Contacts of the strand formed by residues 440 - 450 (chain A) in PDB entry 5I4A
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 ASN 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A LYS* 3.6 15.5 + - - +
438A GLU 3.1 3.6 + - - +
439A LYS* 1.3 83.9 - - - +
441A LEU* 1.3 60.3 + - - +
442A TYR* 3.1 43.8 + - + +
463A VAL 4.6 2.1 - - - +
464A ASP* 4.6 4.7 - - - -
500A TYR* 3.5 13.7 - - - -
510A ASN* 2.7 38.0 + - - +
512A PHE* 3.6 16.4 - - + -
590A TYR* 3.0 23.0 + - - -
598A GLN* 3.4 6.9 + - - -
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Residues in contact with LEU 441 (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 ASN* 1.3 72.2 - - - +
442A TYR* 1.3 59.4 + - - +
443A ILE* 3.7 24.0 + - + -
462A ALA* 3.9 18.4 - - + -
463A VAL 4.1 1.8 - - - +
470A LEU* 3.7 29.8 - - + -
496A ALA 4.2 3.4 - - - +
497A PHE* 4.0 31.9 - - + -
500A TYR* 3.9 9.0 - - + -
508A PRO* 3.7 28.7 - - + -
510A ASN 2.9 9.9 + - - +
511A VAL* 3.4 5.6 - - + +
512A PHE 2.8 33.0 + - - +
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Residues in contact with TYR 442 (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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434A MET* 3.5 22.0 - - + +
437A LYS* 3.5 12.4 - - - +
440A ASN* 3.1 31.9 + - + -
441A LEU* 1.3 70.0 - - - +
443A ILE* 1.3 60.3 + - - +
461A ALA 3.8 0.7 - - - +
462A ALA* 3.2 2.9 - - - -
463A VAL* 2.8 58.2 + - + +
464A ASP 4.1 7.4 - - - -
465A ASN* 4.1 9.6 - - - -
512A PHE* 3.5 39.9 - + + -
514A LEU* 5.5 0.2 - - + -
598A GLN* 2.6 29.3 + - + -
602A LEU* 3.6 37.0 - - + -
619A PRO* 4.0 5.7 - - + +
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Residues in contact with ILE 443 (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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441A LEU* 3.7 25.4 - - + -
442A TYR* 1.3 78.3 - - - +
444A GLY* 1.3 62.7 + - - +
445A ILE* 3.6 26.5 - - + -
460A ILE* 4.5 11.0 - - + -
461A ALA 3.2 7.4 - - - +
462A ALA* 3.8 14.4 - - + -
493A TYR* 3.5 39.3 - - + -
496A ALA* 4.4 7.9 - - + -
511A VAL* 3.9 6.5 - - + -
512A PHE 2.8 14.2 + - - +
513A ILE* 4.7 6.5 - - + -
514A LEU* 2.9 30.7 + - - +
619A PRO* 3.9 3.8 - - - +
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Residues in contact with GLY 444 (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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443A ILE* 1.3 74.7 - - - +
445A ILE* 1.3 65.5 + - - +
460A ILE* 3.2 6.9 - - - +
461A ALA 2.7 35.8 + - - -
514A LEU* 3.4 6.1 - - - -
619A PRO* 3.4 16.3 - - - +
620A LEU* 3.7 14.8 - - - -
623A ALA* 4.0 4.8 - - - +
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Residues in contact with ILE 445 (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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443A ILE* 3.6 16.6 - - + -
444A GLY* 1.3 84.2 - - - +
446A ASP* 1.3 61.8 + - - +
447A LEU* 4.4 15.3 - - + -
458A LEU* 4.5 10.1 - - + -
459A CYS 3.8 1.3 - - - -
460A ILE* 3.6 20.6 - - + -
489A LEU* 5.1 20.6 - - + -
493A TYR* 6.3 2.5 - - + -
513A ILE* 3.9 23.6 - - + -
514A LEU 2.8 16.7 + - - +
515A ARG* 3.7 25.6 - - - +
516A ASP* 3.0 27.5 + - - +
519A PHE* 5.9 1.6 - - + -
620A LEU* 3.5 5.3 - - - +
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Residues in contact with ASP 446 (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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445A ILE* 1.3 72.3 - - - +
447A LEU* 1.3 67.7 + - - +
448A SER* 4.5 6.8 + - - -
457A ASN 3.7 1.6 - - - +
458A LEU* 3.4 2.3 - - - +
459A CYS* 2.8 41.5 + - - +
516A ASP* 3.8 12.7 - - - +
623A ALA* 3.7 21.3 - - + +
624A ASN* 2.6 41.6 - - - +
627A ALA* 4.0 13.8 - - + +
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Residues in contact with LEU 447 (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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445A ILE* 4.0 6.1 + - + -
446A ASP* 1.3 78.9 + - - +
448A SER* 1.3 60.8 + - - +
449A HIS* 3.2 28.6 - - + +
456A THR* 4.7 3.8 - - + -
457A ASN 3.1 8.1 - - - +
458A LEU* 3.8 29.2 - - + -
485A ASN* 5.1 11.4 - - + +
489A LEU* 4.7 18.2 - - + -
515A ARG* 3.3 33.0 + - - +
516A ASP* 5.1 4.9 + - - +
521A GLU* 2.9 31.9 - - + +
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Residues in contact with SER 448 (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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446A ASP* 4.4 7.2 + - - -
447A LEU* 1.3 74.6 - - - +
449A HIS* 1.3 71.5 + - - +
450A ASP* 4.9 9.2 + - - -
457A ASN* 2.8 54.7 + - - +
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Residues in contact with HIS 449 (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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447A LEU* 3.2 31.2 - - + +
448A SER* 1.3 77.6 + - - +
450A ASP* 1.3 66.8 + - - +
455A LYS 3.6 3.8 - - - +
456A THR* 2.6 40.9 + - + -
480A LEU* 3.6 26.1 - - + +
485A ASN* 3.4 15.0 + - + -
520A ILE* 6.2 3.6 - - + -
521A GLU* 3.3 14.2 + - - +
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Residues in contact with ASP 450 (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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448A SER* 4.9 8.5 + - - -
449A HIS* 1.3 80.4 + - - +
453A ALA* 3.2 37.0 - - + +
454A ARG* 3.6 1.4 - - - -
455A LYS* 3.1 35.0 + - + +
457A ASN* 5.5 9.7 + - - +
480A LEU* 4.2 5.6 - - - +
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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