Contacts of the strand formed by residues 469 - 478 (chain A) in PDB entry 2IUK
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 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A GLU* 3.1 21.2 - - - +
371A ALA* 3.6 42.6 - - + +
372A ARG* 5.1 0.6 - - - +
374A VAL* 4.9 0.4 - - + -
375A ILE* 3.9 34.8 - - + -
383A ILE* 4.2 4.7 - - + -
431A PHE* 4.1 17.9 - - + -
461A LEU* 3.9 30.7 - - + -
462A PHE 3.1 22.4 - - - +
463A LEU* 4.2 8.3 - - + +
468A THR* 1.3 79.2 - - - +
470A LYS* 1.3 58.4 + - - +
631A ILE* 4.3 9.4 - - + -
833A ASN* 4.4 4.9 + - - +
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Residues in contact with LYS 470 (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 ASP* 4.4 10.0 + - - +
368A GLU* 2.9 26.6 + - - +
415A ASN* 4.4 19.3 - - + +
461A LEU* 3.3 4.2 - - - -
462A PHE* 2.8 40.4 + - + +
464A LYS* 3.4 31.6 - - + +
469A LEU* 1.3 76.6 - - - +
471A PRO* 1.3 103.4 - - - +
472A LEU* 3.5 19.7 + - + -
495A PRO* 5.4 5.4 - - - -
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Residues in contact with PRO 471 (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 ASP* 3.3 29.8 - - + +
370A PHE* 3.5 26.0 - - + -
371A ALA* 3.8 9.9 - - + -
415A ASN* 5.4 0.2 - - - +
459A THR* 4.9 1.3 - - + -
460A ILE 3.5 9.2 - - - +
461A LEU* 4.1 4.5 - - + -
469A LEU 4.3 0.2 - - - +
470A LYS* 1.3 110.7 - - - +
472A LEU* 1.3 58.2 + - - +
473A ALA 3.7 0.2 - - - -
495A PRO* 3.4 14.6 - - - +
505A TRP* 3.2 28.7 - - + -
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Residues in contact with LEU 472 (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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411A GLN 4.0 2.3 - - - +
412A LEU* 3.7 31.6 - - + +
415A ASN* 3.5 33.7 + - + +
416A MET* 3.5 24.7 - - + -
430A LEU* 3.8 22.0 - - + -
460A ILE* 3.0 14.3 + - + +
462A PHE* 3.6 27.1 - - + -
470A LYS* 3.7 19.3 - - + +
471A PRO* 1.3 73.1 - - - +
473A ALA* 1.3 63.4 - - - +
494A LEU* 3.9 4.3 - - - +
495A PRO* 3.1 23.2 - - - +
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Residues in contact with ALA 473 (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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407A ILE* 4.2 18.2 - - + -
411A GLN* 5.1 0.4 - - + -
412A LEU* 4.1 18.4 - - + -
458A ARG 3.8 0.9 - - - +
459A THR* 3.5 2.4 - - - +
460A ILE* 3.0 28.3 + - - +
471A PRO 3.7 1.0 - - - -
472A LEU* 1.3 82.8 - - - +
474A ILE* 1.3 63.4 + - - +
475A GLU 4.2 0.4 - - - -
492A VAL* 4.2 4.7 - - + -
493A VAL 3.7 8.1 - - - -
494A LEU* 3.7 18.4 - - + -
505A TRP* 4.1 3.7 - - - -
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Residues in contact with ILE 474 (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 PHE* 4.0 6.7 - - + -
458A ARG 3.3 4.7 - - - +
459A THR* 3.8 15.5 - - + -
473A ALA* 1.3 75.2 - - - +
475A GLU* 1.3 67.7 + - - +
476A LEU* 4.2 6.7 - - + +
491A ILE 4.1 0.3 - - - +
492A VAL* 3.8 2.2 - - - -
493A VAL* 2.9 41.6 + - - +
505A TRP* 3.6 20.0 - - + -
508A ALA* 3.8 14.8 - - + +
509A LYS* 3.5 45.3 - - + +
512A VAL* 3.3 25.6 - - + -
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Residues in contact with GLU 475 (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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405A SER* 2.7 25.5 + - - -
406A THR* 2.7 38.0 + - - +
407A ILE* 3.8 16.7 - - + +
436A GLN* 5.4 1.3 - - - +
456A ALA 4.0 0.2 - - - +
457A THR* 3.3 8.3 - - - -
458A ARG* 2.7 68.2 + - + +
473A ALA 4.2 0.8 - - - -
474A ILE* 1.3 73.7 - - - +
476A LEU* 1.3 67.6 + - - +
477A SER* 4.3 2.9 - - - +
490A SER* 3.6 13.8 + - - -
491A ILE 3.3 12.8 - - - +
492A VAL* 4.4 1.8 - - + +
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Residues in contact with LEU 476 (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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455A TYR* 3.5 25.6 - - + -
456A ALA 4.0 2.0 - - - -
457A THR* 3.3 28.7 - - + -
474A ILE* 4.2 15.3 - - + +
475A GLU* 1.3 76.8 - - - +
477A SER* 1.3 60.7 + - - +
489A GLU 3.6 2.1 - - - +
490A SER* 3.5 1.6 - - - -
491A ILE* 3.0 59.7 + - + +
493A VAL* 4.1 11.0 - - + -
508A ALA* 4.3 7.2 - - - +
511A HIS* 3.8 18.2 - - + -
741A ILE* 3.9 22.2 - - + -
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Residues in contact with SER 477 (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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436A GLN* 3.5 29.4 + - - -
440A ILE* 3.9 13.2 - - - -
443A LEU* 3.4 3.0 - - - +
455A TYR* 3.3 3.3 - - - -
456A ALA 2.8 33.7 + - - -
475A GLU* 4.3 3.5 + - - +
476A LEU* 1.3 72.7 - - - +
478A LYS* 1.3 71.0 + - - +
488A PRO* 3.9 5.8 - - - +
489A GLU 3.4 5.4 - - - -
490A SER* 2.6 29.3 + - - -
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Residues in contact with LYS 478 (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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440A ILE* 4.5 0.7 - - - -
443A LEU* 4.1 3.4 - - + -
447A ASN* 3.7 11.2 - - - +
454A ALA 3.4 16.8 - - - +
455A TYR* 4.0 16.4 - - + -
477A SER* 1.3 81.3 - - - +
479A PRO* 1.3 75.1 - - + +
480A HIS* 3.0 32.8 + - + +
488A PRO* 4.3 3.1 - - - -
489A GLU* 2.7 54.0 + - - +
740A PHE* 3.3 43.1 - - + -
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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