Contacts of the strand formed by residues 478 - 481 (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 CYS 478 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B THR* 5.1 6.1 - - - -
213B TYR* 4.2 24.2 - - + -
468B TYR* 3.4 5.4 - - - +
469B LEU 2.9 29.0 + - - +
471B PRO* 5.9 0.4 - - - -
476B LYS 5.4 1.8 - - - -
477B TRP* 1.3 80.7 - - - +
479B LYS* 1.3 60.7 + - - +
480B PHE* 3.7 21.7 - - + -
485B VAL* 4.2 8.3 - - + -
486B SER* 3.0 17.3 - - - +
487B ARG* 4.0 17.9 - - - -
488B CYS* 3.7 5.6 - - - -
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Residues in contact with LYS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B VAL* 4.4 14.5 - - + +
467B VAL 3.9 1.3 - - - +
468B TYR* 3.5 46.3 + - + +
478B CYS* 1.3 73.7 - - - +
480B PHE* 1.3 63.1 + - - +
481B ASP* 4.2 29.6 + - + +
484B VAL 3.6 1.4 - - - +
485B VAL* 3.3 6.2 - - - +
486B SER* 2.6 46.1 + - - +
488B CYS* 3.8 4.6 - - + -
492B GLU* 3.9 9.9 + - - +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.8 26.9 - + + -
214B VAL 4.5 1.1 - - - -
215B GLY* 5.3 0.2 - - - -
227B SER* 4.8 1.4 + - - -
230B GLN* 3.6 28.3 - - + -
234B PHE* 3.5 31.0 - + - -
466B VAL* 3.7 3.0 - - - -
467B VAL* 2.8 47.1 + - + +
469B LEU* 3.6 31.0 - - + -
471B PRO* 4.6 2.5 - - + -
478B CYS* 3.7 28.7 - - + -
479B LYS* 1.3 72.9 - - - +
481B ASP* 1.3 60.7 + - - +
482B ASP 3.7 5.4 + - - +
484B VAL 3.9 2.9 - - - -
485B VAL* 3.7 28.3 - - + -
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Residues in contact with ASP 481 (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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464B HIS* 2.7 30.9 + - - -
466B VAL* 3.3 23.9 - - + +
479B LYS* 3.8 21.8 + - + -
480B PHE* 1.3 71.1 - - - +
482B ASP* 1.3 72.3 + - - +
483B ASP* 3.1 0.5 + - - +
484B VAL* 2.9 32.9 + - + +
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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
------------------------------------------------------------
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