Contacts of the helix formed by residues 337 - 349 (chain 6) 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 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186 LYS* 3.8 20.9 - - + -
266 ALA* 4.5 11.2 - - + -
276 PRO* 3.6 43.3 - - + -
306 VAL* 4.1 17.7 - - + +
3346 GLU* 2.8 15.9 + - + +
3366 LYS* 1.3 124.4 + - + +
3386 SER* 1.4 61.7 + - - -
3396 VAL* 3.3 3.6 - - - -
3406 TRP* 3.0 8.5 + - + +
3416 ILE* 2.9 38.9 + - + +
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Residues in contact with SER 338 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1406 LEU 3.8 0.2 - - - +
1416 SER* 3.2 27.5 + - - -
1446 ALA* 3.5 12.0 - - - +
2986 VAL* 5.9 1.1 - - - +
2996 MET 4.4 2.6 + - - -
3006 SER* 3.7 16.0 - - - -
3326 PRO* 5.2 5.5 - - - +
3346 GLU* 3.8 8.7 + - - -
3356 ARG* 3.3 25.0 + - - +
3366 LYS 3.8 0.2 - - - -
3376 TYR* 1.4 72.7 - - - +
3396 VAL* 1.3 55.7 + - - +
3416 ILE* 3.1 8.2 + - - +
3426 GLY* 2.8 32.1 + - - -
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Residues in contact with VAL 339 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 ASP* 3.4 35.2 - - + +
1066 THR* 4.2 1.8 - - + -
1376 GLN* 4.0 25.1 - - + +
1406 LEU* 3.3 26.8 - - + +
1416 SER* 3.1 24.5 - - - +
1546 ASP* 4.2 17.9 - - - +
3006 SER* 4.5 3.8 - - - +
3356 ARG 6.1 0.2 - - - +
3376 TYR* 5.0 1.1 - - - -
3386 SER* 1.3 81.6 - - - +
3406 TRP* 1.3 60.8 + - - +
3436 GLY 3.2 14.4 + - - -
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Residues in contact with TRP 340 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 VAL* 2.8 43.2 + - + +
116 ASP* 4.0 10.3 + - + +
186 LYS* 3.4 38.1 + - + -
196 ALA* 3.6 6.1 - - - +
206 GLY* 3.6 27.8 - - - -
216 PHE 3.5 22.7 - - - -
246 ASP* 3.8 17.5 - - + -
256 ASP 4.3 0.7 - - - -
266 ALA* 3.5 29.2 - - - -
276 PRO* 3.7 16.8 - - + -
1066 THR* 6.2 0.2 - - - -
3376 TYR* 3.0 17.7 + - + +
3396 VAL* 1.3 78.3 - - - +
3416 ILE* 1.3 67.8 + - + +
3436 GLY* 3.0 3.6 + - - -
3446 SER* 2.9 34.2 + - - -
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Residues in contact with ILE 341 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256 ASP* 3.5 28.3 - - - +
266 ALA* 4.9 0.4 - - + -
1446 ALA* 4.5 6.7 - - + +
3346 GLU* 3.7 41.1 - - + +
3376 TYR* 2.9 35.2 + - + +
3386 SER* 3.6 5.2 - - - +
3406 TRP* 1.3 85.7 - - + +
3426 GLY* 1.3 56.2 + - - +
3446 SER* 3.0 7.2 + - - -
3456 ILE* 3.0 46.4 + - + +
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Residues in contact with GLY 342 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1406 LEU* 3.4 30.9 - - - +
1436 TYR* 3.7 7.8 - - - -
1446 ALA* 3.5 15.1 - - - +
3386 SER 2.8 11.4 + - - -
3396 VAL 3.8 0.4 - - - -
3406 TRP 3.2 0.2 - - - -
3416 ILE* 1.3 76.1 - - - +
3436 GLY* 1.3 54.7 + - - +
3456 ILE* 4.4 2.5 - - - -
3466 LEU* 3.1 30.3 + - - +
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Residues in contact with GLY 343 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 VAL* 3.8 14.8 - - - -
1046 LEU* 4.3 7.1 - - - +
1406 LEU* 3.8 19.4 - - - +
3396 VAL 3.2 8.6 + - - -
3406 TRP 3.0 7.8 + - - -
3426 GLY* 1.3 75.5 - - - +
3446 SER* 1.3 53.7 + - - +
3466 LEU* 3.8 1.5 - - - +
3476 ALA* 2.8 38.5 + - - +
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Residues in contact with SER 344 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 VAL* 3.9 10.7 - - - +
216 PHE 3.7 2.1 + - - -
226 ALA* 3.4 4.1 - - - +
236 GLY* 2.8 28.5 + - - -
246 ASP 3.0 15.9 + - - -
3406 TRP* 2.9 30.0 + - - -
3416 ILE* 3.0 11.2 + - - -
3436 GLY* 1.3 72.7 - - - +
3456 ILE* 1.3 57.0 + - - +
3486 SER* 2.7 36.7 + - - -
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Residues in contact with ILE 345 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436 TYR* 3.5 29.4 - - + +
1446 ALA* 4.4 18.8 - - - +
3416 ILE* 3.0 40.0 + - + +
3426 GLY 3.8 3.4 - - - +
3446 SER* 1.3 75.6 - - - +
3466 LEU* 1.3 66.0 + - - +
3486 SER* 2.7 20.8 + - - -
3496 LEU* 2.9 21.1 + - + +
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Residues in contact with LEU 346 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046 LEU* 4.2 12.3 - - + -
1336 TYR* 4.5 8.7 - - + +
1356 ALA* 4.7 0.9 - - + -
1406 LEU* 3.7 25.1 - - + -
1436 TYR* 3.8 24.9 - - + +
3426 GLY 3.1 13.6 + - - +
3436 GLY 3.8 1.3 - - - +
3456 ILE* 1.3 79.1 - - - +
3476 ALA* 1.3 61.3 + - - +
3496 LEU* 3.1 24.6 - - + +
3526 PHE* 3.2 47.9 - - + +
3556 MET* 5.5 3.6 - - + -
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Residues in contact with ALA 347 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36 ASP 5.7 0.2 - - - +
76 ALA* 4.3 7.8 - - + +
96 VAL* 4.5 2.0 - - + -
226 ALA* 3.9 16.2 - - + -
1046 LEU* 4.2 16.8 - - + -
3436 GLY 2.8 22.9 + - - +
3466 LEU* 1.3 75.5 - - - +
3486 SER* 1.3 59.3 + - - +
3496 LEU 3.6 4.0 + - - +
3526 PHE* 3.9 12.1 - - - -
3566 TRP* 4.1 30.3 + - + -
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Residues in contact with SER 348 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46 GLU* 5.0 19.4 - - - +
76 ALA* 5.7 0.2 - - - -
226 ALA* 3.9 6.5 - - - +
236 GLY* 4.0 20.7 + - - -
3446 SER 2.7 23.9 + - - -
3456 ILE* 2.7 14.2 + - - -
3476 ALA* 1.3 76.8 - - - +
3496 LEU* 1.3 67.0 + - - +
3506 SER* 3.6 1.7 + - - -
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Residues in contact with LEU 349 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436 TYR* 4.2 20.4 - - - +
3456 ILE* 2.9 23.8 + - + +
3466 LEU* 3.1 19.9 + - + +
3476 ALA 4.3 2.6 - - - +
3486 SER* 1.3 81.4 - - - +
3506 SER* 1.3 79.5 - - - +
3516 THR* 3.2 29.4 - - - +
3526 PHE* 3.3 19.1 + - + +
3536 GLN* 4.2 4.2 + - - +
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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
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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