Contacts of the strand formed by residues 543 - 548 (chain A) in PDB entry 1Q8Z
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 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A GLN* 3.2 15.5 - - - +
304A ILE* 3.6 5.4 - - - +
305A VAL* 2.9 40.5 + - + +
306A ASP* 2.8 30.4 + - + +
541A GLU* 3.9 20.4 - - + +
542A ASN* 1.3 78.7 - - - +
544A ILE* 1.3 64.7 + - - +
710A LEU* 3.6 33.7 - - + +
711A GLY* 3.7 11.9 - - - +
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Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 5.2 0.7 - - + -
269A TYR* 3.6 57.7 - - + +
272A GLN* 3.0 20.0 + - + +
273A ILE* 3.9 19.5 - - + -
276A GLN* 3.1 19.7 + - - +
302A MET* 4.4 18.2 - - + -
303A GLU 3.7 7.4 - - - +
304A ILE* 4.1 25.1 - - + -
305A VAL* 3.5 9.2 - - - +
542A ASN 4.8 0.4 - - - -
543A LEU* 1.3 79.8 - - - +
545A GLN* 1.3 63.5 + - - +
546A ILE* 5.5 0.7 - - + -
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Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASN* 3.3 29.6 + - - +
224A HIS* 3.9 9.9 + - + +
276A GLN* 3.1 11.2 - - - +
302A MET* 3.4 3.8 - - - +
303A GLU* 3.2 55.3 + - + +
305A VAL* 4.1 12.0 - - + +
544A ILE* 1.3 77.0 - - - +
546A ILE* 1.3 72.8 + - - +
547A LYS* 4.0 14.1 - - - +
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Residues in contact with ILE 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A HIS* 2.9 31.5 - - + +
249A LEU* 5.1 0.4 - - - -
253A LEU* 4.4 1.3 - - + -
273A ILE* 3.8 35.0 - - + +
276A GLN* 2.8 28.6 + - + +
277A LEU* 3.8 27.1 - - + +
300A VAL* 3.8 22.9 - - + -
301A LEU 3.0 13.7 - - - +
302A MET* 3.6 15.9 - - + -
544A ILE* 5.4 1.3 - - + -
545A GLN* 1.3 79.0 - - - +
547A LYS* 1.3 77.1 + - - +
548A ILE* 4.5 3.6 - - + +
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Residues in contact with LYS 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASN* 2.8 35.8 + - - +
224A HIS 3.3 8.1 - - - -
225A ILE 4.2 12.3 + - - +
226A LEU* 3.9 16.6 - - + +
247A GLU* 2.9 27.9 + - - +
249A LEU* 3.1 37.9 - - + -
300A VAL* 3.5 1.1 - - - -
301A LEU* 2.8 35.5 + - - +
545A GLN* 4.0 17.3 - - - +
546A ILE* 1.3 84.6 - - - +
548A ILE* 1.3 64.4 + - - +
549A ALA 3.4 1.0 + - - -
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A HIS 2.7 21.4 + - - +
225A ILE* 3.5 11.8 - - + +
226A LEU 2.8 23.9 + - - +
277A LEU* 3.6 32.1 - - + +
280A GLY* 3.9 6.1 - - - -
281A LEU* 3.8 31.9 - - + +
284A MET* 4.3 12.8 - - - -
292A HIS* 3.6 28.0 - - + +
295A ILE* 3.9 13.0 - - + -
299A ASN 3.6 6.7 - - - +
300A VAL* 4.6 4.3 - - + +
546A ILE* 4.8 5.4 - - + -
547A LYS* 1.3 71.2 - - - +
549A ALA* 1.3 61.0 + - - +
551A LEU* 5.5 1.9 - - + +
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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