Contacts of the strand formed by residues 335 - 339 (chain B) in PDB entry 3SMP
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 THR 335 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B PHE* 4.3 4.3 - - - -
333B HIS* 3.3 21.2 + - - +
334B THR* 1.3 98.4 + - - +
336B LEU* 1.3 63.5 + - - +
337B CYS* 4.3 3.7 - - - -
356B LEU* 5.1 3.1 - - - -
357B GLN* 3.2 28.9 - - + +
359B HIS* 4.8 11.7 - - + -
591B LEU* 5.8 6.6 - - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 4.1 28.5 - - + +
241B MET* 3.6 36.8 - - + -
250B LEU* 5.7 0.4 - - + -
320B PHE* 4.3 9.2 - - + -
329B PHE* 4.5 17.7 - - + -
335B THR* 1.3 76.4 - - - +
337B CYS* 1.3 69.2 + - - +
338B ALA 3.6 0.5 + - - -
350B PHE* 3.8 23.8 - - + -
356B LEU* 4.7 15.7 - - + -
357B GLN 2.9 7.3 + - - +
358B LEU* 3.5 13.8 - - + +
359B HIS* 2.8 24.3 + - - -
591B LEU* 6.4 0.2 - - - -
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Residues in contact with CYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B PHE 4.9 5.7 + - - +
240B GLY* 3.9 2.6 - - - -
241B MET* 3.1 26.9 + - - +
335B THR* 5.8 3.4 - - - -
336B LEU* 1.3 76.2 - - - +
338B ALA* 1.3 60.0 + - - +
359B HIS* 3.6 22.9 - - - -
361B LEU* 4.0 6.3 - - + -
587B ALA* 3.2 30.6 - - - +
590B GLU* 4.0 15.3 - - - -
591B LEU* 4.0 25.7 - - - +
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B MET* 3.2 21.1 - - + +
243B ILE* 4.0 13.5 - - + -
336B LEU 3.6 0.2 + - - -
337B CYS* 1.3 75.8 - - - +
339B THR* 1.3 61.3 + - - +
343B ALA* 4.8 2.0 - - + +
358B LEU* 4.0 31.9 - - + -
359B HIS 3.0 10.4 + - - +
360B LYS* 3.3 6.8 - - - +
361B LEU* 2.9 24.6 + - - +
587B ALA* 4.3 3.1 - - - +
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Residues in contact with THR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B MET 3.0 10.8 + - - +
242B ASP* 3.8 22.0 - - - -
243B ILE* 2.8 22.2 + - - +
338B ALA* 1.3 75.4 - - - +
340B GLY* 1.3 68.1 + - - +
343B ALA* 4.0 6.4 - - - +
360B LYS* 4.3 3.1 - - - -
361B LEU 2.7 24.9 + - - -
363B GLU* 3.2 23.1 - - + +
366B CYS* 3.9 17.5 - - + -
583B GLY* 3.8 26.5 - - - +
587B ALA* 4.5 0.8 - - + +
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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