Contacts of the strand formed by residues 462 - 469 (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 GLY 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLN* 3.0 17.0 - - - -
458B GLY* 3.5 1.9 - - - -
459B ASP* 3.0 32.4 + - - +
460B ASN 3.5 0.6 - - - -
461B HIS* 1.3 80.6 - - - +
463B GLY* 1.3 59.5 + - - -
374C ARG 3.3 14.3 - - - +
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Residues in contact with GLY 463 (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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293B GLN* 2.7 13.9 + - - +
457B SER 2.8 12.8 - - - -
458B GLY* 4.2 2.0 - - - -
462B GLY* 1.3 75.2 - - - -
464B HIS* 1.3 61.7 + - - +
374C ARG 3.6 2.9 + - - -
375C GLY* 3.8 5.2 - - - -
376C GLZ 3.1 18.9 + - - -
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Residues in contact with HIS 464 (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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223B CYS* 3.7 23.3 - - + -
455B VAL 3.8 0.9 - - - +
456B HIS* 3.6 3.2 + - - -
457B SER* 2.7 51.2 + - - -
463B GLY* 1.3 74.1 + - - +
465B TYR* 1.3 67.7 + - - +
466B VAL* 3.6 21.7 - - + +
481B ASP* 2.7 31.9 + - - -
482B ASP* 3.5 19.3 - - - -
375C GLY* 4.3 0.4 - - - -
376C GLZ 4.0 4.7 - - - -
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Residues in contact with TYR 465 (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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223B CYS* 3.3 25.8 - - - +
224B TYR* 3.5 21.3 - - + -
227B SER* 3.4 15.7 + - - +
294B HIS 3.2 21.1 - - - -
296B VAL* 3.4 37.3 + - + -
454B LEU* 5.2 2.9 - - + -
455B VAL 3.5 15.9 - - - -
456B HIS* 3.7 22.7 - + + -
464B HIS* 1.3 81.7 + - - +
466B VAL* 1.3 72.7 + - - +
481B ASP* 4.3 1.7 - - - +
482B ASP* 4.8 1.9 + - - +
514B TYR* 3.5 20.9 - + + -
373C LEU* 2.4 27.9 + - - +
375C GLY* 3.6 19.3 - - - -
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Residues in contact with VAL 466 (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* 3.4 10.5 + - - -
454B LEU* 3.7 2.3 - - - +
455B VAL* 3.0 47.2 + - + +
464B HIS* 3.6 11.9 - - + +
465B TYR* 1.3 80.4 - - - +
467B VAL* 1.3 64.5 + - - +
468B TYR* 4.1 16.8 - - + +
479B LYS* 4.4 13.2 - - + +
480B PHE 3.7 9.9 - - - +
481B ASP* 3.3 36.3 - - + +
482B ASP 5.7 0.2 - - - +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B SER* 3.6 32.3 - - - +
230B GLN* 4.1 3.6 - - + -
231B THR* 3.7 18.6 - - - +
452B ALA* 4.2 0.7 - - + -
453B VAL 3.4 9.2 - - - +
454B LEU* 4.0 13.2 - - + -
466B VAL* 1.3 78.6 - - - +
468B TYR* 1.3 78.3 + - - +
469B LEU* 3.8 18.4 - - + -
480B PHE* 2.8 53.1 + - + +
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Residues in contact with TYR 468 (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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452B ALA* 3.1 5.4 - - - +
453B VAL* 2.8 35.2 + - + +
455B VAL* 3.9 18.6 - - + -
466B VAL* 4.1 13.4 - - + +
467B VAL* 1.3 77.0 - - - +
469B LEU* 1.3 62.5 + - - +
477B TRP* 3.5 5.2 - - + -
478B CYS 3.4 4.3 - - - +
479B LYS* 3.5 37.0 + - + -
488B CYS* 3.5 24.2 - - - -
492B GLU* 3.1 42.6 + - - +
493B ALA* 3.6 23.8 - - + -
496B HIS* 4.7 5.5 - - - -
497B ASN* 3.6 24.1 + - - -
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Residues in contact with LEU 469 (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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230B GLN* 4.0 9.6 - - + +
231B THR* 4.3 9.9 - - + -
234B PHE* 3.9 25.6 - - + -
451B HIS* 3.4 30.1 - - + +
452B ALA* 3.5 23.3 - - + -
467B VAL* 3.8 22.0 - - + -
468B TYR* 1.3 77.5 - - - +
470B ASN* 1.3 57.4 + - - +
471B PRO* 3.3 11.7 - - + +
477B TRP* 3.2 8.4 - - - -
478B CYS* 2.9 32.7 + - - +
480B PHE* 3.6 32.3 - - + -
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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