Contacts of the helix formed by residues 337 - 349 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410M ASN* 4.9 5.8 - - + -
18Z LYS* 3.8 20.2 - - + -
26Z ALA* 4.5 11.0 - - + -
27Z PRO* 3.6 43.5 - - + -
30Z VAL* 4.1 17.9 - - + +
334Z GLU* 2.8 12.4 + - + +
336Z LYS* 1.3 123.5 + - + +
338Z SER* 1.4 62.5 + - - -
339Z VAL* 3.3 3.4 - - - -
340Z TRP* 3.0 8.6 + - + -
341Z ILE* 2.9 38.4 + - + +
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Residues in contact with SER 338 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636M LYS 5.2 1.1 - - - -
637M LYS* 4.9 5.0 + - - +
140Z LEU 3.8 0.2 - - - +
141Z SER* 3.2 29.2 + - - -
144Z ALA* 3.5 11.2 - - - +
298Z VAL* 5.9 0.5 - - - +
299Z MET 4.4 2.4 + - - -
300Z SER* 3.7 15.6 - - - -
332Z PRO* 5.2 5.9 - - - +
334Z GLU* 3.8 7.6 + - - -
335Z ARG* 3.3 24.3 + - - +
337Z TYR* 1.4 71.9 - - - +
339Z VAL* 1.3 55.2 - - - +
341Z ILE* 3.1 7.6 + - - +
342Z GLY* 2.8 31.2 + - - -
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Residues in contact with VAL 339 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z ASP* 3.4 35.0 - - + +
106Z THR* 4.2 2.0 - - + -
137Z GLN* 4.0 24.9 - - + +
140Z LEU* 3.3 26.7 - - + +
141Z SER* 3.1 24.8 + - - +
154Z ASP* 4.2 17.3 - - - +
300Z SER* 4.5 3.8 - - - +
335Z ARG 6.1 0.2 - - - +
337Z TYR* 5.0 1.1 - - - -
338Z SER* 1.3 81.3 - - - +
340Z TRP* 1.3 61.7 + - - +
343Z GLY 3.2 14.6 + - - -
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Residues in contact with TRP 340 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642M LYS* 2.5 72.3 + - + -
9Z VAL* 2.8 45.1 + - + +
11Z ASP* 4.0 9.8 + - + +
18Z LYS* 3.4 39.1 + - + -
19Z ALA* 3.6 7.0 - - - +
20Z GLY* 3.6 26.9 - - - -
21Z PHE 3.5 10.3 - - - -
24Z ASP* 3.8 3.1 - - + -
25Z ASP 4.3 0.7 - - - -
26Z ALA* 3.5 28.5 - - - -
27Z PRO* 3.7 17.5 - - + -
106Z THR* 6.2 0.2 - - - -
337Z TYR* 3.0 18.1 + - + +
339Z VAL* 1.3 77.5 - - - +
341Z ILE* 1.3 60.7 + - + +
343Z GLY* 3.0 4.5 + - - -
344Z SER 2.9 10.9 + - - -
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Residues in contact with ILE 341 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633M GLY* 5.5 2.9 - - - -
635M GLY* 2.7 64.8 - - - +
636M LYS 3.2 14.4 - - - +
637M LYS 3.4 9.0 - - - -
638M GLY* 2.0 36.2 - - - -
639M GLY 4.9 0.7 - - - +
642M LYS* 2.9 16.0 + - - +
25Z ASP 3.5 15.9 - - - +
26Z ALA* 4.9 0.4 - - + -
334Z GLU* 3.7 16.2 - - + +
337Z TYR* 2.9 35.7 + - + +
338Z SER 3.6 3.8 - - - +
340Z TRP* 1.3 80.1 - - + +
342Z GLY* 1.3 53.5 - - - +
344Z SER* 5.3 0.2 - - - -
345Z ILE 3.0 2.3 + - - -
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Residues in contact with GLY 342 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637M LYS 3.9 0.2 - - - -
638M GLY* 3.7 4.7 - - - -
140Z LEU* 3.4 32.1 - - - -
143Z TYR* 3.7 7.3 - - - -
144Z ALA* 3.5 12.9 - - - +
338Z SER 2.8 10.7 + - - -
339Z VAL 3.4 0.9 + - - -
341Z ILE* 1.3 75.9 - - - +
343Z GLY* 1.3 54.5 + - - +
345Z ILE* 3.8 0.2 - - - +
346Z LEU* 3.1 30.1 + - - +
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Residues in contact with GLY 343 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Z VAL* 3.9 15.3 - - - -
104Z LEU* 4.3 7.1 - - - +
140Z LEU* 3.8 18.6 - - - +
339Z VAL 3.2 8.8 + - - -
340Z TRP 3.0 8.0 + - - -
342Z GLY* 1.3 74.6 - - - +
344Z SER* 1.3 54.0 + - - +
346Z LEU* 3.8 1.9 - - - +
347Z ALA* 2.8 38.1 + - - +
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Residues in contact with SER 344 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639M GLY* 2.4 26.2 + - - -
642M LYS* 0.7 191.7 - - - +
9Z VAL* 3.9 6.0 - - - +
22Z ALA* 3.7 1.6 - - - +
23Z GLY 2.8 1.4 + - - -
24Z ASP 3.8 0.2 - - - -
340Z TRP 2.9 0.8 + - - -
341Z ILE* 4.2 0.4 - - - -
343Z GLY* 1.3 69.9 - - - +
345Z ILE* 1.3 56.3 + - - +
348Z SER* 2.7 24.1 + - - -
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Residues in contact with ILE 345 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541M MET* 2.1 78.3 - - + +
637M LYS* 0.8 52.3 - - - +
638M GLY* 0.6 205.7 - - - +
639M GLY* 1.9 17.1 - - - +
640M LYS* 4.7 2.5 - - + +
143Z TYR* 3.5 4.3 - - + -
341Z ILE* 3.7 0.2 - - + -
342Z GLY 3.8 1.8 - - - +
344Z SER* 1.3 64.1 - - - +
346Z LEU* 1.3 55.7 - - - +
348Z SER* 2.7 12.1 + - - -
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Residues in contact with LEU 346 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538M GLU* 4.2 5.6 - - - +
541M MET* 1.5 83.2 - - + +
542M PHE* 4.2 24.9 - - + -
104Z LEU* 4.2 12.3 - - + -
133Z TYR* 4.5 7.6 - - + +
135Z ALA* 4.7 1.8 - - + -
140Z LEU* 3.7 24.7 - - + -
143Z TYR* 3.8 9.2 - - + -
342Z GLY 3.1 14.0 + - - +
343Z GLY 3.8 1.3 - - - +
345Z ILE* 1.3 71.3 - - - +
347Z ALA* 1.3 59.3 + - - +
349Z LEU* 3.1 3.3 + - - +
352Z PHE* 3.2 43.0 - - + +
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Residues in contact with ALA 347 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641M LYS* 4.7 1.0 + - - -
3Z ASP 5.7 0.2 - - - +
7Z ALA* 4.3 7.7 - - + +
9Z VAL* 4.5 2.2 - - + -
22Z ALA* 3.9 15.5 - - + -
104Z LEU* 4.2 17.3 - - + -
343Z GLY 2.8 22.8 + - - +
346Z LEU* 1.3 73.6 - - - +
348Z SER* 1.3 59.8 + - - +
349Z LEU 3.3 3.9 - - - +
352Z PHE* 3.9 13.0 - - - +
356Z TRP* 4.1 29.4 + - + -
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Residues in contact with SER 348 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541M MET* 4.4 0.3 - - - +
639M GLY* 3.0 8.1 - - - -
641M LYS* 1.8 39.2 + - - +
647M GLN* 1.1 140.8 - - - +
4Z GLU 5.1 0.2 - - - -
7Z ALA* 5.7 0.2 - - - -
22Z ALA* 3.9 3.6 - - - +
23Z GLY 4.0 1.6 - - - -
344Z SER 2.7 23.6 + - - -
345Z ILE 2.7 11.5 + - - -
347Z ALA* 1.3 75.8 - - - +
349Z LEU* 1.3 56.4 + - - +
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Residues in contact with LEU 349 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537M GLU 1.7 32.8 - - - +
538M GLU* 1.8 60.1 - - + +
540M CYS* 3.3 9.4 - - + +
541M MET* 1.6 96.8 - - + +
641M LYS* 4.0 2.7 + - - -
647M GLN* 4.3 9.6 - - + +
346Z LEU 3.1 2.2 + - - +
347Z ALA 4.3 2.3 - - - +
348Z SER* 1.3 72.7 + - - +
350Z SER* 1.3 64.2 - - - +
351Z THR 3.3 0.2 - - - -
352Z PHE* 3.3 15.1 + - - +
353Z GLN* 4.2 4.3 + - - +
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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