Contacts of the strand formed by residues 625 - 633 (chain B) in PDB entry 3UOA
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 ILE 625 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596B CYS* 3.7 47.3 - - + +
598B VAL* 4.0 3.8 - - + -
621B LYS* 3.0 40.4 + - + -
622B PRO* 3.1 22.8 + - + +
623B PRO 3.0 5.7 - - - +
624B GLU* 1.3 78.0 - - - +
626B ILE* 1.3 59.5 + - - +
627B MET 3.5 23.8 - - - +
628B CYS* 4.3 2.2 - - + -
690B TYR* 3.8 18.6 - - + -
691B GLN 3.4 9.4 - - - +
692B TYR* 3.7 22.9 - - + -
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Residues in contact with ILE 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LYS* 3.4 15.1 + - - +
623B PRO 5.1 0.7 - - - -
624B GLU 3.8 0.8 + - - -
625B ILE* 1.3 73.1 - - - +
627B MET* 1.3 66.5 + - + +
691B GLN* 3.0 53.0 + - + +
692B TYR 4.1 6.1 - - - +
693B SER* 3.4 31.0 - - - +
694B GLY 5.3 0.4 - - - +
695B LEU 5.0 0.2 - - - +
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Residues in contact with MET 627 (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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621B LYS* 4.5 4.7 - - - +
625B ILE* 3.4 5.1 - - - +
626B ILE* 1.3 88.3 - - + +
628B CYS* 1.3 72.3 + - - +
629B ASP* 4.9 11.4 - - - +
690B TYR* 3.3 19.2 - - - -
691B GLN* 3.5 7.2 + - + +
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Residues in contact with CYS 628 (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 VAL* 3.9 21.1 - - + -
618B ILE* 3.8 37.6 - - - +
621B LYS* 4.0 17.8 - - - +
625B ILE* 4.3 2.7 - - + -
627B MET* 1.3 80.9 - - - +
629B ASP* 1.3 73.4 + - - +
688B LEU* 4.1 6.7 - - + -
689B SER 3.0 13.0 - - - +
690B TYR* 3.7 11.2 - - + -
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Residues in contact with ASP 629 (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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618B ILE* 4.9 1.3 - - - -
627B MET* 4.9 12.9 - - - +
628B CYS* 1.3 82.8 - - - +
630B ALA* 1.3 62.1 + - - +
631B TYR* 4.3 9.3 - - + -
668B LEU* 6.5 0.7 - - + -
687B CYS 3.8 0.3 - - - +
688B LEU* 3.3 5.6 - - - -
689B SER* 2.8 42.9 + - - +
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Residues in contact with ALA 630 (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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600B ILE* 3.2 46.4 - - + -
616B THR* 4.1 9.4 + - - +
617B SER* 5.9 0.9 - - - -
618B ILE* 4.0 12.4 - - + +
629B ASP* 1.3 76.0 - - - +
631B TYR* 1.3 64.7 + - - +
668B LEU* 3.4 20.4 - - - +
686B VAL* 4.6 2.5 - - + -
687B CYS 3.1 6.3 - - - +
688B LEU* 4.0 0.7 - - + -
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Residues in contact with TYR 631 (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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616B THR* 4.9 3.1 - - - -
629B ASP* 4.3 10.5 - - + -
630B ALA* 1.3 81.2 - - - +
632B VAL* 1.3 66.2 + - - +
633B THR* 3.4 29.8 - - + -
647B ASN* 3.3 25.1 - - + +
668B LEU* 4.5 3.6 - - + -
686B VAL* 3.6 4.2 - - - +
687B CYS* 2.8 59.1 + - + +
689B SER* 4.2 20.8 + - - -
700B GLU* 4.9 7.3 + - - -
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Residues in contact with VAL 632 (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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614B ILE* 4.8 7.6 - - + -
616B THR* 4.0 24.5 - - + -
631B TYR* 1.3 75.8 - - - +
633B THR* 1.3 67.2 + - - +
635B PHE* 3.4 29.5 - - + -
646B ALA* 4.9 2.0 - - + +
647B ASN* 2.9 28.9 + - - +
670B THR* 3.4 28.5 - - + +
684B PHE* 4.1 12.1 - - + -
685B THR 3.3 5.8 - - - +
686B VAL* 4.1 18.6 - - + -
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Residues in contact with THR 633 (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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631B TYR* 3.4 32.5 - - + -
632B VAL* 1.3 82.4 - - - +
634B ASP* 1.3 78.7 + - - +
635B PHE* 3.4 10.6 + - - -
643B PRO* 6.6 0.4 - - + -
647B ASN* 5.0 1.1 - - - +
684B PHE* 3.6 3.6 - - - +
685B THR* 2.9 36.1 + - - +
687B CYS* 3.7 17.4 - - - -
702B LYS* 5.7 0.7 + - - -
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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