Contacts of the strand formed by residues 341 - 346 (chain C) in PDB entry 5C5B
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 CYS 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C TRP* 3.7 22.4 - - - -
332C ALA* 3.6 0.7 - - - +
333C VAL 2.8 39.3 + - - +
335C CYS 4.3 6.5 - - - +
338C ARG* 3.4 37.4 + - - +
339C ARG 3.4 0.2 - - - -
340C TYR* 1.3 77.3 - - - +
342C PHE* 1.3 59.7 + - - +
354C ILE* 3.7 14.6 - - + -
355C LEU 3.2 3.6 - - - -
356C GLN* 3.9 13.2 - - - -
363C HIS* 3.1 10.6 + - - -
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Residues in contact with PHE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 3.9 19.7 - - + -
309C LEU* 6.2 0.2 - - + -
330C VAL* 3.9 15.9 - - + -
331C MET 3.3 15.9 - - - +
332C ALA* 4.0 2.5 - - - -
333C VAL* 3.8 5.4 - - - +
340C TYR 4.3 0.9 - - - -
341C CYS* 1.3 75.4 - - - +
343C GLN* 1.3 66.6 + - - +
344C ILE* 4.6 2.7 - - + -
354C ILE* 3.8 1.3 - - - -
355C LEU* 2.8 74.2 + - + +
357C ALA* 4.8 4.3 - - + -
363C HIS* 3.9 28.0 - + - +
366C TRP* 3.7 31.9 - + + -
367C ILE* 4.4 9.2 - - + -
370C ILE* 4.1 20.0 - - + -
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Residues in contact with GLN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C VAL* 3.4 3.5 - - - +
331C MET* 2.9 34.9 + - + +
333C VAL* 3.9 23.2 - - + +
342C PHE* 1.3 77.7 - - - +
344C ILE* 1.3 70.2 + - - +
345C THR* 4.8 4.1 + - - +
351C LYS* 3.3 37.4 - - - +
352C SER* 3.0 32.4 + - - +
353C SER 4.0 4.7 - - - +
354C ILE* 4.2 21.0 - - + +
355C LEU* 5.8 0.2 - - - -
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Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C LEU* 3.7 24.5 - - + -
323C MET* 3.8 22.9 - - + -
325C ILE* 3.9 11.9 - - + -
328C CYS* 3.8 22.4 - - + -
329C SER 3.5 12.6 - - - +
330C VAL* 4.1 7.4 - - + +
342C PHE* 4.6 5.4 - - + -
343C GLN* 1.3 76.4 - - - +
345C THR* 1.3 68.6 + - - +
346C SER 4.2 0.2 - - - -
351C LYS* 3.3 5.7 - - - +
352C SER* 3.0 40.8 + - - +
355C LEU* 4.7 4.0 - - + -
370C ILE* 3.6 30.5 - - + -
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Residues in contact with THR 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C CYS* 3.3 3.7 - - - +
329C SER* 2.9 52.2 + - - +
330C VAL* 5.8 0.2 - - - -
331C MET* 6.1 1.6 - - - +
343C GLN* 4.8 4.5 + - - +
344C ILE* 1.3 76.7 + - - +
346C SER* 1.3 73.7 + - - +
349C GLY* 4.1 21.1 - - - +
350C LYS 3.5 2.2 - - - +
351C LYS* 4.0 24.1 - - + +
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Residues in contact with SER 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C MET* 4.2 12.5 - - - +
324C ASP 5.0 5.0 + - - -
327C ASN 4.0 3.3 + - - -
328C CYS* 4.0 9.6 - - - -
329C SER* 5.4 0.2 + - - -
345C THR* 1.3 84.3 - - - +
347C PHE* 1.3 67.7 + - - +
348C ASP* 2.9 24.6 + - - +
349C GLY* 2.9 15.9 + - - -
350C LYS* 2.7 32.8 + - - -
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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