Contacts of the strand formed by residues 679 - 685 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A GLU 3.5 1.6 - - - +
615A VAL* 3.1 10.7 - - - +
616A PHE* 2.8 46.6 + - + +
622A ILE* 5.3 0.2 - - + -
635A ILE* 5.6 0.4 - - - -
637A HIS 3.3 3.8 - - - +
638A GLY* 3.9 11.7 - - - -
639A VAL 3.5 24.5 - - - -
640A VAL* 4.0 11.9 - - - -
675A ALA* 3.8 11.2 - - + -
677A THR 3.5 10.1 - - - -
678A TYR* 1.3 83.3 - - - +
680A ARG* 1.3 62.7 + - - +
681A LEU* 3.8 15.9 + - + +
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Residues in contact with ARG 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A HIS 6.0 2.2 - - - -
613A PHE* 3.7 28.5 - - + -
614A GLU 3.8 3.4 - - - -
615A VAL* 4.8 7.2 - - + +
635A ILE 3.9 0.3 - - - -
636A GLN* 2.8 54.6 + - + +
637A HIS* 2.7 60.6 + - - +
678A TYR* 5.9 1.3 - - + -
679A CYS* 1.3 73.4 - - - +
681A LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A PHE* 3.5 8.0 - - - -
614A GLU* 2.7 40.3 + - + +
616A PHE* 3.5 35.0 - - + -
622A ILE* 4.0 18.4 - - + -
633A TYR* 3.6 24.0 - - + -
634A PHE 3.3 7.6 - - - +
635A ILE* 3.8 33.9 - - + -
640A VAL* 5.2 1.3 - - + -
658A PHE* 4.2 8.7 - - + -
679A CYS* 4.2 15.9 - - + -
680A ARG* 1.3 81.4 - - - +
682A TYR* 1.3 61.9 + - - +
683A SER 4.2 0.2 - - - -
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Residues in contact with TYR 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A ASN* 4.9 7.8 + - - +
586A CSO 3.7 28.0 + - - -
589A LEU* 4.5 7.2 - - + -
611A LEU* 3.9 34.8 - - + -
612A ARG 3.1 7.6 - - - -
613A PHE* 3.6 47.2 - + + +
633A TYR* 3.4 2.5 - - - -
634A PHE* 2.9 41.6 + - + +
636A GLN* 3.6 44.4 + - + -
681A LEU* 1.3 77.1 - - - +
683A SER* 1.3 62.0 + - - +
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Residues in contact with SER 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A LYS 4.0 1.0 - - - +
611A LEU* 3.2 9.3 - - - -
612A ARG* 2.6 46.8 + - - +
614A GLU* 2.7 29.3 + - - +
631A LYS* 3.5 20.7 - - - -
632A MET 3.2 10.8 - - - -
633A TYR* 3.9 11.0 - - - -
681A LEU 4.2 0.6 - - - -
682A TYR* 1.3 73.1 - - - +
684A LEU* 1.3 62.2 + - - +
685A SER 4.3 0.4 - - - -
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Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A MET* 3.7 43.1 - - + +
610A LYS* 3.8 23.8 - - + +
611A LEU* 3.8 10.3 - - + -
631A LYS* 3.7 1.5 - - - -
632A MET* 2.9 39.2 + - + +
634A PHE* 4.1 13.5 - - + -
663A LEU* 3.7 1.2 - - - +
683A SER* 1.3 74.9 - - - +
685A SER* 1.3 71.4 + - - +
688A ASN* 3.8 26.9 - - + +
689A PHE* 3.7 32.1 - - + +
692A VAL* 5.2 0.4 - - + -
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Residues in contact with SER 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A LYS 5.3 0.4 + - - -
630A LYS 3.4 11.4 - - - -
631A LYS* 4.4 8.6 - - - +
683A SER 4.3 0.2 - - - -
684A LEU* 1.3 77.9 - - - +
686A VAL* 1.3 60.2 + - - +
687A ASP* 4.0 6.6 + - - +
688A ASN* 3.2 34.4 + - - +
689A PHE* 2.9 28.9 + - - +
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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