Contacts of the strand formed by residues 446 - 455 (chain B) in PDB entry 1D0N
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 446 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B ARG* 3.7 1.7 - - - +
425B VAL* 3.0 33.6 + - - +
445B ASP* 1.3 73.1 + - - +
447B TYR* 1.3 67.4 + - - +
466B TRP 3.3 9.2 - - - -
467B GLN* 3.7 14.7 - - - -
471B SER* 3.3 19.5 + - - -
475B GLU* 4.2 8.2 + - - -
476B VAL* 3.9 10.9 - - - +
479B SER* 3.8 23.0 + - - -
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Residues in contact with TYR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ILE* 4.3 9.6 - - + -
423B TRP 3.3 19.1 - - - +
424B ARG* 3.7 23.3 - - + -
425B VAL 4.9 0.2 - - - +
433B VAL* 4.0 15.5 - - + -
440B GLN 4.3 3.8 + - - -
441B PHE* 3.4 39.6 - + + -
442B TYR* 3.2 31.0 + - - -
445B ASP* 3.1 33.6 + - + -
446B SER* 1.3 74.3 - - - +
448B ILE* 1.3 66.4 + - - +
449B ILE* 4.8 1.8 - - + -
464B TYR 4.2 0.4 - - - -
465B ASN* 3.2 9.2 + - - -
466B TRP* 2.9 51.3 + + + +
525B SER* 3.4 11.0 + - - -
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Residues in contact with ILE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ILE* 3.6 2.1 - - - -
423B TRP* 2.9 57.4 + - + +
425B VAL* 3.8 20.6 - - + -
430B LYS* 4.0 13.2 - - + -
447B TYR* 1.3 79.2 - - - +
449B ILE* 1.3 63.9 + - - +
450B LEU 4.2 0.2 - - - -
463B ILE* 4.0 22.4 - - + -
464B TYR 3.3 3.1 - - - +
465B ASN* 4.5 1.6 - - - +
479B SER 3.8 11.4 - - - +
482B LEU* 3.6 32.5 - - + +
483B THR* 3.9 14.8 - - - +
486B LEU* 4.5 6.5 - - + -
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LYS* 4.7 7.0 - - + -
421B GLN 3.4 8.5 - - - +
422B ILE* 4.1 26.0 - - + -
441B PHE* 4.0 25.8 - - + -
447B TYR* 4.8 2.7 - - + -
448B ILE* 1.3 84.0 - - - +
450B LEU* 1.3 69.0 + - - +
451B TYR* 3.8 1.5 + - + +
462B ILE 3.4 2.1 - - - +
463B ILE* 3.2 5.1 - - - -
464B TYR* 2.8 53.4 + - + +
466B TRP* 5.3 4.7 - - + -
508B LEU* 3.6 29.8 - - + -
511B LEU* 4.3 20.4 - - + -
512B PHE* 5.1 0.7 - - + -
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLN 4.1 0.2 - - - +
420B LYS* 3.2 6.1 - - - +
421B GLN* 2.9 37.6 + - + +
423B TRP* 3.9 30.4 - - + -
448B ILE 4.2 0.6 - - - -
449B ILE* 1.3 71.9 - - - +
451B TYR* 1.3 63.0 + - - +
452B ASN* 4.8 3.1 - - - +
461B GLN* 4.1 26.5 - - + +
462B ILE 3.7 2.7 - - - +
463B ILE* 4.0 18.6 - - + +
486B LEU* 4.5 9.0 - - + -
490B LEU* 4.0 32.3 - - + -
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Residues in contact with TYR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ASP* 2.9 16.6 + - - -
416B GLY* 3.0 23.0 - - - -
418B GLY* 2.7 43.5 + - - -
419B GLN 3.4 10.1 - - - -
420B LYS* 3.8 13.0 - - + -
449B ILE* 4.8 7.6 - - + -
450B LEU* 1.3 75.1 - - - +
452B ASN* 1.3 77.1 + - - +
453B TYR* 3.6 16.6 - - + -
461B GLN* 3.2 6.8 - - - +
462B ILE* 2.8 49.0 + - + +
464B TYR* 5.0 3.6 - - + -
507B HIS* 3.5 25.4 - + - -
511B LEU* 4.1 20.2 - - + -
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Residues in contact with ASN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B GLY* 3.6 12.1 - - - -
419B GLN* 3.0 31.1 + - + +
450B LEU* 4.8 3.3 - - - +
451B TYR* 1.3 87.9 - - - +
453B TYR* 1.3 61.6 + - - +
454B ARG* 4.2 6.1 + - + +
460B GLY 3.5 4.0 - - - +
461B GLN* 3.0 36.3 + - - +
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Residues in contact with TYR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ASP* 4.0 20.2 - - + +
414B ASP* 3.2 18.6 - - + +
451B TYR* 3.6 13.3 + - + -
452B ASN* 1.3 74.5 - - - +
454B ARG* 1.3 64.8 + - - +
455B HIS 4.3 0.4 - - - -
458B ARG* 3.7 34.8 - - + +
459B GLN* 3.5 10.4 + - - +
460B GLY* 3.0 60.8 + - - +
461B GLN 3.7 4.7 - - - -
462B ILE* 3.9 26.7 - - + -
495B VAL* 4.9 3.0 - - + +
724B PHE 4.7 4.5 + - - -
725B GLU 4.2 1.9 + - - -
726B PRO* 3.7 21.3 - - + +
727B PRO* 3.6 20.9 - - + -
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B HIS* 5.0 4.5 - - - +
414B ASP* 2.9 26.1 + - - +
417B THR 5.6 2.6 + - - -
418B GLY* 5.0 13.3 - - - -
419B GLN* 4.8 17.6 - - - +
452B ASN* 4.5 7.1 + - + +
453B TYR* 1.3 79.4 - - - +
455B HIS* 1.3 59.8 + - - +
456B GLY 4.2 0.4 - - - -
458B ARG 4.2 2.0 - - - -
459B GLN* 4.6 11.2 - - + -
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Residues in contact with HIS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B LEU* 3.0 22.8 + - + -
401B HIS* 3.6 25.6 - - + -
402B THR 4.7 0.9 - - - -
403B SER 3.3 26.1 + - - -
404B THR* 3.9 10.1 - - + -
407B ALA* 4.2 5.3 - - + +
413B ASP 3.5 26.5 - - - +
414B ASP* 4.8 1.6 - - - -
453B TYR* 4.5 1.1 - - + -
454B ARG* 1.3 73.5 - - - +
456B GLY* 1.3 55.2 + - - +
457B SER* 2.4 47.2 + - - -
458B ARG 2.5 35.8 + - - +
459B GLN* 4.9 2.4 - - - +
727B PRO* 3.6 21.8 - - + +
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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