Contacts of the strand formed by residues 427 - 430 (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 LEU 427 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306P TYR* 6.2 1.3 - - + -
395P LYS 3.5 1.4 - - - +
396P ALA* 3.2 6.6 - - - -
397P HIS* 2.9 41.4 + - + +
400P THR* 4.2 10.8 - - + +
423P HIS* 3.8 45.7 - - + +
425P PRO 5.3 1.6 - - - +
426P LEU* 1.3 72.7 - - - +
428P LEU* 1.3 58.2 + - - +
429P TYR* 3.9 28.3 - - + +
440P ASN* 3.2 28.5 - - + +
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Residues in contact with LEU 428 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P TYR* 4.0 21.1 - - + -
395P LYS 3.5 9.4 - - - +
426P LEU* 3.8 14.8 - - + -
427P LEU* 1.3 73.1 - - - +
429P TYR* 1.4 65.8 + - - +
439P TYR 3.6 0.3 - - - +
440P ASN* 3.0 18.8 - - - +
441P LEU* 2.7 43.0 + - + +
442P LEU* 4.2 13.7 - - + -
452P VAL* 3.7 37.5 - - + +
455P ALA* 4.6 6.7 - - + -
456P LEU* 4.7 3.6 - - + -
459P LEU* 3.5 31.9 - - + -
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Residues in contact with TYR 429 (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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299P ARG* 4.7 5.8 + - - -
306P TYR* 5.8 3.0 - + - -
394P TYR* 3.2 9.0 - - - -
395P LYS* 2.8 38.7 + - + +
397P HIS* 3.4 35.2 - + - -
427P LEU* 3.9 34.1 - - + +
428P LEU* 1.4 76.4 - - - +
430P ASP* 1.3 63.8 - - - +
431P LEU* 3.7 18.6 - - + -
434P ASP* 3.5 20.6 - - - +
437P GLU* 3.4 40.2 + - + -
438P ASN 3.9 1.2 - - - -
439P TYR 3.5 24.9 - - - -
440P ASN* 3.7 7.7 - - - +
441P LEU* 4.5 0.7 - - - -
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Residues in contact with ASP 430 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393P LYS* 3.2 34.6 + - - +
394P TYR* 4.1 8.6 + - + -
429P TYR* 1.3 74.0 - - - +
431P LEU* 1.3 59.5 + - - +
432P SER* 2.6 29.0 + - - -
433P LYS* 3.2 31.3 + - + -
434P ASP* 2.8 34.2 + - + +
439P TYR 5.3 0.4 + - - -
441P LEU* 3.9 23.7 - - + +
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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
------------------------------------------------------------
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