Contacts of the strand formed by residues 280 - 283 (chain C) in PDB entry 5Y1Z
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 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C HIS 3.8 9.6 - - - +
279C PRO* 1.3 73.0 - - - +
281C VAL* 1.3 63.0 + - - +
293C ALA 3.3 6.1 - - - +
294C LYS* 4.3 6.7 - - + -
308C PHE* 4.0 16.8 - - + -
323C LEU* 3.7 0.3 - - - -
324C MET* 2.9 26.2 + - + -
346C MET* 3.6 34.1 - - + -
349C TYR* 3.5 42.4 - - + -
350C VAL* 4.1 5.2 - - + -
360C PHE* 4.0 20.9 - - + -
376C GLN* 2.7 33.3 + - - +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PRO 4.1 1.1 - - - +
280C LEU* 1.3 80.0 - - - +
282C TRP* 1.3 60.7 + - - +
283C ALA* 4.4 2.7 - - + +
291C TRP 3.4 2.1 - - - +
292C PRO* 3.5 3.8 - - - +
293C ALA* 2.9 49.1 + - + +
294C LYS 4.6 0.2 - - - -
295C ALA* 4.1 22.7 - - + +
303C VAL* 5.2 0.7 - - + -
305C ALA* 5.1 2.9 - - + -
321C CYS* 3.7 17.7 - - - -
322C TYR 3.1 13.9 - - - +
323C LEU* 4.3 2.7 - - + -
324C MET* 3.6 8.4 - - - +
369C TYR* 3.5 36.8 - - + -
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Residues in contact with TRP 282 (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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281C VAL* 1.3 71.3 - - - +
283C ALA* 1.3 60.8 + - - +
290C PHE* 3.8 18.8 - - + -
291C TRP 3.6 21.5 - - - -
292C PRO 4.2 0.4 - - - -
320C ASN 4.0 2.1 - - - +
321C CYS* 3.5 11.4 - - - -
322C TYR* 2.7 32.9 + - + +
323C LEU 3.7 15.7 - - - -
324C MET* 3.4 26.2 - - + -
325C SER* 3.3 36.2 + - - +
326C LYS 5.3 0.7 - - - -
327C GLU 4.3 0.4 - - - -
328C ILE* 3.8 41.5 - - + -
329C PRO* 3.4 26.2 - - + +
339C PHE* 4.0 7.4 - + - -
343C MET* 3.3 39.0 - - + -
366C ARG 6.3 0.2 - - - -
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Residues in contact with ALA 283 (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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281C VAL* 3.6 4.1 + - + -
282C TRP* 1.3 74.3 - - - +
284C LYS* 1.3 61.0 + - - +
285C LEU 4.3 0.2 - - - -
289C PRO 4.1 1.0 - - - +
290C PHE* 3.3 5.0 - - - -
291C TRP* 2.9 34.5 + - - +
293C ALA* 3.9 4.9 - - + -
305C ALA* 3.7 22.9 - - + -
307C PHE* 3.6 26.6 - - + -
316C VAL* 3.9 14.4 - - + -
321C CYS* 4.7 1.8 - - - -
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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