Contacts of the strand formed by residues 668 - 672 (chain B) in PDB entry 3UO8
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 668 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B ILE 3.8 0.2 - - - +
615B TYR* 3.0 5.0 - - - -
616B THR* 2.9 41.0 + - - +
629B ASP* 6.1 1.6 - - + +
630B ALA 3.6 24.0 - - - +
631B TYR* 4.9 2.2 - - + -
647B ASN* 3.9 35.9 - - + +
648B LYS 3.2 15.3 - - - +
649B GLY* 4.1 6.3 - - - +
667B CYS* 1.3 80.2 - - - +
669B TYR* 1.3 61.9 + - - +
670B THR* 5.3 0.6 + - - -
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Residues in contact with TYR 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ILE* 4.2 7.6 - - + -
614B ILE 3.3 6.1 - - - +
615B TYR* 3.4 30.5 - + + -
647B ASN 3.2 4.0 + - - -
648B LYS 2.8 37.3 + - - +
649B GLY 3.3 14.8 + - - -
650B THR 3.7 0.9 - - - -
651B PRO* 3.6 50.2 - - + +
654B THR* 3.4 12.7 - - + +
660B SER* 5.6 2.8 + - - -
663B LEU* 4.2 13.2 - - + -
664B PRO 2.8 27.8 + - - -
665B LYS* 3.6 1.7 - - - -
666B HIS 3.5 6.6 + - - -
667B CYS* 3.2 35.0 + - + -
668B LEU* 1.3 73.2 - - - +
670B THR* 1.3 63.6 + - - +
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Residues in contact with THR 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ILE* 3.5 6.0 - - - +
614B ILE* 2.9 38.6 + - - +
632B VAL* 3.4 19.7 - - - +
635B PHE* 4.1 14.8 - - + -
641B ILE* 4.9 4.0 - - + -
645B ASP 5.4 0.2 - - - +
646B ALA* 3.7 19.2 - - + +
647B ASN* 3.0 23.4 + - - +
654B THR* 4.2 3.6 - - - -
668B LEU 5.3 0.3 + - - -
669B TYR* 1.3 72.2 + - - +
671B ARG* 1.3 63.5 + - - +
672B LEU* 3.6 23.4 + - + +
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Residues in contact with ARG 671 (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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363B LEU* 3.8 19.8 - - - +
384B LEU* 4.1 12.5 - - - +
607B GLU* 3.1 32.3 + - - -
611B VAL* 3.6 21.6 - - + +
613B ILE* 3.5 13.9 - - + -
641B ILE* 4.2 10.6 - - - +
645B ASP 5.1 2.4 + - - -
654B THR* 3.5 40.5 + - - +
655B GLY 3.5 12.9 + - - -
656B SER* 3.5 14.5 - - - +
670B THR* 1.3 74.3 - - - +
672B LEU* 1.3 67.7 + - - +
673B SER* 3.7 24.1 + - - +
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Residues in contact with LEU 672 (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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611B VAL* 3.4 3.5 - - - -
612B MET* 2.8 45.5 + - + +
614B ILE* 3.2 33.2 - - + -
635B PHE* 4.0 15.3 - - + -
639B LEU* 4.7 4.3 - - + -
641B ILE* 4.0 24.5 - - + -
670B THR* 3.6 22.9 - - + +
671B ARG* 1.3 80.3 - - - +
673B SER* 1.3 63.0 + - - +
675B LEU* 3.8 17.2 - - + +
682B LEU* 4.0 25.6 - - + -
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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