Contacts of the helix formed by residues 335 - 344 (chain P) in PDB entry 1E33
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 335 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331P ALA* 3.8 4.0 - - - -
332P SER 2.7 24.9 + - - +
334P LEU* 1.3 77.9 - - - +
336P LEU* 1.3 58.7 + - + +
337P LEU 3.6 0.7 - - - -
338P PRO* 3.7 2.4 - - - +
339P THR* 2.4 33.4 + - - -
355P GLY* 2.9 0.2 - - - -
356P PHE* 2.6 45.3 + - - +
358P LEU* 3.9 22.3 - - + +
370P ARG* 2.7 42.7 + - - +
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Residues in contact with LEU 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P LEU* 4.5 19.3 - - + -
62P PHE* 4.5 18.4 - - + -
76P LEU* 3.6 32.3 - - + +
107P VAL* 5.4 0.9 - - + -
277P ILE* 4.4 28.9 - - + -
279P THR* 4.7 2.9 - - - +
332P SER 4.0 10.8 - - - +
333P SER* 3.2 16.2 + - - +
335P ASP* 1.3 79.5 - - + +
337P LEU* 1.3 70.8 + - - +
339P THR* 3.2 8.5 + - + +
340P LEU* 3.0 32.9 + - + +
358P LEU* 5.3 4.9 - - + -
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Residues in contact with LEU 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P LEU 4.5 4.8 + - - +
77P LEU 3.6 20.4 - - - +
78P THR 3.7 20.0 - - - +
79P GLY* 4.3 8.5 - - - +
105P VAL 3.9 12.3 - - - +
106P THR 4.2 1.3 - - - +
107P VAL* 4.1 31.5 - - + +
110P VAL* 4.7 10.7 - - + +
333P SER 4.7 0.4 + - - -
334P LEU 4.5 1.4 + - - -
336P LEU* 1.3 79.1 - - - +
338P PRO* 1.3 72.0 - - + +
340P LEU* 3.1 1.0 + - - +
341P ALA* 2.8 29.6 + - + +
348P LEU* 3.8 20.6 - - + -
349P PRO* 4.3 16.8 - - + -
353P LEU* 4.4 6.5 - - + -
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Residues in contact with PRO 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P GLY* 4.9 2.0 - - - -
334P LEU 3.9 11.0 - - - +
335P ASP 3.7 9.6 - - - +
336P LEU 3.8 0.7 - - - -
337P LEU* 1.3 101.9 - - + +
339P THR* 1.3 60.1 + - - +
341P ALA* 3.6 0.3 - - - +
342P ALA* 3.0 22.9 + - - +
348P LEU* 3.8 27.9 - - + +
353P LEU* 4.5 11.0 - - + -
355P GLY* 4.0 6.1 - - - +
356P PHE* 3.9 30.1 - - - +
357P ASP* 4.0 7.7 - - + +
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Residues in contact with THR 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335P ASP 2.4 27.0 + - - -
336P LEU* 3.2 9.8 + - + +
338P PRO* 1.3 77.5 - - - +
340P LEU* 1.3 62.9 + - + +
342P ALA* 3.4 2.9 + - - +
343P LEU* 2.9 35.2 + - + +
356P PHE 3.3 1.2 + - - -
357P ASP* 3.7 9.0 - - - +
358P LEU* 3.0 34.2 + - + +
359P SER 3.8 11.0 - - - +
362P LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P ILE* 3.8 35.8 - - + +
25P LEU* 4.8 14.6 - - + -
107P VAL* 4.4 21.1 - - + -
111P LEU* 4.8 5.6 - - + -
220P PHE* 4.9 3.4 - - + -
275P LEU* 3.4 32.5 - - + -
277P ILE* 4.1 18.4 - - + -
336P LEU* 3.0 22.3 + - + +
337P LEU* 3.6 2.9 - - - +
339P THR* 1.3 79.9 - - + +
341P ALA* 1.3 67.8 + - - +
343P LEU* 2.9 9.4 + - + +
344P ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P VAL* 6.0 0.4 - - - +
110P VAL* 4.4 15.7 - - + +
111P LEU* 4.7 3.6 - - - +
337P LEU 2.8 17.0 + - - +
338P PRO 3.6 0.9 - - - +
340P LEU* 1.3 71.0 - - - +
342P ALA* 1.3 66.4 + - - +
344P ALA 3.0 6.8 + - - -
345P GLY 3.1 8.8 + - - -
346P ALA* 3.1 31.6 + - - +
348P LEU* 3.3 34.3 - - + -
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Residues in contact with ALA 342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338P PRO 3.0 10.9 + - - +
339P THR 3.5 8.7 - - - +
341P ALA* 1.3 79.7 - - - +
343P LEU* 1.3 62.6 + - - +
344P ALA 3.0 0.5 + - - -
345P GLY* 3.1 12.1 + - - -
346P ALA 4.3 1.5 + - - -
357P ASP* 3.2 30.1 - - + +
359P SER* 4.1 4.3 - - - +
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Residues in contact with LEU 343 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P PRO* 4.3 1.7 - - - +
21P PRO* 3.3 23.3 - - + +
23P ILE* 5.7 1.6 - - + -
275P LEU* 3.7 30.3 - - + -
318P TRP* 4.2 27.5 - - + -
339P THR* 2.9 25.0 + - + +
340P LEU* 2.9 10.3 + - + +
342P ALA* 1.3 72.3 - - - +
344P ALA* 1.3 57.8 + - + +
345P GLY 3.5 0.4 - - - -
359P SER* 4.0 19.1 - - - -
362P LEU* 4.1 19.3 - - + -
363P LEU* 4.6 11.7 - - + -
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Residues in contact with ALA 344 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P PRO* 3.7 18.2 - - - +
21P PRO* 5.0 0.4 - - + -
23P ILE* 5.2 2.7 - - + -
111P LEU* 4.5 11.2 - - + -
114P ARG* 3.6 14.6 - - + +
116P TYR* 3.6 33.7 - - + +
340P LEU 2.9 16.0 + - - +
341P ALA 3.0 2.2 + - - +
343P LEU* 1.3 76.4 - - + +
345P GLY* 1.3 64.7 + - - +
346P ALA* 2.9 5.5 + - + +
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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