Contacts of the strand formed by residues 679 - 685 (chain B) in PDB entry 3U11
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 CYS 679 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614B GLU 3.7 0.7 - - - +
615B VAL* 3.3 10.6 - - - +
616B PHE* 3.0 38.1 + - + +
635B ILE* 5.7 0.2 - - - -
637B HIS 3.3 6.1 - - - +
638B GLY* 4.2 1.6 - - - -
639B VAL 3.3 32.8 - - - -
640B VAL* 3.7 18.2 - - - -
675B ALA* 3.9 7.0 - - - -
677B THR 3.4 11.9 - - - -
678B TYR* 1.3 75.6 - - - +
680B ARG* 1.3 62.3 + - - +
681B LEU* 3.8 19.7 - - + -
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Residues in contact with ARG 680 (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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645A LYS* 4.2 35.4 - - - +
557B HIS 3.8 16.6 + - - -
558B ARG 4.8 2.2 + - - -
560B GLN* 3.1 26.3 + - - -
613B PHE* 3.5 41.7 - - + -
614B GLU 3.8 3.4 - - - -
615B VAL* 4.7 6.3 - - + +
636B GLN* 2.8 42.8 + - + +
637B HIS* 2.7 40.1 + - + +
678B TYR* 5.7 1.6 - - + -
679B CYS* 1.3 74.7 - - - +
681B LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 681 (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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613B PHE* 3.6 4.0 - - - -
614B GLU* 2.8 36.8 + - + +
616B PHE* 3.5 32.3 - - + -
622B ILE* 4.0 9.6 - - + -
633B TYR* 3.9 16.8 - - + -
634B PHE 3.2 7.6 - - - +
635B ILE* 3.7 35.9 - - + +
640B VAL* 5.2 0.4 - - + -
658B PHE* 3.9 23.8 - - + -
679B CYS* 3.8 21.1 - - + -
680B ARG* 1.3 83.3 - - - +
682B TYR* 1.3 69.5 + - - +
683B SER 4.1 0.4 - - - -
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Residues in contact with TYR 682 (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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585B ASN* 4.7 7.3 + - - +
586B CSO 3.7 31.2 + - - -
589B LEU* 4.5 7.4 - - + -
611B LEU* 3.8 36.8 - - + -
612B ARG 3.2 5.4 - - - -
613B PHE* 3.6 46.3 - + + -
633B TYR* 4.4 1.1 - - - -
634B PHE* 2.8 49.9 + - + +
636B GLN* 3.2 45.6 + - + -
681B LEU* 1.3 76.1 - - - +
683B SER* 1.3 60.9 + - - +
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Residues in contact with SER 683 (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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610B LYS 4.0 1.4 - - - +
611B LEU* 3.4 7.1 - - - -
612B ARG* 3.0 41.8 + - - +
614B GLU* 2.7 32.2 + - - -
631B LYS* 4.0 20.2 - - - +
632B MET 3.0 12.1 - - - -
633B TYR* 4.0 10.5 - - - -
681B LEU 4.1 1.0 - - - -
682B TYR* 1.3 73.4 - - - +
684B LEU* 1.3 59.0 + - - +
685B SER* 4.2 0.7 + - - -
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Residues in contact with LEU 684 (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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607B MET* 4.4 18.8 - - + +
610B LYS* 3.8 23.8 - - + +
611B LEU* 3.8 15.9 - - + -
631B LYS* 3.4 2.0 - - - -
632B MET* 2.5 56.9 + - + +
634B PHE* 4.0 14.1 - - + -
663B LEU* 4.4 0.2 - - - +
682B TYR 3.8 0.8 + - - -
683B SER* 1.3 73.0 - - - +
685B SER* 1.3 65.0 + - - +
688B ASN* 3.8 25.8 - - + +
689B PHE* 3.6 37.0 - - + +
692B VAL* 5.3 2.7 - - + -
703B PHE* 5.6 0.9 - - + -
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Residues in contact with SER 685 (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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610B LYS 4.9 1.0 + - - -
630B LYS 3.5 9.2 - - - -
631B LYS* 4.3 11.7 - - - +
663B LEU* 4.8 0.7 - - - -
683B SER* 4.2 1.4 + - - -
684B LEU* 1.3 75.1 - - - +
686B VAL* 1.3 56.5 + - - +
687B ASP* 4.1 4.5 + - - +
688B ASN* 3.1 32.6 + - - +
689B PHE* 2.7 36.2 + - - +
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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