Contacts of the strand formed by residues 409 - 416 (chain A) in PDB entry 4XH9
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 ILE 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A ASP* 3.7 30.1 - - - +
380A ARG* 3.9 23.3 - - + +
381A ILE* 3.9 24.5 - - + -
384A SER* 4.1 0.2 - - - +
406A PHE* 2.9 47.5 + - + +
408A ASP* 1.3 82.9 - - - +
410A LEU* 1.3 63.6 + - - +
411A VAL* 4.4 0.4 - - + -
430A PRO* 3.6 28.0 - - + -
431A ILE 3.6 15.3 - - - +
432A PRO* 3.9 10.5 - - + -
433A VAL* 3.5 3.7 - - - +
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Residues in contact with LEU 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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403A ILE* 3.9 25.8 - - + -
404A PHE 3.5 4.9 - - - +
405A LEU* 4.0 20.4 - - + -
409A ILE* 1.3 73.1 - - - +
411A VAL* 1.3 63.2 + - - +
412A LEU* 3.7 25.3 + - + +
430A PRO* 3.4 2.3 - - - +
431A ILE* 2.7 49.8 + - + +
433A VAL* 4.6 0.4 - - - +
436A LEU* 4.0 26.0 - - + -
468A ILE* 3.8 24.2 - - + -
496A ILE* 4.2 18.8 - - + -
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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
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369A LEU* 4.4 7.0 - - + -
381A ILE* 3.6 33.7 - - + -
402A TYR 3.9 1.4 - - - +
403A ILE* 3.5 1.4 - - - -
404A PHE* 2.8 47.2 + - + +
406A PHE* 3.8 19.7 - - + -
409A ILE* 4.4 2.7 - - + -
410A LEU* 1.3 78.4 - - - +
412A LEU* 1.3 67.4 + - - +
413A THR* 3.9 18.8 - - + -
426A VAL* 4.1 22.7 - - + -
430A PRO* 4.1 11.4 - - + -
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Residues in contact with LEU 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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401A LEU* 3.9 22.0 - - + -
402A TYR 4.1 2.2 - - - -
403A ILE* 4.0 15.7 - - + -
410A LEU* 3.7 24.7 - - + +
411A VAL* 1.3 72.1 - - - +
413A THR* 1.3 61.6 + - - +
426A VAL* 3.6 2.4 - - - +
427A TYR* 2.7 45.4 + - + +
429A GLN 4.6 4.7 - - - +
430A PRO* 5.3 1.6 - - - +
431A ILE* 4.3 11.4 - - + -
468A ILE* 4.2 8.1 - - + -
477A GLN* 4.5 3.4 - - - +
479A HIS* 3.7 50.9 - - + +
481A LEU* 4.5 3.1 - - + -
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Residues in contact with THR 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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369A LEU* 3.8 29.6 - - + -
401A LEU* 3.4 11.4 - - - +
402A TYR* 2.6 58.1 + - - +
404A PHE* 3.9 7.0 - - + -
411A VAL* 3.9 10.3 - - + -
412A LEU* 1.3 81.4 - - - +
414A ARG* 1.3 65.3 + - - +
424A TYR* 3.5 23.8 - - + +
425A GLN 3.2 9.6 - - - -
426A VAL* 4.1 3.8 - - - -
427A TYR* 3.9 1.1 - - - +
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Residues in contact with ARG 414 (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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395A SER* 4.5 2.2 + - - -
397A SER* 3.8 6.7 + - - -
399A HIS* 3.2 54.9 + - - +
400A LYS 5.3 1.6 - - - +
401A LEU* 3.4 25.9 - - + +
413A THR* 1.3 73.8 - - - +
415A PRO* 1.3 71.6 - - + +
416A VAL* 3.6 2.2 - - + +
425A GLN* 2.7 48.1 + - + +
427A TYR* 3.4 49.3 + - + -
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Residues in contact with PRO 415 (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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392A GLU* 5.3 5.4 - - - +
400A LYS 3.7 20.9 - - - +
401A LEU 5.1 0.4 - - - -
402A TYR* 3.8 26.7 - - + +
413A THR* 3.8 6.0 - - - +
414A ARG* 1.3 87.7 - - + +
416A VAL* 1.3 62.8 + - - +
422A HIS* 4.0 22.4 - - + +
423A SER 3.4 9.9 - - - +
424A TYR* 4.4 9.9 - - + -
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Residues in contact with VAL 416 (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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370A GLU* 4.8 6.1 - - - +
414A ARG* 3.6 11.9 - - + +
415A PRO* 1.3 79.8 - - - +
417A THR* 1.3 81.3 + - - +
418A ARG* 3.3 1.6 + - + -
422A HIS* 3.7 9.9 + - - -
423A SER* 2.9 43.2 + - - +
425A GLN* 3.9 32.1 - - + +
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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