Contacts of the strand formed by residues 660 - 666 (chain A) in PDB entry 4DXT
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 THR 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649A PHE* 3.2 3.7 - - - -
650A GLY 3.0 35.6 + - - -
652A ASP 5.7 0.7 + - - -
658A GLU 4.6 2.8 + - - -
659A GLY* 1.3 72.3 - - - -
661A LEU* 1.3 74.2 + - - +
662A LEU* 3.1 5.0 + - + +
687A TYR* 4.1 23.3 + - - +
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Residues in contact with LEU 661 (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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647A ALA* 3.7 15.5 - - + -
648A ILE 3.8 3.1 - - - +
649A PHE* 3.5 32.1 - - + -
659A GLY 4.0 1.2 + - - -
660A THR* 1.3 75.9 - - - +
662A LEU* 1.3 62.4 + - - +
663A GLY* 3.6 29.6 - - - +
664A LYS* 4.0 27.8 - - + -
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Residues in contact with LEU 662 (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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621A PRO* 4.3 22.7 - - + -
648A ILE* 2.7 25.2 + - + +
649A PHE 4.0 3.6 - - - -
650A GLY* 3.6 23.6 - - - +
660A THR* 3.1 19.4 + - + +
661A LEU* 1.3 77.7 - - - +
663A GLY* 1.3 55.8 + - - +
679A PHE* 3.4 35.9 - - + +
680A GLN 5.3 1.2 + - - -
683A THR* 6.1 0.7 - - - +
687A TYR* 3.8 34.8 - - + +
690A VAL* 4.8 3.4 - - + -
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Residues in contact with GLY 663 (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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647A ALA* 3.2 5.0 - - - +
648A ILE 2.9 26.7 + - - -
661A LEU* 3.6 8.1 - - - +
662A LEU* 1.3 81.8 - - - +
664A LYS* 1.3 63.9 + - - -
665A PHE* 3.9 19.2 - - - -
679A PHE* 4.2 2.3 - - - -
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Residues in contact with LYS 664 (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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646A PHE 3.4 6.3 - - - +
647A ALA* 4.1 10.1 - - + -
649A PHE* 6.2 1.3 - - - -
661A LEU* 4.0 26.4 - - + +
663A GLY* 1.3 75.8 - - - +
665A PHE* 1.3 77.9 + - - +
695A LEU* 4.3 24.3 - - + +
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Residues in contact with PHE 665 (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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624A VAL* 4.6 1.3 - - + -
645A ASP* 3.2 4.5 - - - +
646A PHE* 2.7 66.1 + + + +
648A ILE* 4.5 4.0 - - + -
663A GLY* 3.9 16.6 - - - -
664A LYS* 1.3 85.9 - - - +
666A THR* 1.3 63.7 + - - +
677A PHE* 3.6 39.9 - + + -
678A HIS 3.5 27.1 - - - -
679A PHE* 3.7 35.9 - + - -
680A GLN 5.4 1.1 - - - -
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Residues in contact with THR 666 (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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644A LYS* 3.2 23.1 - - + +
645A ASP* 2.7 25.9 + - - +
646A PHE* 4.1 3.4 - - - -
665A PHE* 1.3 76.6 - - - +
667A TYR* 1.3 74.4 + - - +
668A ASP* 3.6 7.1 + - + +
675A GLN* 4.3 0.7 - - - +
677A PHE* 3.3 17.7 - - - -
698A TRP* 4.6 5.6 - - + -
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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