Contacts of the strand formed by residues 617 - 624 (chain B) in PDB entry 5MJ6
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 PRO 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B TRP* 3.5 24.7 - - + -
616B PHE* 1.3 95.7 - - + +
618B LEU* 1.3 64.4 + - - +
619B VAL* 4.7 0.2 - - + -
632B GLN* 4.5 4.0 - - + -
633B GLU 3.3 10.3 - - - +
635B PHE* 4.3 0.2 - - - -
652B TRP* 3.5 25.4 - - + -
654B ILE* 3.7 28.3 - - + -
699B TYR 3.9 2.2 - - - +
700B TYR* 3.4 16.6 - - + +
701B ILE 3.3 21.0 + - - -
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Residues in contact with LEU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B PHE 3.8 1.2 + - - -
617B PRO* 1.3 73.7 - - - +
619B VAL* 1.3 60.1 + - - +
620B THR* 3.9 11.9 + - - +
631B GLN 3.6 0.9 - - - +
632B GLN* 3.4 4.7 - - - -
633B GLU* 2.7 61.5 + - + +
634B ARG 5.4 0.7 - - - +
635B PHE* 3.9 25.4 - - + +
701B ILE* 3.6 33.0 - - + +
703B HIS* 3.9 26.9 - - + -
738B LEU* 4.0 8.7 - - + -
743B LYS* 4.6 18.2 - - + +
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Residues in contact with VAL 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B PRO* 4.7 0.9 - - + -
618B LEU* 1.3 76.3 - - - +
620B THR* 1.3 64.4 + - - +
621B VAL* 4.1 19.3 - - + -
630B ILE* 4.7 4.5 - - + -
631B GLN 3.4 8.3 - - - +
632B GLN* 4.8 1.8 - - + -
654B ILE* 3.9 27.8 - - + -
656B LEU* 4.2 20.2 - - + -
674B LEU* 5.2 2.9 - - + -
692B VAL* 4.8 0.2 - - + -
700B TYR* 3.6 32.8 - - + -
701B ILE 2.8 15.2 + - - +
702B VAL* 3.4 7.9 - - + +
703B HIS 2.9 26.3 + - - +
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Residues in contact with THR 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B LEU* 3.9 10.2 + - - +
619B VAL* 1.3 74.7 - - - +
621B VAL* 1.3 69.8 + - - +
622B GLN* 6.0 1.6 - - + -
629B PHE 3.6 0.6 - - - +
630B ILE* 3.1 7.1 - - - +
631B GLN* 2.7 51.9 + - + +
633B GLU* 4.1 16.1 + - - -
703B HIS* 3.5 25.0 - - + +
705B ALA 5.7 1.8 - - - +
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Residues in contact with VAL 621 (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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619B VAL* 4.1 12.6 - - + -
620B THR* 1.3 79.0 - - - +
622B GLN* 1.3 64.7 + - - +
623B LYS 4.9 0.4 - - - +
628B LEU* 3.6 23.8 - - + -
629B PHE 3.4 2.9 - - - -
630B ILE* 3.5 23.8 - - + -
690B VAL* 5.6 1.8 - - + -
692B VAL* 3.6 23.3 - - + -
702B VAL* 4.3 5.8 - - + -
703B HIS 2.9 13.3 + - - +
704B TYR* 3.5 25.9 - - + -
705B ALA 3.1 25.8 + - - -
708B ASP* 3.9 3.7 - - + +
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Residues in contact with GLN 622 (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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620B THR* 6.0 2.2 - - + -
621B VAL* 1.3 77.3 - - - +
623B LYS* 1.3 74.6 + - - +
624B LYS* 3.3 32.1 + - - +
628B LEU* 4.1 2.7 - - - -
629B PHE* 2.8 45.4 + - + +
705B ALA* 3.9 21.9 - - + +
708B ASP* 3.4 3.1 - - - +
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Residues in contact with LYS 623 (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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622B GLN* 1.3 78.4 + - - +
624B LYS* 1.3 66.8 + - - +
625B GLY* 3.2 32.7 + - - +
627B GLU 3.7 6.1 - - - +
628B LEU* 4.1 9.7 - - + +
683B LEU* 4.7 6.3 - - + -
686B GLU* 3.7 12.9 + - - -
687B VAL* 3.5 39.1 + - + +
688B LEU 5.4 3.6 - - - -
689B TRP* 5.5 3.8 - - - -
690B VAL* 4.3 9.4 - - + -
707B ASP* 6.0 1.2 - - - +
708B ASP* 2.7 35.8 + - - +
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Residues in contact with LYS 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B GLN* 3.3 35.7 + - + +
623B LYS* 1.3 77.0 - - - +
625B GLY* 1.3 60.1 + - - +
626B LYS 3.1 0.7 + - - -
627B GLU* 2.7 32.1 + - - +
629B PHE* 3.9 39.2 - - + +
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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