Contacts of the helix formed by residues 332 - 340 (chain Z) in PDB entry 5WTI
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 ASP 332 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E T 3.6 31.7 + - + +
4E A 3.3 14.0 - - - +
272Z ARG* 2.9 38.9 + - - -
286Z TYR* 4.2 0.9 + - - -
292Z GLY* 3.0 26.4 + - - -
319Z PHE* 4.2 0.4 - - - -
331Z GLY* 1.3 70.9 - - - -
333Z TYR* 1.3 76.0 + - - +
334Z SER* 3.4 8.3 + - - -
335Z VAL* 3.4 20.0 + - + +
336Z TYR* 3.4 17.3 + - - -
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Residues in contact with TYR 333 (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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120B A 3.5 20.4 - - - +
121B U 3.5 58.1 + - - +
3E T 5.2 1.6 + - - -
316Z LEU* 3.5 30.9 - - + +
319Z PHE* 3.7 27.3 - + + -
320Z LYS* 5.0 2.5 - - + -
331Z GLY 3.7 3.8 + - - -
332Z ASP* 1.3 76.5 + - - +
334Z SER* 1.3 68.8 + - - +
335Z VAL 3.0 0.5 + - - -
336Z TYR* 3.2 3.1 + - - +
337Z GLU* 2.3 66.4 + - - +
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Residues in contact with SER 334 (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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120B A 4.5 5.7 + - - -
268Z TYR* 3.1 18.8 + - - -
272Z ARG* 3.6 36.2 + - - -
332Z ASP* 3.4 4.4 + - - -
333Z TYR* 1.3 93.9 - - - +
335Z VAL* 1.3 61.9 + - - +
337Z GLU* 4.0 10.1 + - - +
338Z PHE* 3.6 9.5 + - - +
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Residues in contact with VAL 335 (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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268Z TYR* 3.4 20.0 - - + +
286Z TYR* 3.5 17.5 - - - +
288Z LEU* 4.1 17.5 - - + -
292Z GLY* 4.4 8.3 - - - +
293Z LEU* 3.5 29.6 - - + -
332Z ASP* 3.6 27.4 - - + +
333Z TYR 3.0 0.8 - - - -
334Z SER* 1.3 74.5 - - - +
336Z TYR* 1.3 58.6 + - - +
337Z GLU 3.1 1.6 - - - -
338Z PHE* 2.6 26.5 + - - +
339Z LEU* 3.1 27.3 - - + +
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Residues in contact with TYR 336 (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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292Z GLY 3.3 20.4 - - - -
293Z LEU* 3.7 15.7 - - + -
295Z GLY 3.4 4.4 + - - -
296Z TRP* 3.2 50.5 + + - +
299Z ILE* 3.8 31.2 - - + -
303Z TRP* 3.8 24.5 - + + -
316Z LEU* 3.8 5.0 - - + +
319Z PHE* 3.4 40.4 - + + -
331Z GLY* 4.4 5.8 - - - -
332Z ASP 3.4 16.4 + - - -
333Z TYR 3.2 5.9 + - - +
335Z VAL* 1.3 80.0 - - + +
337Z GLU* 1.3 61.0 + - - +
339Z LEU* 3.6 7.1 + - + -
340Z SER* 3.2 25.1 + - - -
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Residues in contact with GLU 337 (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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316Z LEU* 3.5 22.4 - - + +
333Z TYR* 2.3 55.6 + - + +
334Z SER* 4.0 11.4 + - - +
336Z TYR* 1.3 75.9 - - - +
338Z PHE* 1.3 61.9 + - - +
340Z SER* 2.7 21.1 + - - +
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Residues in contact with PHE 338 (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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264Z SER* 3.5 37.2 - - - -
265Z LEU* 4.1 19.5 - - + -
268Z TYR* 3.8 41.3 - + + -
334Z SER 3.6 10.2 + - - +
335Z VAL 2.6 17.6 + - - +
337Z GLU* 1.3 77.5 - - - +
339Z LEU* 1.3 75.1 + - + +
340Z SER 3.2 6.2 + - - +
341Z LYS 5.1 2.8 - - - -
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Residues in contact with LEU 339 (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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265Z LEU* 4.7 14.6 - - + -
268Z TYR* 6.2 0.2 - - + -
288Z LEU* 5.5 0.7 - - + -
293Z LEU* 5.2 3.4 - - + -
296Z TRP* 4.6 10.3 - - + -
303Z TRP* 4.0 22.1 - - + -
335Z VAL* 3.1 48.8 + - + +
336Z TYR* 3.6 5.4 + - + +
338Z PHE* 1.3 91.5 - - + +
340Z SER* 1.3 61.4 + - - +
341Z LYS 3.3 4.8 + - - -
355Z PRO* 3.7 35.7 - - + -
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Residues in contact with SER 340 (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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303Z TRP* 4.2 7.4 - - - -
312Z SER* 4.0 14.9 + - - -
315Z TYR* 3.7 24.9 - - - -
316Z LEU* 3.9 15.0 - - - +
336Z TYR 3.2 14.3 + - - -
337Z GLU* 2.7 30.1 + - - +
338Z PHE 4.0 2.4 - - - +
339Z LEU* 1.3 73.9 - - - +
341Z LYS* 1.3 72.5 + - - +
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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