Contacts of the strand formed by residues 611 - 619 (chain B) in PDB entry 4NPJ
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 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605B ARG* 3.4 17.7 - - - +
606B ASP* 2.8 41.1 + - - +
609B HIS* 4.1 17.7 - - - +
610B GLN* 1.3 79.6 - - - +
612B SER* 1.3 68.4 + - - +
613B LEU* 5.8 1.8 - - - -
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Residues in contact with SER 612 (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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549B PRO* 5.8 0.2 - - - +
603B GLU* 3.6 21.5 + - - +
604B VAL 3.7 4.8 + - - -
605B ARG* 4.0 11.1 - - - +
611B CYS* 1.3 81.8 - - - +
613B LEU* 1.3 63.6 + - - +
614B GLY* 3.5 18.8 + - - -
615B ASN* 4.8 3.5 - - - +
639B ASN* 5.4 8.9 + - - -
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Residues in contact with LEU 613 (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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548B LEU* 3.9 13.6 - - + +
549B PRO* 3.7 46.7 - - + +
558B PRO* 4.2 22.2 - - + -
560B PRO* 4.3 11.7 - - + -
604B VAL* 2.9 28.0 + - + +
605B ARG 3.6 26.2 - - - +
606B ASP* 3.6 19.3 - - + +
611B CYS* 3.7 2.2 + - - -
612B SER* 1.3 76.9 - - - +
614B GLY* 1.3 53.0 + - - +
639B ASN 5.2 0.2 - - - -
640B SER* 2.6 25.8 + - - -
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Residues in contact with GLY 614 (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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603B GLU* 3.6 2.4 - - - +
604B VAL* 3.0 28.9 + - - +
612B SER* 3.5 10.1 + - - -
613B LEU* 1.3 81.4 - - - +
615B ASN* 1.3 64.3 + - - +
637B LEU* 4.1 11.2 - - - -
638B SER 4.0 1.1 - - - -
639B ASN 4.5 4.0 + - - -
640B SER* 3.6 19.3 - - - -
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Residues in contact with ASN 615 (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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601B GLU* 5.5 4.9 + - - +
602B VAL 3.5 9.8 + - - -
603B GLU* 4.4 15.7 - - + +
612B SER* 4.8 3.4 - - - +
614B GLY* 1.3 75.5 - - - +
616B LEU* 1.3 65.9 + - - +
617B LYS* 4.9 9.8 + - - +
637B LEU* 3.8 5.2 - - - +
638B SER* 3.0 43.4 + - - +
639B ASN* 4.3 16.4 - - + +
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Residues in contact with LEU 616 (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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601B GLU* 3.5 2.6 - - - +
602B VAL* 2.7 58.3 + - + +
615B ASN* 1.3 76.3 + - - +
617B LYS* 1.3 77.9 + - - +
618B VAL* 3.6 24.5 - - + -
635B PHE* 3.7 31.0 - - + -
636B GLN 3.6 20.9 - - - +
637B LEU* 4.2 13.2 - - + +
638B SER* 5.4 4.3 - - - +
646B ILE* 4.1 14.1 - - + -
648B MET* 4.7 4.7 - - + -
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Residues in contact with LYS 617 (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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599B ASP* 3.8 25.9 + - + -
600B LEU 3.5 3.6 - - - +
601B GLU* 3.5 34.8 + - - +
615B ASN* 4.5 12.1 + - - +
616B LEU* 1.3 86.2 - - - +
618B VAL* 1.3 66.3 + - - +
619B PRO* 3.9 7.7 - - + +
638B SER* 6.2 0.2 - - - -
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Residues in contact with VAL 618 (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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599B ASP* 4.3 2.6 - - - +
600B LEU* 2.9 53.9 + - + +
602B VAL* 5.2 0.2 - - + -
616B LEU* 3.6 30.3 - - + -
617B LYS* 1.3 80.1 - - - +
619B PRO* 1.3 70.9 - - - +
620B LEU* 3.2 4.8 + - + +
622B GLN* 4.1 15.7 - - + +
623B LEU* 6.0 5.6 - - + -
631B VAL* 6.0 2.9 - - + -
635B PHE* 4.3 23.3 - - + -
650B ILE* 4.7 12.1 - - + -
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Residues in contact with PRO 619 (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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598B GLN 4.0 0.7 - - - +
599B ASP* 3.3 23.5 - - - +
617B LYS* 3.9 7.2 - - + +
618B VAL* 1.3 86.3 - - - +
620B LEU* 1.3 64.0 + - - +
621B SER* 3.1 16.8 + - - +
622B GLN* 3.2 48.0 + - + +
623B LEU* 4.5 1.0 + - - +
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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