Contacts of the helix formed by residues 337 - 349 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y LYS* 3.8 20.2 - - + -
26Y ALA* 4.5 10.8 - - + -
27Y PRO* 3.6 42.8 - - + -
30Y VAL* 4.1 18.3 - - + +
334Y GLU* 2.8 15.7 + - + +
336Y LYS* 1.3 123.7 + - + +
338Y SER* 1.3 63.3 + - - -
339Y VAL* 3.3 3.4 - - - -
340Y TRP* 3.0 8.6 + - + -
341Y ILE* 2.9 39.6 + - + +
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Residues in contact with SER 338 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Y LEU 3.8 0.2 - - - +
141Y SER* 3.2 27.7 + - - -
144Y ALA* 3.5 11.8 - - - +
298Y VAL* 5.9 1.0 - - - +
299Y MET 4.4 2.4 + - - -
300Y SER* 3.7 15.8 - - - -
332Y PRO* 5.2 5.9 - - - +
334Y GLU* 3.8 8.8 + - - -
335Y ARG* 3.3 24.1 + - - +
337Y TYR* 1.3 71.5 - - - +
339Y VAL* 1.3 54.4 - - - +
341Y ILE* 3.1 7.8 + - - +
342Y GLY* 2.8 31.5 + - - -
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Residues in contact with VAL 339 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Y ASP* 3.4 35.4 - - - +
106Y THR* 4.2 2.5 - - + -
137Y GLN* 4.0 25.1 - - + +
140Y LEU* 3.3 26.4 - - + +
141Y SER* 3.1 24.7 + - - +
154Y ASP* 4.2 16.6 - - - +
300Y SER* 4.5 4.7 - - - +
337Y TYR* 5.0 1.1 - - - -
338Y SER* 1.3 81.0 - - - +
340Y TRP* 1.3 61.6 + - - +
343Y GLY 3.2 14.4 + - - -
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Residues in contact with TRP 340 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y VAL* 2.8 43.8 + - + +
11Y ASP* 4.0 9.4 + - + +
18Y LYS* 3.4 38.9 + - + -
19Y ALA* 3.6 6.6 - - - +
20Y GLY* 3.6 27.4 - - - -
21Y PHE 3.5 23.1 - - - -
24Y ASP* 3.8 18.2 - - + -
25Y ASP 4.3 0.4 - - - -
26Y ALA* 3.5 28.9 - - - -
27Y PRO* 3.7 17.5 - - + -
106Y THR* 6.2 0.4 - - - -
337Y TYR* 3.0 17.7 + - + +
339Y VAL* 1.3 77.5 - - - +
341Y ILE* 1.3 67.7 + - + +
343Y GLY* 3.0 4.5 + - - -
344Y SER* 2.9 33.7 + - - -
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Residues in contact with ILE 341 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y ASP* 3.5 28.9 - - - +
144Y ALA* 4.5 6.1 - - + +
334Y GLU* 3.7 42.0 - - + +
337Y TYR* 2.9 36.1 + - + +
338Y SER* 3.6 5.4 - - - +
340Y TRP* 1.3 84.5 - - + +
342Y GLY* 1.3 58.1 + - - +
344Y SER* 3.0 6.9 + - - -
345Y ILE* 3.0 46.5 + - + +
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Residues in contact with GLY 342 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Y LEU* 3.4 32.3 - - - +
143Y TYR* 3.7 8.0 - - - -
144Y ALA* 3.5 14.3 - - - +
338Y SER 2.8 10.7 + - - -
339Y VAL 3.4 1.3 + - - -
341Y ILE* 1.3 75.5 - - - +
343Y GLY* 1.3 54.5 + - - +
345Y ILE* 3.8 2.9 - - - +
346Y LEU* 3.1 29.6 + - - +
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Residues in contact with GLY 343 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y VAL* 3.8 14.6 - - - -
104Y LEU* 4.3 7.3 - - - +
140Y LEU* 3.8 19.3 - - - +
339Y VAL 3.2 8.6 + - - -
340Y TRP 3.0 8.2 + - - -
342Y GLY* 1.3 75.4 - - - +
344Y SER* 1.3 53.7 + - - +
346Y LEU* 3.8 1.3 - - - +
347Y ALA* 2.8 38.5 + - - +
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Residues in contact with SER 344 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y VAL* 3.9 10.2 - - - +
21Y PHE 3.7 1.9 + - - -
22Y ALA* 3.4 5.0 - - - +
23Y GLY 2.8 28.8 + - - -
24Y ASP 3.0 15.7 + - - -
340Y TRP* 2.9 29.9 + - - -
341Y ILE* 3.3 10.8 - - - -
343Y GLY* 1.3 73.2 - - - +
345Y ILE* 1.3 58.4 + - - +
348Y SER* 2.7 36.0 + - - -
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Residues in contact with ILE 345 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143Y TYR* 3.5 28.7 - - + +
144Y ALA* 4.4 20.0 - - - +
341Y ILE* 3.0 39.6 + - + +
342Y GLY 3.8 3.4 - - - +
344Y SER* 1.3 73.5 - - - +
346Y LEU* 1.3 66.4 + - - +
348Y SER* 2.7 21.7 + - - -
349Y LEU* 2.9 21.6 + - + +
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Residues in contact with LEU 346 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Y LEU* 4.2 12.6 - - + -
133Y TYR* 4.5 7.9 - - + -
135Y ALA* 4.7 1.6 - - + -
140Y LEU* 3.7 24.2 - - + -
143Y TYR* 3.8 24.7 - - + +
342Y GLY 3.1 13.8 + - - +
343Y GLY 3.8 1.1 - - - +
345Y ILE* 1.3 80.6 - - - +
347Y ALA* 1.3 61.9 + - - +
349Y LEU* 3.1 24.1 + - + +
352Y PHE* 3.2 48.5 - - + +
355Y MET* 5.5 3.4 - - + -
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Residues in contact with ALA 347 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y ASP 5.7 0.2 - - - +
7Y ALA* 4.3 8.2 - - + +
9Y VAL* 4.5 2.0 - - + -
22Y ALA* 3.9 15.9 - - + -
104Y LEU* 4.2 17.3 - - + -
343Y GLY 2.8 22.9 + - - +
346Y LEU* 1.3 74.7 - - - +
348Y SER* 1.3 59.6 + - - +
349Y LEU 4.3 4.0 - - - +
352Y PHE* 3.9 12.4 - - - -
356Y TRP* 4.1 29.3 + - + -
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Residues in contact with SER 348 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Y GLU* 5.0 18.6 - - - +
7Y ALA* 5.7 0.2 - - - -
22Y ALA* 3.9 7.4 - - - +
23Y GLY* 4.0 20.6 + - - -
344Y SER 2.7 24.4 + - - -
345Y ILE* 2.7 14.9 + - - -
347Y ALA* 1.3 76.1 - - - +
349Y LEU* 1.3 65.0 + - - +
350Y SER* 3.6 1.9 + - - -
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Residues in contact with LEU 349 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y TYR* 4.2 18.6 - - - +
345Y ILE* 2.9 24.2 + - + +
346Y LEU* 3.1 19.4 + - + +
347Y ALA 4.3 2.1 - - - +
348Y SER* 1.3 81.6 + - - +
350Y SER* 1.3 79.9 - - - +
351Y THR* 3.2 28.7 - - - +
352Y PHE* 3.3 18.7 + - + +
353Y 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
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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