Contacts of the strand formed by residues 345 - 350 (chain A) in PDB entry 3HYW
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 ALA 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ILE* 6.5 0.9 - - + -
313A THR* 3.4 27.8 - - + +
315A MET* 3.8 5.2 - - - -
316A MET* 4.2 0.2 - - + -
344A SER* 1.3 75.4 - - - +
346A ILE* 1.3 58.1 + - - +
347A CSS 3.9 14.5 - - - -
358A PHE 3.8 0.9 - - - +
359A PHE* 3.2 8.5 - - - -
360A ALA* 3.0 34.6 + - + +
363A VAL* 3.3 20.6 - - + +
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Residues in contact with ILE 346 (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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313A THR* 5.0 0.3 + - - -
315A MET* 3.5 31.7 - - + +
345A ALA* 1.3 71.6 - - - +
347A CSS 1.3 65.4 + - - +
348A ILE* 4.5 3.1 - - + -
357A PHE* 3.4 28.9 - - + -
358A PHE 3.5 3.4 - - - -
359A PHE* 3.7 11.0 - - + -
407A LEU* 4.1 3.8 - - + -
411A LEU* 3.1 36.8 - - + -
441A FAD 4.4 2.3 - - - +
500A DCQ 3.3 65.2 - - + +
600A LMT 4.8 5.6 - - + -
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Residues in contact with CSS 347 (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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199A ILE* 5.7 4.9 - - + -
313A THR* 3.7 32.1 - - - -
345A ALA* 3.9 12.1 - - - -
346A ILE* 1.3 80.1 - - - +
348A ILE* 1.3 62.7 + - - +
349A ALA 4.0 0.2 - - - -
356A GLY 3.6 1.6 - - - +
357A PHE* 3.7 1.2 - - - -
358A PHE* 2.7 51.8 + - + +
441A FAD 4.8 4.0 - - - -
800A PS9 3.5 37.0 - - - -
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Residues in contact with ILE 348 (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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162A GLU* 3.5 0.2 - - - +
346A ILE* 4.2 0.8 + - + -
347A CSS 1.3 77.2 - - - +
349A ALA* 1.3 58.4 + - - +
355A ALA* 3.7 13.9 - - + -
356A GLY 3.2 8.7 - - - +
357A PHE* 3.7 29.6 - - + -
378A ALA* 3.4 29.6 - - + +
381A PHE* 3.4 35.9 - - + -
382A LYS* 2.7 52.8 + - + +
441A FAD 5.4 1.8 + - - -
500A DCQ 3.8 20.9 + - - +
800A PS9 4.0 7.1 - - - -
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Residues in contact with ALA 349 (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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158A GLY 4.9 3.1 - - - +
161A TYR* 5.3 3.8 - - + -
162A GLU* 3.6 17.3 - - + +
194A PHE* 6.3 0.7 - - + -
347A CSS 4.0 1.4 + - - -
348A ILE* 1.3 70.3 - - - +
350A ASP* 1.3 61.3 + - - +
351A PHE* 3.2 24.6 - - + -
355A ALA* 3.2 4.3 - - - -
356A GLY 2.8 37.1 + - - +
358A PHE* 4.4 8.1 - - + -
800A PS9 3.9 19.2 - - - -
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Residues in contact with ASP 350 (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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47A HIS* 2.8 28.5 + - - +
52A TRP* 5.5 0.7 - - - -
162A GLU* 2.8 35.7 + - - +
166A MET* 3.4 23.5 - - + +
348A ILE 3.6 2.0 + - - -
349A ALA* 1.3 69.8 - - - +
351A PHE* 1.3 66.8 + - - +
352A GLY* 3.5 6.1 + - - +
354A ASP 3.5 5.5 - - - +
355A ALA* 3.8 5.8 - - + -
379A HIS* 2.9 39.4 + - - +
382A LYS* 4.1 18.9 - - + +
383A THR* 5.0 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