Contacts of the strand formed by residues 543 - 549 (chain B) in PDB entry 2NUP
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 LYS 543 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B PRO* 5.4 5.4 - - + -
504B PRO 2.8 9.9 + - - +
505B VAL* 3.3 22.7 - - + -
506B TYR* 2.9 24.1 + - - +
541B ARG 3.8 9.2 - - - +
542B THR* 1.3 83.9 - - - +
544B ILE* 1.3 60.7 + - - +
582B GLU 5.5 2.4 + - - -
585B LEU* 3.9 34.0 + - + +
586B VAL 3.1 10.5 - - - +
587B ASN* 4.5 13.5 - - - +
630B THR* 5.7 6.5 - - + -
21C GLN* 5.7 2.2 + - - -
120C GLN* 4.8 12.3 + - - +
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Residues in contact with ILE 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B TYR* 3.2 14.8 - - + +
508B PHE* 3.3 35.9 - - + -
529B LEU* 5.1 3.4 - - + -
533B LEU* 5.3 2.5 - - + -
536B LEU* 4.4 13.9 - - + -
542B THR* 5.3 1.3 - - + -
543B LYS* 1.3 75.0 - - - +
545B GLY* 1.3 61.2 + - - +
546B PHE* 3.6 22.6 - - + -
558B LEU* 5.9 0.5 - - - +
584B LEU 3.8 0.5 - - - +
585B LEU* 3.5 4.8 - - - -
586B VAL* 2.7 56.5 + - + +
588B LEU* 3.7 32.8 - - + -
595B VAL* 4.0 10.8 - - + -
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Residues in contact with GLY 545 (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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506B TYR 2.7 13.2 + - - -
507B LEU* 3.4 8.5 - - - -
508B PHE* 3.2 14.6 + - - -
544B ILE* 1.3 75.8 - - - +
546B PHE* 1.3 83.8 + - - -
584B LEU 3.8 7.6 - - - -
585B LEU* 3.6 17.2 - - - +
626B LEU* 5.9 0.2 - - - -
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Residues in contact with PHE 546 (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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507B LEU* 3.4 3.4 - - - +
508B PHE* 3.4 19.5 - + + -
510B PHE* 4.1 13.7 - + + -
529B LEU* 3.9 16.6 - - + -
533B LEU* 6.0 0.7 - - + -
544B ILE* 3.6 29.4 - - + -
545B GLY* 1.3 91.8 - - - -
547B ILE* 1.3 71.7 + - - +
548B THR* 6.2 0.2 - - + -
555B PHE* 4.3 0.3 - - - -
556B TYR* 3.8 34.6 + - + +
558B LEU* 4.7 6.1 - - + -
584B LEU* 4.6 4.0 + - - +
595B VAL* 4.2 23.6 - - + -
598B LEU* 4.0 23.6 - - + -
599B LEU* 3.6 35.9 - - + -
602B LEU* 4.8 6.7 - - + -
626B LEU* 5.5 1.5 - - - +
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Residues in contact with ILE 547 (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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507B LEU* 4.2 8.1 - - + -
508B PHE 3.0 10.1 + - - +
509B VAL* 3.2 18.9 - - + +
510B PHE* 2.8 26.3 + - - +
546B PHE* 1.3 84.8 - - - +
548B THR* 1.3 76.7 + - - +
549B PHE* 4.7 2.9 - - + -
553B ILE* 4.1 15.0 - - + -
554B HIS 3.3 8.3 - - - +
555B PHE* 3.5 38.6 - - + -
556B TYR* 4.3 0.4 - - - -
619B ALA* 5.3 5.4 - - + +
622B ALA* 5.0 0.4 - - + -
623B ALA* 4.1 24.0 - - + +
626B LEU* 3.8 15.9 - - + -
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Residues in contact with THR 548 (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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510B PHE* 3.1 20.9 - - + +
512B VAL* 3.8 24.0 - - + -
522B LEU* 5.8 0.2 - - + -
547B ILE* 1.3 82.5 - - - +
549B PHE* 1.3 65.7 + - - +
554B HIS* 2.8 52.4 + - - +
556B TYR* 2.9 31.5 + - + +
602B LEU* 3.6 20.0 - - + -
606B PHE* 3.9 0.8 - - + -
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Residues in contact with PHE 549 (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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509B VAL* 3.4 29.6 - - + -
510B PHE 3.0 40.5 + - - -
511B ASP* 3.5 13.6 - - + +
512B VAL* 2.8 34.1 + - - +
547B ILE* 4.7 1.8 - - + -
548B THR* 1.3 80.7 - - - +
550B ASP* 1.3 65.4 + - - +
552B THR 3.3 14.8 - - - +
553B ILE* 4.2 4.5 - - - -
554B HIS* 3.8 3.6 - - - -
614B SER* 3.5 23.8 - - - -
615B ALA 4.4 1.1 - - - -
616B LEU* 3.7 29.6 - - + -
619B ALA* 3.5 23.1 - - + -
636B VAL* 5.2 0.9 - - + -
637B PHE 4.6 1.8 - - - -
638B GLN* 3.4 18.6 - - - -
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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