Contacts of the strand formed by residues 471 - 482 (chain A) in PDB entry 3IJE
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 SER 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A LEU* 4.9 3.9 - - - +
455A ASN 2.4 31.8 + - - -
456A GLN* 3.8 19.1 - - - -
458A ASN* 2.9 19.8 + - - +
459A LYS* 3.5 4.0 - - - +
470A VAL* 1.3 70.4 - - - +
472A CYS* 1.3 61.1 + - - +
473A PHE* 4.6 2.4 - - - -
541A TYR 3.9 0.2 - - - -
542A LEU* 3.1 40.9 + - - +
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Residues in contact with CYS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO* 4.8 1.0 - - - +
454A LEU* 5.2 1.9 - - - +
460A THR* 5.2 0.2 - - - -
461A CYS* 2.0 58.1 - - - -
470A VAL 3.1 1.9 + - - +
471A SER* 1.3 75.4 + - - +
473A PHE* 1.3 65.4 + - - +
514A LEU* 5.6 0.4 - - + -
539A ILE* 5.3 9.4 - - + -
540A ALA 3.4 15.0 - - - +
541A TYR* 3.7 13.2 - - + +
1F NAG 3.2 31.8 + - - -
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Residues in contact with PHE 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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449A VAL* 4.1 16.4 - - + -
451A PRO* 3.6 18.2 - - + +
454A LEU* 3.4 50.5 - - + -
471A SER 4.6 1.8 - - - -
472A CYS* 1.3 78.5 - - - +
474A ASN* 1.3 65.1 + - - +
475A VAL* 3.5 26.5 - - + -
499A LEU* 4.2 10.5 - - + -
511A ALA* 4.3 11.0 - - + -
539A ILE* 3.4 8.2 - - - +
540A ALA* 2.8 57.9 + - + +
541A TYR 4.3 10.8 - - - -
555A ILE* 5.4 1.6 - - + -
557A ILE* 4.2 9.0 - - + -
590A ALA* 5.3 4.5 - - + -
1F NAG 5.4 0.7 - - - -
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Residues in contact with ASN 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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448A GLU 3.9 0.3 - - - +
449A VAL* 3.2 27.0 - - - +
450A TYR* 3.3 12.6 + - + -
451A PRO* 3.5 14.2 - - + +
473A PHE* 1.3 76.9 - - - +
475A VAL* 1.3 61.9 + - - +
476A ARG* 5.7 0.2 - - - -
537A GLU* 2.8 39.5 + - - +
538A LEU 3.3 14.8 - - - +
539A ILE* 3.2 22.5 - - + +
2F NAG 5.5 12.0 + - - -
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 4.3 9.4 - - + -
448A GLU 3.7 3.1 - - - -
449A VAL* 3.8 8.5 - - + -
473A PHE* 3.5 31.2 - - + -
474A ASN* 1.3 74.4 - - - +
476A ARG* 1.3 63.8 + - - +
477A PHE* 4.3 1.4 + - - -
497A LEU* 3.9 25.8 - - + -
499A LEU* 4.6 7.9 - - + -
513A PHE* 4.9 3.6 - - + -
536A GLU 4.4 0.5 - - - +
537A GLU* 3.6 0.9 - - - -
538A LEU* 2.7 47.6 + - + +
540A ALA* 4.3 12.8 - - + -
557A ILE* 4.0 18.6 - - + -
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Residues in contact with ARG 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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446A GLY 4.5 0.5 - - - -
447A LEU* 3.5 6.5 - - - -
448A GLU* 3.0 60.5 + - + +
450A TYR* 3.7 33.3 + - + -
475A VAL* 1.3 77.2 - - - +
477A PHE* 1.3 67.4 + - - +
478A CYS* 5.4 0.3 - - - +
535A CYS* 4.0 21.7 - - - -
536A GLU 3.9 8.7 - - - +
537A GLU* 3.4 35.6 + - + +
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Residues in contact with PHE 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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446A GLY 3.4 5.6 - - - +
447A LEU* 4.3 5.2 - - + -
475A VAL 5.2 0.7 - - - -
476A ARG* 1.3 75.8 - - - +
478A CYS* 1.3 67.2 + - - +
479A LEU* 5.9 0.9 - - + -
495A VAL* 4.2 14.4 - - + -
497A LEU* 3.3 41.7 - - + -
521A HIS* 5.9 0.2 - - - -
523A LYS* 4.0 25.1 - - + -
525A MET* 3.8 22.4 - - - -
535A CYS* 3.2 13.3 - - - -
536A GLU* 3.4 51.3 + - + -
538A LEU* 4.4 16.8 - - + -
559A MET* 3.6 25.6 - - + -
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Residues in contact with CYS 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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445A ALA* 3.4 3.8 - - - +
446A GLY* 2.8 34.6 + - - +
476A ARG* 5.9 0.2 - - - +
477A PHE* 1.3 76.0 - - - +
479A LEU* 1.3 65.2 + - - +
525A MET* 5.3 0.2 - - - -
533A MET* 3.3 39.0 - - + +
534A GLN 3.2 13.7 - - - -
535A CYS* 2.0 48.2 - - - -
559A MET* 4.9 0.9 - - - +
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Residues in contact with LEU 479 (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 VAL* 5.0 6.3 - - + -
444A ASN 3.8 1.3 - - - +
445A ALA* 3.8 25.4 - - + +
477A PHE* 5.9 0.9 - - + -
478A CYS* 1.3 82.6 - - - +
480A LYS* 1.3 58.6 + - - +
493A PHE* 3.9 30.3 - - + -
495A VAL* 3.7 29.4 - - + -
525A MET* 4.6 10.3 - - - +
527A ILE* 3.6 28.3 - - + +
532A LEU 3.8 1.2 - - - +
533A MET* 3.5 3.9 - - - -
534A GLN 3.1 28.9 + - - +
559A MET* 4.9 5.2 - - + -
561A TYR* 4.3 22.2 - - + -
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Residues in contact with LYS 480 (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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442A THR* 4.7 4.1 + - - +
443A VAL* 3.3 1.5 - - - -
444A ASN* 2.6 69.3 + - + +
479A LEU* 1.3 72.7 - - - +
481A ALA* 1.3 68.6 + - - +
482A ASP* 4.1 15.9 + - - +
527A ILE* 4.2 0.4 - - - -
531A GLY* 3.5 48.9 - - - +
532A LEU 4.4 2.2 - - - +
533A MET* 3.8 24.0 - - + +
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Residues in contact with ALA 481 (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 ILE* 5.5 1.6 - - + -
442A THR 3.4 4.9 - - - -
443A VAL* 3.8 20.6 - - + +
480A LYS* 1.3 75.7 - - - +
482A ASP* 1.3 65.9 + - - +
491A LEU* 4.1 21.2 - - + +
493A PHE* 4.2 0.9 - - + -
527A ILE* 3.2 29.0 - - + +
528A SER 4.3 5.0 + - - +
529A ARG 3.2 5.5 - - - +
530A GLY* 3.2 17.7 + - - -
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Residues in contact with ASP 482 (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 ILE* 3.8 8.6 - - - +
442A THR* 2.7 44.8 + - - +
480A LYS* 4.1 15.4 + - - +
481A ALA* 1.3 76.0 - - - +
483A GLY* 1.3 74.7 + - - +
487A LEU* 5.9 0.2 - - - +
491A LEU* 5.8 0.7 - - - -
529A ARG 2.9 20.3 - - - +
530A GLY* 3.6 15.0 - - - -
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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