Contacts of the helix formed by residues 332 - 337 (chain D) in PDB entry 5H2U
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 GLY 332 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D GLU* 5.8 0.5 - - - +
239D MET* 3.5 11.7 - - - +
308D TYR* 3.6 16.6 + - - -
310D HIS 2.9 19.2 + - - -
311D ARG* 4.8 0.4 - - - -
331D PHE* 1.3 71.1 - - - +
333D LEU* 1.3 62.4 + - - +
334D ALA 3.2 2.7 - - - -
335D ARG* 3.2 20.2 + - - +
336D LEU* 3.5 4.3 + - - +
503D GOL 3.6 18.2 - - - -
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Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TYR* 3.4 12.6 - - + +
202D PHE* 4.0 14.8 - - + -
219D LYS* 3.8 21.3 - - + -
221D ILE* 4.3 9.4 - - + -
239D MET* 4.0 9.0 - - + -
262D ILE* 3.8 17.3 - - + -
310D HIS 4.5 0.2 + - - -
330D ASP* 3.1 49.2 + - - +
331D PHE 3.2 2.4 + - - -
332D GLY* 1.3 74.1 - - - +
334D ALA* 1.3 65.4 + - - +
336D LEU* 3.0 38.4 + - + +
337D ILE* 3.5 10.9 + - + +
504D 1N1 4.6 7.9 - - + -
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Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TYR* 3.2 21.3 + - - +
310D HIS 5.1 0.2 + - - -
311D ARG* 3.9 23.3 - - + -
312D ASP* 4.5 5.5 - - + +
330D ASP 4.6 1.0 + - - -
332D GLY 3.2 0.4 - - - -
333D LEU* 1.3 76.4 - - - +
335D ARG* 1.3 53.8 + - - +
337D ILE* 3.0 16.6 + - - +
342D TYR* 3.9 19.9 - - + +
502D GOL 2.6 39.6 + - - -
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Residues in contact with ARG 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU* 3.2 41.4 - - - +
231D MET* 2.9 35.2 - - - +
235D GLU* 2.6 28.7 + - + +
311D ARG* 3.7 32.4 - - - +
332D GLY* 3.2 13.2 + - - +
333D LEU 3.2 0.2 - - - -
334D ALA* 1.3 80.2 - - - +
336D LEU* 1.3 61.6 + - - +
337D ILE 3.4 1.7 + - - +
502D GOL 4.2 13.8 + - - -
503D GOL 3.3 23.3 + - - +
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D LEU* 3.5 10.0 - - + +
227D LEU* 3.0 29.2 + - - +
232D LEU* 3.9 29.1 - - + +
235D GLU* 3.3 34.3 - - + -
236D ILE* 4.3 10.3 - - + +
239D MET* 3.8 20.2 - - + -
262D ILE* 3.5 32.8 - - + -
332D GLY 3.5 11.4 + - - +
333D LEU* 3.0 16.2 + - + +
335D ARG* 1.3 77.1 - - - +
337D ILE* 1.3 63.7 + - + +
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Residues in contact with ILE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TYR* 3.9 26.0 - - + -
202D PHE* 4.2 16.6 - - + -
221D ILE* 4.1 38.1 - - + -
225D ASN* 3.2 15.9 - - + +
226D LEU* 4.2 2.2 - - + -
227D LEU* 3.9 4.8 - - - +
333D LEU* 3.5 16.4 + - + +
334D ALA 3.0 16.3 + - - +
335D ARG 3.2 5.2 - - - +
336D LEU* 1.3 87.7 - - + +
338D LYS* 1.3 79.5 + - - +
339D GLU 3.4 0.7 + - - -
341D VAL* 3.8 20.6 - - + -
342D TYR* 4.0 3.1 - - + +
502D GOL 3.1 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