -
538A GLU* 4.2 6.1 - - - +
541A MET* 1.5 82.7 - - + +
542A PHE* 4.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38 ASP 5.7 0.3 - - - +
78 ALA* 4.3 7.4 - - + +
98 VAL* 4.5 2.0 - - + -
228 ALA* 3.9 16.6 - - + -
1048 LEU* 4.2 17.3 - - + -
3438 GLY 2.8 21.5 + - - +
3468 LEU* 1.3 75.2 - - - +
3488 SER* 1.3 60.7 + - - +
3498 LEU 4.3 3.5 - - - +
3528 PHE* 3.9 13.1 - - - -
3568 TRP* 4.1 29.9 + - + -
641A LYS* 4.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48 GLU 5.1 0.2 - - - -
78 ALA* 5.7 0.2 - - - -
228 ALA* 3.9 3.3 - - - +
238 GLY 4.0 2.5 - - - -
3448 SER 2.7 23.8 + - - -
3458 ILE 2.7 10.9 + - - -
3478 ALA* 1.3 75.7 - - - +
3498 LEU* 1.3 57.1 + - - +
541A MET* 4.4 0.5 - - - +
639A GLY* 3.0 8.1 - - - -
641A LYS* 1.8 37.6 + - - -
647A GLN* 1.1 141.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3468 LEU 3.1 1.7 + - - +
3478 ALA 4.3 1.9 - - - +
3488 SER* 1.3 73.1 + - - +
3508 SER* 1.3 64.7 - - - +
3528 PHE* 3.3 15.1 + - - +
3538 GLN* 4.2 4.2 + - - +
537A GLU 1.7 33.0 - - - +
538A GLU* 1.8 60.1 - - + +
540A CYS* 3.3 9.4 - - + +
541A MET* 1.6 99.5 - - + +
641A LYS* 4.0 2.4 + - - -
647A GLN* 4.3 10.5 - - + +
----------------------------------------------------------
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