Contacts of the strand formed by residues 447 - 459 (chain B) in PDB entry 1NBF
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 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B LEU 3.8 1.8 - - - -
432B PRO* 3.5 29.1 - - - +
433B LEU 4.6 0.2 - - - +
434B ASP* 5.6 3.0 - - - +
445B PRO* 2.8 34.1 + - + +
446B ALA* 1.3 71.5 - - - +
448B TYR* 1.3 56.0 + - - +
520B ARG* 3.6 3.1 - - - +
521B GLU* 2.7 57.4 + - + +
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Residues in contact with TYR 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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398B LEU* 3.0 32.6 + - + +
399B PRO 2.7 30.5 + - - -
400B PRO 3.9 1.8 - - - -
402B LEU* 4.0 15.7 - - + -
429B GLU 3.9 0.2 - - - +
430B GLN* 3.5 5.5 - - - +
431B LEU* 2.8 43.8 + - + +
433B LEU* 3.8 15.0 - - + -
446B ALA* 3.4 35.0 - - + -
447B ASN* 1.3 73.9 - - - +
449B ILE* 1.3 64.9 + - - +
518B TYR* 3.6 30.2 - - + -
519B ILE 3.6 4.5 - - - -
520B ARG* 3.2 39.6 + - + -
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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
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429B GLU* 3.6 8.7 - - + +
430B GLN* 3.7 32.5 - - + +
447B ASN 5.4 0.2 - - - -
448B TYR* 1.3 80.6 - - - +
450B LEU* 1.3 76.3 + - - +
451B HIS* 3.2 2.3 + - - +
470B ASN* 5.3 0.7 - - - +
473B GLY* 4.4 15.5 - - - +
518B TYR* 3.2 3.7 - - - -
519B ILE* 2.9 40.4 + - - +
521B GLU* 3.9 25.8 - - + +
524B LEU* 4.0 24.9 - - + -
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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
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427B PHE* 3.9 19.1 - - + -
428B PRO 3.9 7.4 - - - +
429B GLU* 2.8 25.9 + - + +
449B ILE* 1.3 82.5 - - - +
451B HIS* 1.3 58.2 + - - +
452B ALA 3.7 15.0 - - - +
453B VAL* 4.1 4.9 - - + -
470B ASN* 3.0 17.2 + - - +
473B GLY* 5.2 0.5 - - - -
477B TRP* 3.6 29.8 - - + -
494B ILE* 3.8 25.4 - - + -
516B LEU* 4.6 2.5 - - + -
517B VAL 3.6 15.7 - - - +
518B TYR* 3.5 32.6 - - + +
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Residues in contact with HIS 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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231B THR* 4.9 2.5 + - - +
234B PHE* 3.3 28.0 - - + -
235B THR* 4.7 6.3 + - - -
449B ILE 3.2 1.0 + - - +
450B LEU* 1.3 73.9 - - - +
452B ALA* 1.3 57.0 + - - +
469B LEU* 3.4 20.1 - - + +
470B ASN* 3.0 50.5 + - - +
471B PRO* 3.0 28.2 + - - +
473B GLY* 4.5 3.1 - - - -
477B TRP* 3.7 2.2 - - - -
517B VAL* 2.8 27.8 + - + +
519B ILE* 3.3 38.8 - - + +
528B LEU* 3.6 6.7 - - + +
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Residues in contact with ALA 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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231B THR* 4.6 3.8 - - + +
450B LEU* 3.7 5.4 - - - +
451B HIS* 1.3 82.8 - - - +
453B VAL* 1.3 69.2 + - - +
454B LEU* 4.1 3.6 - - + -
467B VAL* 4.2 7.6 - - + -
468B TYR 3.1 7.4 - - - +
469B LEU* 3.5 24.9 - - + -
477B TRP* 4.2 1.1 - - - -
516B LEU* 3.7 3.3 - - - -
517B VAL* 3.1 43.6 + - + -
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Residues in contact with VAL 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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427B PHE* 4.0 20.6 - - + -
450B LEU* 4.1 7.9 - - + -
452B ALA* 1.3 78.9 - - - +
454B LEU* 1.3 62.1 + - - +
455B VAL* 3.3 21.1 + - + +
467B VAL* 3.4 0.9 - - - -
468B TYR* 2.8 35.3 + - + -
477B TRP* 4.1 14.6 - - + -
493B ALA 3.5 25.6 - - - +
497B ASN* 4.2 0.7 - - - +
513B ALA* 3.7 30.7 - - + -
515B MET 3.8 2.7 - - - -
516B LEU* 4.0 3.6 - - + -
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Residues in contact with LEU 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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227B SER* 3.8 20.2 - - - +
228B LEU* 4.3 2.2 - - - +
231B THR* 3.4 28.5 - - + +
296B VAL* 4.0 29.8 - - + -
452B ALA* 4.2 3.6 - - + -
453B VAL* 1.3 72.1 - - - +
455B VAL* 1.3 61.4 + - - +
465B TYR* 5.2 3.6 - - + -
466B VAL 3.7 6.1 - - - +
467B VAL* 4.0 7.2 - - + -
513B ALA* 3.9 1.0 - - - -
514B TYR* 3.0 25.1 + - - +
515B MET* 2.9 44.3 + - + +
517B VAL* 4.2 22.0 - - + -
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Residues in contact with VAL 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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453B VAL* 3.7 21.8 - - + +
454B LEU* 1.3 72.5 - - - +
456B HIS* 1.3 60.4 + - - +
457B SER* 5.1 0.4 - - - +
464B HIS 3.8 0.9 - - - +
465B TYR* 3.5 9.2 - - - -
466B VAL* 3.0 45.7 + - + +
468B TYR* 3.9 9.0 - - + -
497B ASN* 3.3 37.5 - - + +
511B THR* 3.5 30.3 - - + -
512B ASN 3.1 18.8 - - - +
513B ALA* 4.3 0.2 - - - -
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Residues in contact with HIS 456 (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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420B LYS* 2.7 42.6 + - + +
454B LEU 4.1 1.0 + - - -
455B VAL* 1.3 74.3 - - - +
457B SER* 1.3 72.5 + - - +
458B GLY 3.5 6.5 - - - -
459B ASP* 3.3 37.3 + - - -
462B GLY 4.1 0.4 + - - -
464B HIS 3.6 3.4 - - - -
465B TYR* 3.7 24.7 - + + -
510B CYS 3.3 0.5 - - - +
511B THR* 3.4 1.0 - - - -
512B ASN* 3.0 24.6 + - - +
514B TYR* 4.2 14.8 - - + +
373C LEU* 3.6 32.0 + - + +
374C ARG 3.0 23.3 + - - -
375C GLY* 4.6 0.9 - - - -
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Residues in contact with SER 457 (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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455B VAL* 5.1 0.5 - - - +
456B HIS* 1.3 76.5 - - - +
458B GLY* 1.3 59.7 + - - +
463B GLY* 2.8 7.0 - - - -
464B HIS* 2.7 54.4 + - - -
507B VAL* 4.4 13.7 - - - +
510B CYS* 3.3 4.7 - - - -
511B THR* 2.7 32.0 + - - +
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Residues in contact with GLY 458 (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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420B LYS* 3.3 15.4 - - - +
422B ASN* 5.0 0.9 + - - -
456B HIS* 3.5 4.0 - - - -
457B SER* 1.3 72.8 - - - +
459B ASP* 1.3 63.8 + - - +
462B GLY 3.5 6.1 - - - -
463B GLY* 4.2 2.5 - - - -
510B CYS* 3.1 35.7 + - - +
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Residues in contact with ASP 459 (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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420B LYS* 4.1 16.2 - - + +
456B HIS* 3.3 19.5 + - - -
458B GLY* 1.3 75.5 - - - +
460B ASN* 1.3 65.4 + - - +
461B HIS* 2.7 30.0 + - - +
462B GLY 3.0 25.4 + - - +
373C LEU* 4.2 2.5 - - - -
374C ARG 3.5 1.9 + - - +
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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