Contacts of the helix formed by residues 337 - 349 (chain 5) 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 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185 LYS* 3.8 20.6 - - + -
265 ALA* 4.5 11.2 - - + -
275 PRO* 3.6 42.2 - - + -
305 VAL* 4.1 18.3 - - + +
3345 GLU* 2.8 15.9 + - + +
3365 LYS* 1.3 124.4 + - + +
3385 SER* 1.4 62.8 + - - -
3395 VAL* 3.3 3.1 - - - -
3405 TRP* 3.0 8.8 + - + +
3415 ILE* 2.9 38.8 + - + +
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Residues in contact with SER 338 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1405 LEU 3.8 0.2 - - - +
1415 SER* 3.2 28.3 + - - -
1445 ALA* 3.5 11.6 - - - +
2985 VAL* 5.9 1.3 - - - +
2995 MET 4.4 2.3 + - - -
3005 SER* 3.7 15.6 - - - -
3325 PRO* 5.2 6.4 - - - +
3345 GLU* 3.8 8.5 + - - -
3355 ARG* 3.3 25.3 + - - +
3375 TYR* 1.4 72.2 - - - +
3395 VAL* 1.3 55.7 + - - +
3415 ILE* 3.1 7.7 + - - +
3425 GLY* 2.8 31.7 + - - -
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Residues in contact with VAL 339 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 ASP* 3.4 34.5 - - + +
1065 THR* 4.2 2.5 - - + -
1375 GLN* 4.0 25.6 - - + +
1405 LEU* 3.3 26.1 - - + +
1415 SER* 3.1 24.7 + - - +
1545 ASP* 4.2 17.3 - - - +
3005 SER* 4.5 3.6 - - - +
3375 TYR* 5.0 1.1 - - - -
3385 SER* 1.3 81.9 - - - +
3405 TRP* 1.3 61.8 + - - +
3435 GLY 3.2 14.0 + - - -
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Residues in contact with TRP 340 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 VAL* 2.8 43.9 + - + +
115 ASP* 4.0 9.6 + - + +
185 LYS* 3.4 39.3 + - + -
195 ALA* 3.6 6.1 - - - +
205 GLY* 3.6 27.4 - - - -
215 PHE 3.5 22.7 - - - -
245 ASP* 3.8 17.9 - - + -
255 ASP 4.3 0.4 - - - -
265 ALA* 3.5 28.3 - - - -
275 PRO* 3.7 16.8 - - + -
1065 THR* 6.2 0.2 - - - -
3375 TYR* 3.0 18.7 + - + +
3395 VAL* 1.3 78.6 - - - +
3415 ILE* 1.3 67.1 + - + +
3435 GLY* 3.0 4.7 + - - +
3445 SER* 2.9 33.0 + - - -
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Residues in contact with ILE 341 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255 ASP* 3.5 28.3 - - - +
265 ALA* 4.9 0.4 - - + -
1445 ALA* 4.5 6.3 - - + +
3345 GLU* 3.7 41.5 - - + +
3375 TYR* 2.9 37.6 + - + +
3385 SER* 3.6 4.9 - - - +
3405 TRP* 1.3 84.8 - - + +
3425 GLY* 1.3 58.8 + - - +
3445 SER* 3.0 6.6 + - - -
3455 ILE* 3.0 46.1 + - + +
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Residues in contact with GLY 342 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1405 LEU* 3.4 31.1 - - - +
1435 TYR* 3.7 8.1 - - - -
1445 ALA* 3.5 14.5 - - - +
3385 SER 2.8 11.6 + - - -
3395 VAL 3.8 0.9 - - - -
3415 ILE* 1.3 76.6 - - - +
3435 GLY* 1.3 53.7 + - - +
3455 ILE* 3.7 3.2 + - - +
3465 LEU* 3.1 29.6 + - - +
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Residues in contact with GLY 343 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 VAL* 3.8 15.2 - - - +
1045 LEU* 4.3 7.1 - - - +
1405 LEU* 3.8 18.3 - - - +
3395 VAL 3.2 8.2 + - - -
3405 TRP 3.0 8.4 + - - -
3425 GLY* 1.3 76.1 - - - +
3445 SER* 1.3 54.1 + - - +
3465 LEU* 3.8 2.1 - - - +
3475 ALA* 2.8 38.6 + - - +
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Residues in contact with SER 344 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 VAL* 3.9 10.9 - - - +
215 PHE 3.7 1.9 + - - -
225 ALA* 3.4 4.6 - - - +
235 GLY 2.8 28.5 + - - -
245 ASP 3.0 15.5 + - - -
3405 TRP* 2.9 30.8 + - - -
3415 ILE* 3.0 11.6 + - - -
3435 GLY* 1.3 71.0 - - - +
3455 ILE* 1.3 59.8 + - - +
3485 SER* 2.7 36.8 + - - -
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Residues in contact with ILE 345 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435 TYR* 3.5 29.6 - - + +
1445 ALA* 4.4 19.7 - - - +
3415 ILE* 3.0 39.0 + - + +
3425 GLY 3.8 3.4 - - - +
3445 SER* 1.3 74.3 - - - +
3465 LEU* 1.3 67.1 + - - +
3485 SER* 2.7 21.3 + - - -
3495 LEU* 2.9 21.1 + - + +
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Residues in contact with LEU 346 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045 LEU* 4.2 12.6 - - + -
1335 TYR* 4.5 7.9 - - + -
1355 ALA* 4.7 1.1 - - + -
1405 LEU* 3.7 25.4 - - + -
1435 TYR* 3.8 24.2 - - + +
3425 GLY 3.1 13.8 + - - +
3435 GLY 3.8 1.3 - - - +
3455 ILE* 1.3 81.0 - - - +
3475 ALA* 1.3 60.8 + - - +
3495 LEU* 3.1 24.7 - - + +
3525 PHE* 3.2 47.9 - - + +
3555 MET* 5.5 3.6 - - + -
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Residues in contact with ALA 347 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35 ASP 5.7 0.3 - - - +
75 ALA* 4.3 7.8 - - + +
95 VAL* 4.5 1.8 - - + -
225 ALA* 3.9 16.2 - - + -
1045 LEU* 4.2 17.5 - - + -
3435 GLY 2.8 22.1 + - - +
3465 LEU* 1.3 74.6 - - - +
3485 SER* 1.3 60.6 + - - +
3495 LEU 4.3 4.0 - - - +
3525 PHE* 3.9 12.7 - - - -
3565 TRP* 4.1 30.2 + - + -
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Residues in contact with SER 348 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45 GLU* 5.0 19.7 - - - +
75 ALA* 5.7 0.2 - - - -
225 ALA* 3.9 6.7 - - - +
235 GLY* 4.0 20.6 + - - -
3445 SER 2.7 24.1 + - - -
3455 ILE* 2.7 14.6 + - - -
3475 ALA* 1.3 75.9 - - - +
3495 LEU* 1.3 65.2 + - - +
3505 SER* 3.6 1.7 + - - -
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Residues in contact with LEU 349 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435 TYR* 4.2 20.0 - - - +
3455 ILE* 2.9 22.1 + - + +
3465 LEU* 3.1 20.1 + - + +
3475 ALA 4.3 2.1 - - - +
3485 SER* 1.3 81.1 + - - +
3505 SER* 1.3 79.7 + - - +
3515 THR* 3.2 28.5 - - - +
3525 PHE* 3.3 18.6 + - + +
3535 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