Contacts of the strand formed by residues 612 - 619 (chain B) in PDB entry 1J1B
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 LEU 612 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B GLY* 3.5 26.6 - - - -
546B GLN* 4.3 3.6 + - - +
598B LEU* 3.8 25.1 - - + -
601B MET* 3.6 32.4 + - + +
602B ARG* 3.9 18.8 - - + +
610B VAL 3.8 2.8 + - - -
611B ARG* 1.3 80.5 - - - +
613B ARG* 1.3 63.3 + - - +
614B TYR 3.5 22.0 - - - +
615B PHE* 4.4 2.9 - - + -
630B LEU* 3.7 31.4 - - + -
631B VAL 3.7 5.2 - - - +
632B LEU* 3.8 7.4 - - + -
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Residues in contact with ARG 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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544B PRO* 3.7 1.7 - - - +
545B GLY 2.7 22.6 + - - -
546B GLN 4.6 0.3 + - - -
552B GLN* 5.0 0.2 + - - -
575B LEU* 3.0 33.5 - - - +
580B GLU* 2.6 39.8 + - - +
581B LEU 4.5 3.6 + - - -
582B VAL* 3.4 23.6 - - - +
611B ARG* 3.5 23.2 + - - +
612B LEU* 1.3 72.8 - - - +
614B TYR* 1.3 87.6 + - + +
631B VAL* 2.7 18.7 + - - +
632B LEU 4.8 0.2 - - - -
633B ASP* 2.8 36.6 + - - +
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Residues in contact with TYR 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ALA* 3.7 15.9 - - + -
543B THR 2.9 24.2 - - - +
545B GLY* 3.5 5.2 - - - +
552B GLN* 3.4 37.5 - - + -
554B VAL* 3.7 33.3 - - + +
575B LEU* 3.9 20.1 - - + +
612B LEU* 3.5 7.2 - - - +
613B ARG* 1.3 101.1 + - + +
615B PHE* 1.3 64.1 + - - +
616B PHE* 5.6 0.2 - + - -
631B VAL* 2.8 64.7 + - + +
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Residues in contact with PHE 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ALA* 3.5 0.7 - - - +
543B THR* 3.0 65.8 + - + -
544B PRO 3.9 5.2 - - - -
545B GLY* 4.8 0.2 - - - -
598B LEU* 3.8 32.3 - - + -
602B ARG* 3.7 38.6 - - + -
612B LEU* 4.4 6.3 - - + -
614B TYR* 1.3 79.6 - - - +
616B PHE* 1.3 67.5 + - - +
617B TYR* 4.3 16.8 - + - -
628B LEU* 4.0 8.7 - - + -
629B ASN 3.0 13.9 - - - +
630B LEU* 4.0 16.8 - - + -
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Residues in contact with PHE 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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525B SER 6.0 0.2 - - - -
526B MET* 4.7 4.5 - - + -
540B VAL* 3.9 37.5 - - + -
541B VAL 3.8 21.1 - - - +
542B ALA* 4.0 6.7 - - + +
556B TYR* 3.8 26.2 - + - -
584B ILE* 4.6 6.5 - - + -
615B PHE* 1.3 79.5 - - - +
617B TYR* 1.3 78.2 + - - +
618B SER* 4.4 8.3 - - - -
628B LEU* 3.7 0.6 - - - -
629B ASN* 2.7 73.7 + - + +
631B VAL* 3.7 24.9 - - + -
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Residues in contact with TYR 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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523B PHE 3.8 26.0 - - - +
524B GLY* 3.7 25.1 - - - +
525B SER* 4.0 4.3 + - - +
589B GLN* 3.9 25.8 + - + +
595B ASN* 5.7 0.9 - - - +
598B LEU* 4.0 13.2 - - - +
615B PHE* 4.3 19.8 - + - -
616B PHE* 1.3 87.3 - - - +
618B SER* 1.3 61.2 + - - +
626B VAL* 4.1 14.8 - - + -
627B TYR 3.1 15.0 - - - +
628B LEU* 3.8 26.3 - - + +
629B ASN* 4.0 0.2 - - - -
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Residues in contact with SER 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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524B GLY 4.4 4.0 - - - -
525B SER* 5.3 0.4 - - - +
526B MET* 4.3 27.4 - - - -
586B LYS* 3.4 25.0 + - - -
616B PHE* 4.4 4.5 - - - -
617B TYR* 1.3 75.1 - - - +
619B SER* 1.3 63.6 + - - +
620B GLY 3.3 0.7 + - - -
626B VAL* 3.9 3.8 - - - -
627B TYR* 2.9 31.1 + - - +
629B ASN* 3.0 19.8 + - - +
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Residues in contact with SER 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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524B GLY 3.4 17.9 + - - +
525B SER* 4.7 5.9 - - - +
586B LYS* 5.8 0.8 + - - -
618B SER* 1.3 71.9 - - - +
620B GLY* 1.3 61.7 + - - +
621B GLU* 3.0 28.2 + - - +
623B LYS 5.7 2.0 - - - -
625B GLU 4.0 5.4 - - - -
626B VAL* 4.9 4.9 - - - +
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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