Contacts of the strand formed by residues 619 - 624 (chain B) in PDB entry 1JVA
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 LYS 619 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A HIS* 4.5 27.0 - - + +
619A LYS* 5.5 6.5 - - - +
611B TYR 3.9 0.2 - - - +
612B VAL* 3.4 6.0 - - - +
613B THR* 3.0 49.5 + - - +
617B GLY 4.1 5.2 - - - +
618B ILE* 1.3 77.8 - - - +
620B ALA* 1.3 72.3 + - - +
621B THR* 4.5 3.4 - - - +
667B TYR* 4.0 35.5 - - + -
668B MET 3.2 15.3 - - - +
669B SER* 4.6 2.7 - - - -
674B LEU* 3.7 4.5 - - - -
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Residues in contact with ALA 620 (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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606B ILE* 4.0 28.3 - - + -
611B TYR 3.4 6.3 - - - +
612B VAL* 4.5 10.3 - - + -
619B LYS* 1.3 75.8 - - - +
621B THR* 1.3 61.5 + - - +
666B ILE 3.6 1.4 - - - +
667B TYR* 3.6 1.9 - - - -
668B MET* 2.8 45.9 + - + +
674B LEU* 3.9 15.9 - - + +
678B LEU* 4.6 1.1 - - + -
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Residues in contact with THR 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B ILE* 6.1 0.2 - - - -
610B GLY* 3.0 5.2 - - - -
611B TYR* 2.8 82.9 + - + +
613B THR* 5.3 1.7 + - - -
619B LYS* 4.5 6.1 - - - +
620B ALA* 1.3 73.5 - - - +
622B ILE* 1.3 64.4 + - - +
623B LYS* 4.1 15.4 + - + -
665B ALA* 4.5 2.7 - - + -
666B ILE 3.4 7.0 - - - +
667B TYR* 3.2 34.4 - - + +
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Residues in contact with ILE 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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602B LEU* 4.7 3.1 - - + +
605B LEU* 3.6 51.4 - - + -
606B ILE* 4.0 19.1 - - + -
609B ASP 3.7 8.3 - - - +
610B GLY* 4.7 3.4 - - - -
621B THR* 1.3 76.8 - - - +
623B LYS* 1.3 72.1 + - - +
624B THR* 5.4 3.4 - - - -
629B VAL* 5.9 0.7 - - + -
633B LEU* 3.6 32.5 - - + -
664B TYR 3.7 1.2 - - - +
665B ALA* 3.6 2.1 - - - -
666B ILE* 2.9 35.4 + - - +
668B MET* 3.7 23.8 - - + -
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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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500B GLY 5.4 0.5 - - - +
605B LEU* 5.7 0.7 - - - +
609B ASP* 3.3 39.4 + - - +
611B TYR* 4.4 23.6 + - + +
621B THR* 4.1 9.9 - - + -
622B ILE* 1.3 82.3 - - - +
624B THR* 1.3 62.8 + - - +
649B GLU* 3.6 25.9 + - - +
663B SER* 3.2 25.6 + - - +
664B TYR 3.5 1.3 - - - -
665B ALA* 3.7 22.2 - - + -
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Residues in contact with THR 624 (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 ILE* 5.4 2.7 - - - -
623B LYS* 1.3 76.2 - - - +
625B ILE* 1.3 61.2 + - - +
626B HIS* 3.1 27.6 + - - +
629B VAL* 3.4 26.4 - - + +
630B ARG 4.0 9.9 - - - +
633B LEU* 5.6 0.7 - - + -
663B SER* 3.7 1.9 + - - -
664B TYR* 2.7 53.7 + - + +
666B ILE* 3.8 19.1 - - + -
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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