Contacts of the strand formed by residues 338 - 342 (chain B) in PDB entry 4CQ8
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 TYR 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU* 3.9 14.8 - - + -
217B PHE* 5.2 1.1 - + - -
244B PHE* 3.5 23.2 - + - -
246B GLU* 2.7 47.1 + - + +
307B ILE* 4.2 11.2 - - + -
308B VAL 4.0 0.6 + - - -
309B GLY* 3.4 26.7 - - - -
310B VAL 3.0 23.6 + - - -
336B ALA* 3.5 7.3 - - - +
337B ASP* 1.3 80.7 - - - +
339B ILE* 1.3 70.0 + - - +
340B ALA* 4.1 5.4 - - + -
424B PRO* 3.8 1.3 - - - -
425B LEU* 3.3 23.8 - - + +
427B PHE* 3.4 42.2 - + + -
503B ILE* 6.2 0.4 - - + -
526B GLN* 3.5 8.3 + - - -
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Residues in contact with ILE 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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310B VAL* 3.4 15.0 - - + +
312B ILE* 3.6 36.1 - - + -
329B ILE* 4.8 7.0 - - + -
332B ILE* 4.5 8.7 - - + -
333B GLY* 4.3 14.1 - - - -
336B ALA* 3.8 22.4 - - + -
338B TYR* 1.3 76.2 - - - +
340B ALA* 1.3 62.8 + - - +
341B ILE* 3.9 2.2 + - + +
367B VAL* 4.6 13.9 - - + -
371B ILE* 4.2 13.2 - - + -
424B PRO* 3.9 20.6 - - + -
425B LEU 2.8 10.1 + - - +
426B VAL* 3.5 3.5 - - - +
427B PHE* 2.8 27.7 + - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLU* 3.6 30.7 - - - +
310B VAL 2.9 9.6 + - - +
311B SER* 3.3 9.8 + - - +
312B ILE* 2.9 28.9 + - - +
338B TYR* 4.1 5.1 - - + -
339B ILE* 1.3 74.1 - - - +
341B ILE* 1.3 62.5 + - - +
342B ASN 3.4 0.5 + - - -
427B PHE* 3.5 5.6 - - - -
429B LYS* 5.4 2.7 - - + -
455B ILE* 3.7 20.2 - - + -
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Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 4.1 5.6 - - + -
325B LEU* 4.1 15.7 - - + -
339B ILE* 4.8 4.9 - - + -
340B ALA* 1.3 69.7 - - - +
342B ASN* 1.3 61.2 + - - +
343B VAL* 3.5 19.9 + - + -
360B LEU* 5.8 0.4 - - + -
363B ILE* 3.7 22.2 - - + -
364B ILE* 4.3 24.7 - - + -
367B VAL* 3.8 30.5 - - + -
426B VAL* 3.6 27.4 - - + -
427B PHE 2.8 18.2 + - - +
428B VAL* 3.8 8.1 - - + +
429B LYS* 3.0 25.3 + - - -
451B ILE* 4.7 1.3 - - + -
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Residues in contact with ASN 342 (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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249B THR* 2.8 26.7 + - + +
278B PHE* 3.4 14.8 - - + -
311B SER* 3.7 11.7 - - - +
312B ILE 3.1 22.3 + - - +
313B GLY* 4.5 3.1 - - - -
321B ILE* 4.5 3.6 - - - +
325B LEU* 5.7 0.3 - - - +
340B ALA 3.4 0.8 + - - -
341B ILE* 1.3 71.1 - - - +
343B VAL* 1.3 59.3 + - - +
344B SER* 3.1 21.2 + - - -
345B SER 3.2 9.7 + - - -
351B LEU* 3.4 18.9 - - - +
429B LYS* 4.7 6.3 - - + -
458B ASN* 4.3 0.7 - - - -
800B FMN 3.2 10.8 + - - +
900B ORO 2.8 22.8 + - - +
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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