Contacts of the strand formed by residues 505 - 511 (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 VAL 505 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B PRO* 3.5 18.9 + - + +
504B PRO* 1.3 77.9 - - - +
506B TYR* 1.3 68.8 + - - +
543B LYS* 3.3 16.6 - - + +
585B LEU* 3.8 37.7 - - + -
627B MET* 4.3 9.6 - - + +
630B THR* 3.1 28.9 - - + +
631B GLY 3.4 15.0 - - - +
632B GLY* 4.7 0.4 - - - -
633B ARG 2.9 28.9 + - - +
745B PHE* 4.4 5.5 - - - -
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Residues in contact with TYR 506 (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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504B PRO* 4.2 9.6 - - + +
505B VAL* 1.3 78.6 - - - +
507B LEU* 1.3 54.3 + - - +
508B PHE* 3.7 20.9 - + + -
536B LEU* 3.7 30.3 - - + -
537B PRO* 2.6 50.6 + - + +
542B THR* 4.1 20.9 - - + -
543B LYS 2.9 9.8 + - - -
544B ILE* 3.2 10.2 - - + +
545B GLY 2.7 31.9 + - - +
633B ARG* 3.6 41.7 - - + -
743B ILE* 3.9 10.6 - - + +
745B PHE* 4.2 15.0 - + - -
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Residues in contact with LEU 507 (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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505B VAL* 4.1 0.6 - - + -
506B TYR* 1.3 72.3 - - - +
508B PHE* 1.3 69.0 + - - +
509B VAL* 4.2 6.5 - - + -
545B GLY* 3.4 5.2 - - - -
546B PHE* 3.4 32.5 - - - +
547B ILE* 4.2 9.0 - - + -
585B LEU* 4.5 6.3 - - + -
623B ALA* 3.6 40.8 - - + +
626B LEU* 4.1 19.7 - - + -
627B MET* 3.8 29.4 - - + -
633B ARG 2.9 9.1 + - - -
634B MET* 3.4 5.0 - - + +
635B SER 3.0 23.0 + - - +
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Residues in contact with PHE 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B TYR* 3.7 13.9 - + + -
507B LEU* 1.3 75.6 - - - +
509B VAL* 1.3 62.5 + - - +
510B PHE* 3.5 22.6 - + + -
525B VAL* 5.5 0.9 - - + -
529B LEU* 3.7 37.0 - - + -
536B LEU* 5.1 1.8 - - + -
544B ILE* 3.3 28.0 - - + -
545B GLY 3.2 14.6 + - - -
546B PHE* 3.4 9.9 - + + -
547B ILE 3.0 25.5 + - - +
633B ARG* 4.2 16.8 - - - -
635B SER* 3.6 29.2 - - - -
637B PHE* 4.2 12.3 - + - -
735B LEU* 6.1 0.7 - - + -
738B TYR* 4.8 1.3 - + - -
739B LEU* 4.2 15.3 - - + -
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 4.2 9.2 - - + -
508B PHE* 1.3 78.7 - - - +
510B PHE* 1.3 62.4 + - - +
547B ILE* 3.2 17.5 - - + +
549B PHE* 3.4 29.9 - - + -
619B ALA* 5.0 4.3 - - + -
620B LEU* 4.9 6.7 - - + -
623B ALA* 4.0 25.4 - - + -
634B MET* 4.1 11.9 - - + -
635B SER 2.7 16.4 + - - +
636B VAL* 3.5 13.9 - - + -
637B PHE* 2.8 30.1 + - - +
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Residues in contact with PHE 510 (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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508B PHE* 3.5 27.1 - + + -
509B VAL* 1.3 72.3 - - - +
511B ASP* 1.3 62.0 + - - +
512B VAL* 3.6 1.2 + - + -
521B TYR* 3.3 17.0 - + + +
522B LEU* 4.1 23.6 - - + -
525B VAL* 3.8 23.1 - - + -
526B CYS* 4.7 5.6 - - - -
529B LEU* 4.7 6.3 - - + -
546B PHE* 4.1 21.8 - + + -
547B ILE 2.8 13.1 + - - +
548B THR* 3.1 25.4 - - + -
549B PHE* 3.0 32.5 + - - -
599B LEU* 5.4 0.2 - - + -
602B LEU* 4.1 14.1 - - + -
637B PHE* 3.6 33.4 - + + -
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Residues in contact with ASP 511 (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* 1.3 70.9 - - - +
512B VAL* 1.3 59.7 + - - +
513B SER* 3.0 27.7 + - - -
516B ALA* 3.1 16.9 - - - +
521B TYR* 3.1 13.2 + - + -
522B LEU* 5.7 0.3 - - - +
549B PHE* 3.5 25.8 - - + +
614B SER* 3.9 5.2 + - - -
637B PHE 3.1 20.9 + - - +
638B GLN* 2.7 29.1 + - - +
639B THR* 2.8 25.1 + - - -
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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