Contacts of the strand formed by residues 447 - 459 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A LEU 3.8 2.9 - - - -
432A PRO* 3.7 22.5 - - + +
434A ASP* 5.7 1.7 + - - +
445A PRO* 2.7 37.1 + - - +
446A ALA* 1.3 72.6 - - - +
448A TYR* 1.3 56.5 + - - +
520A ARG* 3.7 3.3 - - - +
521A GLU* 2.8 64.0 + - + +
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Residues in contact with TYR 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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398A LEU* 3.2 31.4 + - + +
399A PRO 2.5 30.2 + - - -
400A PRO 3.9 2.0 - - - -
402A LEU* 3.9 15.5 - - + -
430A GLN* 3.4 5.4 - - - +
431A LEU* 2.7 47.5 + - + +
433A LEU* 4.2 11.4 - - + -
446A ALA* 3.5 32.3 - - + -
447A ASN* 1.3 77.2 - - - +
449A ILE* 1.3 64.0 + - - +
518A TYR* 3.7 29.2 - - + -
519A ILE 3.3 6.5 - - - -
520A ARG* 3.2 42.1 - - + -
521A GLU* 5.6 0.4 - - - +
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Residues in contact with ILE 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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429A GLU* 3.5 11.0 - - + +
430A GLN* 4.9 12.1 - - + +
448A TYR* 1.3 77.4 - - - +
450A LEU* 1.3 75.1 + - - +
451A HIS* 3.4 0.5 + - - +
470A ASN* 5.2 0.4 - - - +
473A GLY* 4.4 16.8 - - - +
518A TYR* 3.3 3.4 - - - -
519A ILE* 2.8 38.9 + - + +
521A GLU* 3.7 35.4 - - + +
524A LEU* 3.3 33.7 - - + -
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Residues in contact with LEU 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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427A PHE* 3.7 30.3 - - + -
428A PRO 3.9 4.9 - - - +
429A GLU* 2.9 23.7 + - + +
449A ILE* 1.3 81.0 - - - +
451A HIS* 1.3 60.1 + - - +
452A ALA 3.8 14.4 - - - +
453A VAL* 3.9 7.4 - - + -
470A ASN* 2.8 17.0 + - - +
477A TRP* 3.6 29.6 - - + -
494A ILE* 4.0 15.0 - - + -
516A LEU* 4.6 2.2 - - + -
517A VAL 3.6 15.3 - - - +
518A TYR* 3.4 33.9 - - + +
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Residues in contact with HIS 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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231A THR* 5.1 3.4 + - - +
234A PHE* 3.2 26.2 - - + -
235A THR* 4.7 3.0 + - - -
449A ILE* 3.4 0.9 + - + +
450A LEU* 1.3 74.2 - - - +
452A ALA* 1.3 58.4 + - - +
469A LEU* 3.2 26.3 - - + +
470A ASN* 3.1 47.7 + - - +
471A PRO* 3.0 25.2 + - - +
473A GLY* 4.3 2.9 - - - -
477A TRP* 3.5 2.6 - - - -
517A VAL* 2.8 27.1 + - + +
519A ILE* 3.5 33.4 - - + +
528A LEU* 3.5 15.6 - - + +
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Residues in contact with ALA 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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231A THR* 4.6 3.8 - - + +
450A LEU* 3.8 3.4 - - - +
451A HIS* 1.3 84.3 - - - +
453A VAL* 1.3 66.7 + - - +
454A LEU* 4.1 10.8 - - + -
467A VAL* 4.2 1.6 - - + -
468A TYR 3.1 8.3 - - - +
469A LEU* 3.6 23.3 - - + -
477A TRP* 4.2 0.8 - - - -
516A LEU* 3.6 3.1 - - - -
517A VAL* 2.8 50.2 + - + +
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Residues in contact with VAL 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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427A PHE* 3.9 9.9 - - + -
450A LEU* 3.9 24.9 - - + -
452A ALA* 1.3 77.8 - - - +
454A LEU* 1.3 64.4 + - - +
455A VAL* 3.4 18.6 + - + +
467A VAL* 3.5 0.5 - - - -
468A TYR* 2.8 35.8 + - + +
477A TRP* 4.3 9.4 - - + -
493A ALA 3.7 23.8 - - - +
497A ASN* 4.3 0.9 - - + -
513A ALA* 3.7 28.7 - - + -
515A MET 3.8 2.2 - - - -
516A LEU* 3.9 7.2 - - + -
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Residues in contact with LEU 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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227A SER* 4.3 15.7 - - - +
228A LEU* 4.5 2.9 - - + +
231A THR* 3.6 27.1 - - + +
296A VAL* 3.9 33.9 - - + -
452A ALA* 4.1 12.3 - - + -
453A VAL* 1.3 71.7 - - - +
455A VAL* 1.3 60.1 + - - +
465A TYR* 5.2 3.6 - - + -
466A VAL 3.8 5.4 - - - +
467A VAL* 3.6 11.2 - - + -
513A ALA* 3.7 1.7 - - - -
514A TYR* 2.9 27.4 + - - +
515A MET* 2.7 50.4 + - + +
517A VAL* 4.4 10.5 - - + -
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Residues in contact with VAL 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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453A VAL* 3.8 13.5 - - + +
454A LEU* 1.3 75.0 - - - +
456A HIS* 1.3 62.4 - - - +
457A SER* 4.8 0.9 - - - +
464A HIS 3.5 1.7 - - - +
465A TYR* 3.4 9.8 - - - -
466A VAL* 2.9 40.2 + - + +
468A TYR* 3.8 17.0 - - + -
497A ASN* 3.3 44.2 - - + +
511A THR* 3.7 21.3 - - + -
512A ASN 3.3 17.3 - - - +
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Residues in contact with HIS 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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420A LYS* 2.8 45.2 + - + +
454A LEU 4.1 1.2 + - - -
455A VAL* 1.3 74.6 - - - +
457A SER* 1.3 64.6 + - - +
458A GLY 3.1 28.3 - - - -
459A ASP 4.2 7.2 - - - -
463A GLY* 4.0 5.0 - - - -
464A HIS 3.6 2.2 - - - -
465A TYR* 3.7 37.0 - + + -
512A ASN 2.9 23.2 + - - +
514A TYR* 4.2 13.7 - - + +
373D LEU* 3.7 23.3 - - + +
374D ARG 3.1 26.4 + - - -
375D GLY* 4.5 2.0 - - - -
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Residues in contact with SER 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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455A VAL* 5.4 1.1 - - - -
456A HIS* 1.3 75.9 - - - +
458A GLY* 1.3 60.3 + - - +
463A GLY* 2.8 28.1 - - - -
464A HIS* 2.9 27.4 + - - -
507A VAL* 4.4 9.2 + - - +
510A CYS* 3.5 4.8 - - - -
511A THR* 2.6 29.7 + - - -
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Residues in contact with GLY 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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420A LYS* 3.2 16.5 + - - +
456A HIS* 3.1 15.3 - - - -
457A SER* 1.3 74.3 - - - +
459A ASP* 1.3 63.9 + - - -
462A GLY 3.7 6.7 - - - -
510A CYS* 3.0 36.1 + - - +
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Residues in contact with ASP 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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420A LYS* 4.7 10.8 - - + +
422A ASN* 6.2 0.2 - - - +
456A HIS* 4.2 3.4 - - - -
458A GLY* 1.3 77.5 - - - -
460A ASN* 1.3 54.4 + - - +
461A HIS* 2.5 61.2 + - + +
462A GLY 2.6 19.6 + - - +
510A CYS* 5.4 3.3 - - + +
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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