Contacts of the strand formed by residues 336 - 341 (chain B) in PDB entry 1QXP
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 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B TRP* 4.5 14.0 - - - +
215B TYR 3.2 8.8 + - - -
217B LEU* 4.2 2.5 - - - +
239B GLY 5.2 1.8 - - - +
240B CYS* 3.4 5.0 - - - +
241B SER* 2.7 52.7 + - - +
335B PHE* 1.3 103.7 + - + +
337B LYS* 1.3 67.2 + - - +
338B LEU* 4.9 3.6 - - + +
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Residues in contact with LYS 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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214B TRP* 3.2 3.1 - - - +
215B TYR* 2.8 73.3 + - - +
217B LEU* 3.6 22.0 - - + +
224B LEU* 4.3 9.4 - - - -
228B ILE* 3.9 26.5 - - + -
238B LEU* 4.5 11.0 - - + -
239B GLY 3.5 3.6 - - - +
240B CYS* 4.0 18.4 - - - -
266B VAL* 5.5 0.7 - - + -
336B THR* 1.3 75.8 - - - +
338B LEU* 1.3 63.6 + - - +
339B GLU* 3.5 20.9 - - - +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B SER* 6.3 2.2 - - - -
204B PHE* 5.8 7.9 - - + -
212B THR* 5.5 4.5 - - - +
213B GLU 3.5 7.2 - - - +
214B TRP* 4.2 12.3 - - + -
237B LEU 3.9 0.2 - - - +
238B LEU* 3.6 1.0 - - - -
239B GLY* 2.7 38.7 + - - +
336B THR* 4.9 5.6 - - + +
337B LYS* 1.3 76.9 - - - +
339B GLU* 1.4 56.9 + - - +
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Residues in contact with GLU 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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204B PHE* 6.2 0.4 - - - -
211B VAL 3.4 0.7 - - - +
212B THR* 3.2 5.5 + - - -
213B GLU* 2.3 74.7 + - + +
215B TYR* 4.3 5.8 - - - -
227B ILE* 4.8 7.7 - - + +
228B ILE* 5.3 0.9 - - - +
231B ALA* 4.8 9.5 - - + +
236B SER* 4.8 0.9 - - - -
237B LEU 3.1 14.8 - - - +
238B LEU* 3.9 20.0 - - + +
337B LYS* 3.5 28.3 - - - +
338B LEU* 1.4 68.8 - - - +
340B ILE* 1.3 67.0 + - - +
341B CYS* 3.7 10.0 + - - -
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Residues in contact with ILE 340 (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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201B SER* 4.6 4.3 - - - +
204B PHE* 3.3 40.6 - - + +
205B GLU* 4.5 10.1 - - + +
208B THR* 4.0 23.3 - - + +
210B GLY 4.3 7.2 - - - +
211B VAL* 3.1 9.9 - - - +
212B THR* 2.5 44.6 - - - +
236B SER* 3.6 2.4 + - - -
237B LEU* 3.3 35.2 + - + +
339B GLU* 1.3 76.9 - - - +
341B CYS* 1.3 65.7 + - - +
342B ASN* 3.5 16.8 + - - +
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Residues in contact with CYS 341 (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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210B GLY* 3.2 4.0 - - - -
211B VAL* 2.8 44.1 + - + -
213B GLU* 3.3 26.9 - - - -
231B ALA* 5.7 2.5 - - - -
236B SER* 3.3 15.7 - - - -
339B GLU* 4.2 10.1 - - - -
340B ILE* 1.3 74.1 - - - +
342B ASN* 1.4 53.5 + - - +
356B TRP* 3.7 33.2 - - + +
410B LEU* 3.9 5.2 - - + -
503B PHE* 4.1 5.6 - - + -
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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