Contacts of the strand formed by residues 511 - 520 (chain E) 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 THR 511 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455E VAL* 2.8 19.0 - - + +
456E HIS 3.8 5.9 + - - -
457E SER* 3.7 17.9 + - - -
466E VAL* 4.6 12.1 - - - +
468E TYR* 4.4 16.4 - - + +
492E GLU 5.3 0.7 - - - +
496E HIS* 3.2 21.4 - - + +
497E ASN* 2.9 20.7 - - - +
499E GLY 5.2 0.9 - - - +
510E CYS* 1.3 81.6 - - - +
512E ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E ARG* 3.6 33.7 + - - +
420E LYS* 2.9 19.2 + - - +
422E ASN* 2.9 25.9 - - - +
455E VAL* 3.0 7.7 - - - +
456E HIS* 2.6 52.3 + - - +
497E ASN* 3.9 10.3 - - - +
498E TYR 4.3 3.4 - - - +
499E GLY 4.8 7.6 - - - +
500E GLY* 5.9 0.2 - - - -
510E CYS* 4.3 4.5 - - - +
511E THR* 1.3 76.0 - - - +
513E ALA* 1.3 62.8 + - - +
514E TYR* 4.5 0.8 - - - +
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Residues in contact with ALA 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E LEU* 3.9 11.0 - - + +
408E ARG* 3.2 27.3 + - - +
427E PHE* 4.0 12.1 - - + -
453E VAL* 3.5 28.3 - - + -
454E LEU 3.4 7.2 - - - +
455E VAL* 4.2 1.3 - - - +
497E ASN* 3.3 17.6 + - + +
512E ASN* 1.3 76.0 + - - +
514E TYR* 1.3 60.3 + - - +
515E MET 4.5 0.2 - - - +
516E LEU* 4.0 10.5 - - + -
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Residues in contact with TYR 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E TYR* 3.0 27.4 - + + +
227E SER* 4.1 3.5 - - - -
296E VAL* 3.5 35.8 - - + +
405E GLN* 3.7 5.0 - - - +
406E LEU* 3.1 35.8 + - - +
408E ARG* 4.4 4.3 - - + -
409E PHE* 4.2 27.1 - + + -
420E LYS* 6.2 0.7 - - - -
454E LEU* 2.9 55.9 + - + +
455E VAL 3.6 13.0 - - - -
456E HIS* 3.8 17.5 - - + -
465E TYR* 3.6 18.3 - + - -
466E VAL 5.0 0.2 - - - -
512E ASN* 5.0 1.6 - - - +
513E ALA* 1.3 73.6 - - - +
515E MET* 1.3 63.4 + - + +
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Residues in contact with MET 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E LEU* 4.7 11.7 - - + -
296E VAL* 4.2 23.1 - - + -
300E CYS* 5.6 3.1 - - + -
403E HIS* 3.5 46.4 - - + +
404E LEU 3.3 13.0 - - - +
405E GLN* 3.8 21.1 - - + +
406E LEU* 4.4 2.1 - - - +
453E VAL* 3.5 3.3 - - - +
454E LEU* 2.8 63.8 + - + +
513E ALA 3.7 0.8 - - - -
514E TYR* 1.3 87.3 - - + +
516E LEU* 1.3 70.8 + - - +
517E VAL* 4.2 7.0 - - + -
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Residues in contact with LEU 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E ILE* 4.3 13.5 - - + -
402E LEU 4.0 0.3 - - - +
403E HIS* 3.7 0.5 - - - -
404E LEU* 2.7 43.4 + - + +
406E LEU* 4.1 21.1 - - + -
427E PHE* 3.7 44.9 - - + -
450E LEU* 4.2 2.9 - - + -
452E ALA 3.3 2.7 - - - +
453E VAL* 4.0 26.2 - - + -
513E ALA* 4.0 8.7 - - + -
515E MET* 1.3 81.7 - - - +
517E VAL* 1.3 65.8 + - - +
518E TYR* 3.9 26.6 + - + -
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Residues in contact with VAL 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E THR* 3.7 16.4 - - + -
235E THR* 5.6 2.5 - - - +
401E VAL* 4.1 14.8 - - + -
402E LEU 3.4 11.7 - - - +
403E HIS* 3.7 26.2 - - + +
450E LEU* 4.6 1.2 - - - +
451E HIS* 2.7 48.1 + - + +
452E ALA* 2.8 37.6 + - + +
454E LEU* 4.1 10.3 - - + -
515E MET* 4.2 4.0 - - + -
516E LEU* 1.3 77.6 - - - +
518E TYR* 1.3 54.4 + - - +
519E ILE* 4.8 0.7 - - + -
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Residues in contact with TYR 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E ILE* 5.5 0.9 - - + -
401E VAL* 3.4 1.9 - - - +
402E LEU* 2.6 43.3 + - + +
404E LEU* 3.5 32.3 - - + -
427E PHE* 3.8 9.2 - - - +
428E PRO* 2.6 38.1 + - - +
429E GLU 3.8 4.3 - - - -
431E LEU* 4.1 27.4 - - + -
448E TYR* 3.5 24.0 - - + -
449E ILE* 3.3 10.5 - - - -
450E LEU* 3.1 48.4 - - + +
516E LEU* 3.9 18.3 - - + +
517E VAL* 1.3 75.5 - - - +
519E ILE* 1.3 59.5 + - - +
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Residues in contact with ILE 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E THR* 5.9 1.8 - - - +
400E PRO 3.3 13.0 - - - +
401E VAL* 3.8 23.8 - - + -
448E TYR* 3.8 3.6 - - - -
449E ILE* 2.8 31.5 + - - +
451E HIS* 3.7 36.8 - - + +
517E VAL* 4.8 0.9 - - + +
518E TYR* 1.3 79.5 - - - +
520E ARG* 1.3 75.2 + - - +
523E LYS 4.5 0.2 - - - -
524E LEU* 3.7 17.5 - - + +
527E VAL* 3.8 26.2 - - + -
528E LEU* 4.0 22.2 - - + -
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Residues in contact with ARG 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E THR* 5.2 2.4 + - - +
398E LEU* 3.7 29.4 + - - +
399E PRO 4.1 2.5 - - - +
400E PRO* 2.8 14.8 + - - +
437E LEU* 4.6 8.5 - - - +
444E ASP* 2.4 63.2 + - - -
445E PRO 4.1 11.0 + - - -
446E ALA* 4.1 14.0 - - - +
447E ASN 4.0 4.7 - - - +
448E TYR* 3.4 37.0 + - + +
519E ILE* 1.3 73.6 - - - +
521E GLU* 1.3 61.8 + - - +
522E SER* 3.8 3.8 - - - +
523E LYS* 3.4 31.5 - - + +
524E LEU* 2.8 29.6 + - - +
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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