Contacts of the strand formed by residues 566 - 570 (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 GLN 566 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 5.8 1.2 + - - +
184A SER* 3.6 11.4 - - - +
248A GLN* 5.3 0.7 + - - +
556B TYR* 3.3 6.5 - - - -
557B GLY* 2.8 45.2 + - - +
559B GLN* 3.5 12.1 + - - +
562B LEU* 2.9 27.7 - - + +
564B GLN 4.8 1.1 - - - +
565B PRO* 1.3 75.6 - - - +
567B MET* 1.3 60.8 + - - +
568B LEU* 3.3 26.3 + - + +
580B MET* 3.3 31.9 - - - +
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Residues in contact with MET 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ILE* 3.8 21.9 - - + +
184A SER 3.6 6.7 + - - -
185A LYS* 3.3 38.0 - - + +
186A SER 3.3 26.2 + - - +
554B HIS* 3.6 33.2 - - + +
555B PHE 3.2 8.5 - - - +
556B TYR* 3.8 28.3 - - + +
566B GLN* 1.3 67.9 - - - +
568B LEU* 1.3 59.3 + - - +
569B ILE* 3.5 26.7 + - + +
605B MET* 5.0 2.9 - - - +
606B PHE* 4.1 16.4 - - + -
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Residues in contact with LEU 568 (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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174A GLN* 4.4 10.5 - - - +
185A LYS* 6.1 0.2 - - - -
186A SER* 3.8 20.2 - - - +
188A VAL* 3.8 15.0 - - + -
555B PHE* 2.8 45.6 + - + +
557B GLY 4.8 0.9 - - - +
566B GLN* 3.7 45.5 - - + +
567B MET* 1.3 74.8 - - - +
569B ILE* 1.3 60.6 + - - +
579B PRO* 4.0 29.3 - - + +
580B MET* 4.0 21.3 - - + -
584B LEU* 4.7 4.0 - - + -
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Residues in contact with ILE 569 (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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185A LYS* 4.0 15.3 - - + +
186A SER 3.0 15.3 + - - +
187A TYR* 3.4 54.3 - - + +
188A VAL* 2.6 32.4 + - - +
552B THR* 3.5 24.2 - - - +
553B ILE 3.3 4.5 - - - +
554B HIS* 4.1 10.5 - - + +
567B MET* 3.6 36.1 - - + +
568B LEU* 1.3 72.3 - - - +
570B VAL* 1.3 64.3 + - - +
571B SER 3.9 1.3 + - - +
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 4.0 7.2 - - + -
552B THR* 3.8 0.5 - - - -
553B ILE* 3.0 44.7 + - + +
555B PHE* 3.3 36.1 - - + -
569B ILE* 1.3 73.7 - - - +
571B SER* 1.3 60.8 + - - +
572B ASP 3.9 21.1 - - - +
576B VAL* 4.4 19.5 - - + -
577B PHE* 4.2 30.7 - - + +
579B PRO* 5.3 1.6 - - + -
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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