Contacts of the strand formed by residues 409 - 413 (chain A) in PDB entry 4HXG
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 409 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A TYR* 4.5 0.7 - + - -
368A ILE 3.5 14.1 - - - -
369A LYS* 3.5 26.5 - - + -
370A PRO* 3.8 5.7 - - + +
372A ILE* 3.4 32.0 - - + +
378A ALA* 3.6 15.0 - - + -
379A PRO 2.9 13.2 + - - +
380A VAL* 3.7 11.4 - - + -
381A ILE 2.8 27.5 + - - -
407A GLY 4.1 0.2 + - - -
408A TYR* 1.3 72.9 - - - +
410A ILE* 1.3 63.1 + - - +
448A PHE* 3.5 23.3 - + + -
452A GLU* 2.8 38.4 + - + +
454A GLN* 3.5 7.7 - - - +
455A ALA* 3.3 34.8 - - - -
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Residues in contact with ILE 410 (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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367A TYR* 2.9 9.1 - - - +
368A ILE* 2.7 50.4 + - + -
381A ILE* 3.6 4.9 - - + -
383A PHE* 4.0 24.2 - - + -
400A MET* 3.6 46.2 - - + +
403A MET* 3.7 29.6 - - + -
404A ALA* 4.3 2.0 - - + +
408A TYR* 3.9 11.9 - - + +
409A TYR* 1.3 81.1 - - - +
411A VAL* 1.3 62.5 + - - +
412A TYR* 4.0 14.6 - - + -
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PHE* 4.5 8.7 - - + -
366A TRP 3.5 12.8 - - - +
367A TYR* 4.2 4.7 - - + -
380A VAL* 3.9 13.7 - - + -
381A ILE 3.0 9.7 + - - +
382A VAL* 3.2 33.6 - - + +
383A PHE* 2.9 25.6 + - - +
410A ILE* 1.3 76.0 - - - +
412A TYR* 1.3 68.8 + - - +
413A VAL* 5.0 4.0 - - + -
444A GLY 5.1 1.8 - - - +
445A ILE* 4.8 8.3 - - + -
448A PHE* 4.0 34.3 - - + -
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Residues in contact with TYR 412 (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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351A PRO* 3.3 31.4 - - + +
365A GLY* 3.6 0.2 - - - -
366A TRP* 2.9 67.4 + + + +
367A TYR* 4.8 0.9 - - - -
368A ILE* 4.9 5.3 - - + +
382A VAL* 5.2 2.2 - - - -
383A PHE* 3.4 21.5 - - + +
392A TYR* 3.4 37.7 - + + -
393A GLY 3.7 16.2 + - - -
400A MET* 3.6 32.1 - - + -
410A ILE* 4.0 11.4 - - + -
411A VAL* 1.3 80.3 - - - +
413A VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 413 (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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354A PHE* 4.6 6.1 - - + -
356A PHE* 3.7 28.5 - - + -
364A ASP 3.4 11.2 - - - +
365A GLY* 3.8 8.3 - - - -
366A TRP* 4.7 3.4 - - - -
383A PHE 4.5 2.7 + - - +
384A VAL* 6.0 0.5 - - - -
385A HIS* 3.7 9.4 + - - -
392A TYR* 4.0 5.9 - - - -
411A VAL* 5.0 4.3 - - + -
412A TYR* 1.3 83.3 - - - +
414A ASN* 1.3 69.8 + - - +
415A PRO* 3.4 15.0 - - + +
441A ILE* 4.0 39.5 - - + +
444A GLY* 4.4 11.7 - - - -
445A ILE* 6.3 0.4 - - + -
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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