Contacts of the strand formed by residues 409 - 419 (chain A) in PDB entry 5IXM
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A ALA* 4.2 5.6 - - + -
401A GLN 3.4 17.5 - - - +
402A TYR* 3.4 39.3 - - + +
407A GLY 3.7 7.1 - - - +
408A SER* 1.3 85.3 + - - +
410A THR* 1.3 59.1 + - - +
411A LEU 3.5 15.7 - - - +
412A GLY* 5.0 1.1 - - - +
432A TYR* 3.7 19.4 + - + +
434A SER* 3.5 15.9 - - - -
604A C8E 3.5 51.1 - - - -
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Residues in contact with THR 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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401A GLN* 2.9 26.0 + - - +
402A TYR* 4.1 1.7 + - - -
403A ASP* 4.0 21.8 - - + +
406A LEU* 4.1 19.7 - - + +
408A SER 3.5 14.4 - - - +
409A LEU* 1.3 75.2 - - - +
411A LEU* 1.3 71.0 + - - +
432A TYR* 4.4 3.1 - - - -
433A ALA* 3.3 3.3 - - - -
434A SER* 2.7 34.1 + - - -
437A TYR* 3.7 31.7 - - + +
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Residues in contact with LEU 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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309A GLN* 3.2 28.7 - - - +
400A ALA* 3.4 1.5 - - - -
401A GLN* 2.8 59.5 + - + +
409A LEU* 3.5 9.8 - - - +
410A THR* 1.3 82.4 + - - +
412A GLY* 1.3 58.2 + - - +
413A ASN* 6.0 0.9 - - - +
431A ARG* 5.7 0.9 - - - +
432A TYR* 3.5 7.4 - - - +
433A ALA* 3.6 27.8 - - + -
437A TYR* 3.6 26.0 - - + -
77B GLU* 3.6 17.3 - - - +
107B PHE* 3.7 8.5 - - + -
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Residues in contact with GLY 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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399A GLY 3.3 11.4 - - - -
400A ALA* 4.1 1.8 - - - -
409A LEU* 5.0 0.9 - - - -
411A LEU* 1.3 76.3 - - - +
413A ASN* 1.3 66.9 + - - +
431A ARG* 5.6 0.3 + - - -
432A TYR* 2.8 37.3 + - - +
604A C8E 3.7 21.3 - - - -
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Residues in contact with ASN 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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397A LYS* 6.0 3.6 - - - +
398A GLY* 3.2 5.3 - - - -
399A GLY* 2.8 44.8 + - - +
411A LEU* 6.0 0.7 - - - +
412A GLY* 1.3 78.9 + - - +
414A ALA* 1.3 66.7 + - - +
415A ILE* 5.5 5.7 - - - +
430A TYR 3.1 15.3 - - - +
431A ARG* 3.8 38.7 + - + +
604A C8E 3.6 10.6 - - - +
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Residues in contact with ALA 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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396A LEU* 5.5 2.7 - - + -
397A LYS 3.4 8.1 - - - +
398A GLY* 3.9 0.2 - - - -
413A ASN* 1.3 79.1 - - - +
415A ILE* 1.3 63.4 + - - +
429A ASN* 3.2 3.1 - - - +
430A TYR* 2.9 37.9 + - + +
604A C8E 3.8 33.4 - - + +
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Residues in contact with ILE 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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396A LEU* 3.6 5.1 - - - +
397A LYS* 2.8 68.1 + - + +
413A ASN* 5.5 5.6 - - - +
414A ALA* 1.3 76.9 - - - +
416A MET* 1.3 61.8 + - - +
427A GLN* 3.7 33.2 - - + +
428A LEU 3.2 17.3 - - - +
429A ASN* 3.7 12.1 - - + -
553A GLN 5.4 1.6 - - - +
555A ALA* 4.1 20.6 - - + -
556A PHE* 4.0 2.5 - - + -
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Residues in contact with MET 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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390A ILE* 5.4 2.9 - - + -
394A LEU* 4.0 24.2 - - + -
395A GLY 3.3 12.6 - - - +
396A LEU* 3.9 18.8 - - + -
415A ILE* 1.3 76.0 - - - +
417A GLU* 1.3 67.1 + - - +
418A TYR* 5.0 2.2 - - + +
426A ILE* 5.0 13.7 - - + +
427A GLN* 3.4 4.3 - - - +
428A LEU* 2.9 68.9 + - + +
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Residues in contact with GLU 417 (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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393A GLN 3.5 2.1 - - - +
394A LEU* 3.5 5.3 - - - -
395A GLY* 2.8 39.2 + - - -
416A MET* 1.3 76.5 - - - +
418A TYR* 1.3 69.7 + - - +
419A ARG* 4.0 13.1 - - + +
425A MET* 4.1 2.6 - - + +
426A ILE 3.4 11.9 - - - +
427A GLN* 2.6 33.2 + - + +
552A TYR* 2.9 23.3 + - - -
554A SER* 3.7 7.3 + - - -
555A ALA* 2.8 28.6 + - + +
556A PHE* 3.8 16.0 - - + -
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Residues in contact with TYR 418 (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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391A ASN* 5.1 2.5 - - - -
393A GLN* 3.2 36.8 - - + +
394A LEU* 3.9 19.7 - - + +
416A MET* 5.0 2.8 - - + +
417A GLU* 1.3 74.5 - - - +
419A ARG* 1.3 64.5 + - - +
420A LYS* 3.7 35.7 - - + +
424A ARG* 4.5 3.6 - - + -
425A MET* 3.4 4.3 - - - +
426A ILE* 2.8 45.3 + - + +
463A TRP* 3.7 38.2 - + - -
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Residues in contact with ARG 419 (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 ASP 4.9 0.3 - - - +
393A GLN* 2.9 32.6 + - - +
417A GLU* 4.0 15.3 - - + +
418A TYR* 1.3 81.2 - - - +
420A LYS* 1.3 61.0 + - - +
421A ASP 3.0 26.3 + - - +
422A ALA* 4.2 16.6 - - - +
424A ARG 3.4 12.1 - - - +
425A MET* 4.4 6.7 - - + +
552A TYR* 3.0 29.6 + - - -
554A SER* 3.3 20.3 + - - -
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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