Contacts of the strand formed by residues 450 - 461 (chain A) in PDB entry 1SIW
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 VAL 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A TYR* 4.7 14.1 - - + +
430A GLY* 3.9 20.9 - - - -
431A PHE 3.4 6.3 - - - +
448A GLU* 3.2 17.1 - - - +
449A ASN* 1.3 87.2 - - + +
451A LEU* 1.3 63.9 + - - +
452A LEU* 3.8 25.9 - - + +
631A PRO* 3.8 24.5 - - + +
632A MET* 4.2 16.4 - - + -
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Residues in contact with LEU 451 (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 VAL 3.5 1.9 - - - +
431A PHE* 2.8 44.9 + - + +
432A PRO 5.5 1.3 - - - +
433A TYR* 4.0 17.3 - - + -
447A LEU* 4.3 9.6 - - + -
448A GLU* 3.7 38.1 - - + +
450A VAL* 1.3 73.5 - - - +
452A LEU* 1.3 63.8 + - - +
453A HIS* 3.9 17.1 - - + +
491A ASN* 4.0 25.4 - - + +
501A ALA* 3.3 33.9 - - + -
502A TYR* 5.7 1.3 - - + +
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Residues in contact with LEU 452 (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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347A GLY 4.7 3.8 - - - +
348A TYR* 4.1 35.2 - - + -
428A GLU* 3.5 28.7 - - + +
429A VAL 3.3 7.9 - - - +
430A GLY* 4.7 1.6 - - - -
450A VAL* 3.8 27.6 - - + +
451A LEU* 1.3 75.9 - - - +
453A HIS* 1.3 60.6 - - - +
489A ASP* 3.6 6.2 - - - +
491A ASN* 2.6 32.6 + - - +
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Residues in contact with HIS 453 (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 GLU* 3.1 6.5 - - - -
429A VAL 2.9 31.9 + - - -
431A PHE* 3.7 27.5 - + + +
451A LEU* 3.9 22.1 - - + +
452A LEU* 1.3 72.2 + - - +
454A LYS* 1.3 63.5 + - - +
455A LEU* 3.6 16.8 + - + +
479A ALA* 3.2 34.6 + - + -
480A ASN* 4.9 3.4 + - - -
482A GLY* 4.5 4.7 - - - -
489A ASP* 2.8 25.1 + - - +
491A ASN* 3.6 33.0 - - + -
492A CYS* 3.7 8.5 - - - -
501A ALA* 5.2 3.1 + - + -
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Residues in contact with LYS 454 (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* 3.7 18.6 - - + -
427A ALA 3.7 4.9 - - - -
428A GLU* 4.0 27.9 + - + +
453A HIS* 1.3 73.2 - - - +
455A LEU* 1.3 64.7 + - - +
456A PRO* 4.1 1.7 - - - +
479A ALA* 5.4 1.7 - - - +
487A LEU* 2.9 46.3 - - + +
488A ASN* 3.0 23.0 + - - +
489A ASP* 3.0 25.1 + - + +
490A VAL* 4.1 13.1 - - - +
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Residues in contact with LEU 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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426A ILE* 3.4 4.3 - - - -
427A ALA 2.8 37.8 + - - +
429A VAL* 3.9 23.3 - - + -
431A PHE* 3.9 3.1 - - + -
453A HIS* 3.6 28.3 - - + +
454A LYS* 1.3 79.7 - - - +
456A PRO* 1.3 64.6 - - + +
457A VAL* 3.1 11.1 + - + +
471A THR* 4.4 4.9 - - - +
475A ASP* 3.4 46.7 - - + +
476A LEU* 3.8 20.0 - - + +
479A ALA* 3.8 12.1 - - + -
485A ARG* 6.0 0.2 - - - +
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Residues in contact with PRO 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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419A LEU* 3.6 17.0 - - - +
420A LEU* 3.8 33.0 - - + +
423A GLN* 3.7 29.4 - - + +
425A GLU 3.8 6.7 - - - +
426A ILE* 4.6 4.0 - - + -
454A LYS 4.1 4.5 - - - +
455A LEU* 1.3 89.4 - - + +
457A VAL* 1.3 63.9 + - - +
471A THR* 3.8 7.0 + - - -
475A ASP* 3.9 17.3 - - + +
485A ARG* 4.8 4.7 - - - +
487A LEU* 4.2 8.7 - - + -
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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
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342A LEU* 3.3 34.5 - - + -
419A LEU* 4.4 0.7 - - - -
423A GLN* 2.9 24.4 - - - +
424A ASP 3.0 7.0 + - - -
425A GLU* 3.0 44.2 + - + +
427A ALA* 3.5 14.1 - - + +
455A LEU* 3.1 17.2 + - + +
456A PRO* 1.3 73.5 - - - +
458A LYS* 1.3 63.6 + - - +
469A LEU* 3.8 18.8 - - + -
470A VAL 3.6 10.3 - - - +
471A THR* 4.8 2.2 - - - -
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Residues in contact with LYS 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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377A PHE* 3.6 38.4 - - + -
381A GLY* 5.2 7.0 - - - -
419A LEU* 4.0 20.0 - - + -
422A SER* 2.7 32.8 + - - +
423A GLN* 5.0 0.7 - - - -
424A ASP* 3.5 26.3 + - - +
457A VAL* 1.3 80.8 - - - +
459A ARG* 1.3 66.5 + - - +
460A LEU* 3.8 4.6 + - + -
469A LEU* 4.3 2.2 - - - -
470A VAL* 3.1 37.3 + - + +
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Residues in contact with ARG 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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349A TYR* 4.4 7.5 + - - -
424A ASP* 3.0 24.7 + - + +
425A GLU* 3.8 16.8 + - - +
458A LYS* 1.3 72.2 - - - +
460A LEU* 1.3 67.5 + - - +
467A THR* 3.1 42.8 + - - +
468A ALA* 3.4 18.0 - - - +
469A LEU* 3.4 34.6 - - + +
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Residues in contact with LEU 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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339A LEU* 4.7 0.7 - - + -
355A LEU* 3.9 13.5 - - + -
360A LEU* 4.7 7.6 - - + -
377A PHE* 4.2 19.7 - - + -
383A MET* 3.8 30.1 - - + -
458A LYS* 4.0 7.9 - - + +
459A ARG* 1.3 85.0 - - - +
461A GLN* 1.3 63.2 + - - +
462A LEU* 3.7 6.3 + - + +
467A THR* 2.7 26.6 + - - -
468A ALA 2.9 20.5 + - - +
470A VAL* 3.5 38.1 - - + -
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Residues in contact with GLN 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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360A LEU* 4.7 8.1 - - - +
361A VAL* 4.0 17.7 + - + +
460A LEU* 1.3 73.9 - - - +
462A LEU* 1.3 75.5 + - - +
465A GLY* 3.1 30.1 + - - +
466A SER 3.5 7.0 + - - +
467A THR* 3.8 14.9 - - - +
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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