Contacts of the strand formed by residues 454 - 464 (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 ILE 454 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ARG* 3.7 16.8 - - + +
432A TYR* 3.0 13.6 - - - -
433A ALA* 2.9 44.4 + - + +
438A ILE* 4.3 3.4 - - + -
453A GLY* 1.3 83.3 - - - +
455A SER* 1.3 62.6 + - - +
456A GLN* 4.2 11.4 - - + +
480A LYS* 5.8 0.2 - - - -
68B SER* 4.1 22.2 - - - +
69B ILE 3.7 20.4 - - - +
70B PHE* 3.6 26.9 - - + -
76B ALA* 3.8 16.2 - - + -
77B GLU* 4.5 2.9 - - - +
107B PHE* 4.4 5.2 - - + -
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Residues in contact with SER 455 (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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430A TYR* 2.7 27.6 + - - -
431A ARG 3.2 6.1 - - - -
432A TYR* 4.4 2.2 - - - -
453A GLY 4.3 0.6 + - - -
454A ILE* 1.3 76.8 - - - +
456A GLN* 1.3 59.6 + - - +
478A ASP* 3.5 9.9 + - - +
479A THR* 2.9 48.1 + - - +
480A LYS* 3.9 29.5 - - - +
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Residues in contact with GLN 456 (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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429A ASN* 3.9 3.7 + - - +
430A TYR* 3.3 6.4 - - - -
431A ARG* 2.9 41.6 + - + +
454A ILE* 4.2 13.0 - - + +
455A SER* 1.3 74.2 - - - +
457A VAL* 1.3 64.9 + - - +
458A GLY 4.2 0.2 + - - -
476A TYR* 3.4 38.6 - - + -
477A TYR 3.4 12.1 - - - +
478A ASP* 5.3 2.7 - - + -
485A ALA* 4.8 5.8 - - + +
550A LEU* 3.8 9.2 - - - +
67B VAL 2.8 26.6 + - - -
68B SER* 3.3 23.0 - - - +
69B ILE* 3.6 13.3 + - - +
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 5.3 9.6 - - + -
429A ASN 3.5 9.0 - - - +
430A TYR* 3.6 23.1 - - + -
456A GLN* 1.3 74.3 - - - +
458A GLY* 1.3 65.8 + - - +
459A THR* 5.7 2.5 - - + -
475A TYR* 3.9 1.0 - - - +
476A TYR* 3.5 1.9 - - - -
477A TYR* 2.8 39.3 + - + +
479A THR* 3.6 21.5 - - + -
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Residues in contact with GLY 458 (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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428A LEU* 3.4 6.2 - - - +
429A ASN* 2.9 52.1 + - - +
457A VAL* 1.3 76.6 - - - +
459A THR* 1.3 65.6 + - - +
475A TYR 3.4 7.0 - - - -
476A TYR* 3.6 12.6 - - - -
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Residues in contact with THR 459 (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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426A ILE* 6.5 1.6 - - + -
427A GLN 3.2 5.4 - - - +
428A LEU* 3.6 28.7 - - + -
457A VAL* 5.7 2.7 - - + -
458A GLY* 1.3 79.7 - - - +
460A THR* 1.3 68.7 + - - +
473A GLY 5.3 0.2 - - - -
474A ALA* 3.3 1.6 - - - +
475A TYR* 2.9 50.0 + - - +
476A TYR* 4.4 1.6 - - - -
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Residues in contact with THR 460 (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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425A MET* 3.1 16.2 - - + +
426A ILE* 3.5 2.4 - - - +
427A GLN* 2.9 43.6 + - - -
459A THR* 1.3 79.3 + - - +
461A ALA* 1.3 66.0 + - - +
473A GLY 3.3 14.6 - - - +
474A ALA* 4.2 7.4 - - + +
476A TYR* 3.5 23.2 + - - -
545A LEU* 3.9 21.5 - - + -
552A TYR* 4.5 16.7 - - + +
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Residues in contact with ALA 461 (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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425A MET* 3.2 15.5 - - - +
426A ILE* 4.6 11.2 - - + -
460A THR* 1.3 79.3 - - - +
462A SER* 1.3 63.5 + - - +
463A TRP* 5.4 3.6 - - + +
471A ILE 4.6 0.2 - - - -
472A VAL* 3.2 5.4 - - - +
473A GLY* 2.9 36.5 + - - +
545A LEU* 4.1 3.2 - - - +
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Residues in contact with SER 462 (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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423A ASP* 2.7 26.2 + - - +
424A ARG* 3.2 0.2 - - - -
425A MET* 2.9 38.0 + - - +
461A ALA* 1.3 76.2 - - - +
463A TRP* 1.3 58.4 + - - +
470A ALA* 6.0 1.7 - - - +
471A ILE 3.4 6.0 + - - -
472A VAL* 3.4 12.7 - - - +
541A THR* 3.2 28.8 - - - +
545A LEU* 4.2 10.8 - - - -
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Residues in contact with TRP 463 (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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418A TYR* 3.7 26.7 - + - -
423A ASP 4.0 1.1 - - - -
424A ARG* 3.4 36.9 - - + +
425A MET 3.7 14.4 - - - -
426A ILE* 3.6 38.4 - - + -
461A ALA* 4.3 3.3 - - + -
462A SER* 1.3 85.7 + - - +
464A PRO* 1.3 92.9 + - + +
465A ILE* 5.1 4.3 - - + -
470A ALA* 4.7 2.2 - - - +
471A ILE* 2.9 44.3 + - + +
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Residues in contact with PRO 464 (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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423A ASP* 3.3 28.5 - - + +
424A ARG* 3.7 33.6 + - + +
463A TRP* 1.3 110.3 + - + +
465A ILE* 1.3 60.3 + - - +
466A ALA 5.0 5.6 - - - +
469A TRP 3.8 13.5 - - - +
470A ALA* 4.3 4.0 - - + -
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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