Contacts of the strand formed by residues 750 - 757 (chain B) in PDB entry 3HS0
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 SER 750 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A GLY 3.0 27.6 + - - +
548A ASP 3.8 1.6 + - - -
549A PRO* 3.2 28.4 - - - +
740B LEU* 3.6 17.4 + - - +
742B GLU* 3.1 30.5 + - - -
743B GLU 3.7 15.5 - - - -
744B PRO* 4.0 3.4 - - - -
748B GLY 4.1 1.4 - - - -
749B ILE* 1.3 73.0 - - - +
751B SER* 1.3 60.1 + - - +
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Residues in contact with SER 751 (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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544A LYS* 4.0 18.0 + - - +
545A LEU 3.1 3.4 - - - -
546A GLU* 3.5 33.2 + - - -
740B LEU* 4.9 0.4 - - - -
742B GLU* 3.0 26.9 - - - +
743B GLU 4.9 1.8 + - - -
749B ILE* 4.0 4.1 + - - -
750B SER* 1.3 76.2 - - - +
752B LYS* 1.3 61.1 + - - +
753B THR 4.1 0.9 + - - -
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Residues in contact with LYS 752 (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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543A ILE 3.6 0.2 - - - +
544A LYS* 3.4 3.1 - - - -
545A LEU* 2.7 47.6 + - + +
738B LYS* 4.7 24.8 - - + +
739B ASP 3.7 24.5 + - - +
740B LEU* 3.5 22.4 - - + +
741B THR* 4.5 8.7 + - - +
742B GLU* 3.6 24.6 + - + +
751B SER* 1.3 73.5 - - - +
753B THR* 1.3 71.6 + - - +
754B MET* 3.5 5.6 + - + +
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Residues in contact with THR 753 (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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542A LYS* 3.9 29.6 - - + -
543A ILE 3.5 6.7 - - - +
544A LYS* 3.4 29.3 - - + +
742B GLU* 4.5 6.0 + - - +
751B SER* 4.1 2.4 + - - -
752B LYS* 1.3 81.3 - - - +
754B MET* 1.3 63.8 + - - +
755B SER* 5.0 3.2 + - - +
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Residues in contact with MET 754 (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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542A LYS* 3.3 2.7 - - - -
543A ILE* 2.7 58.9 + - + +
545A LEU* 4.7 5.8 - - + -
555A LEU* 3.4 31.6 - - + -
734B LEU* 4.4 12.6 - - + -
736B LEU* 3.9 24.5 - - + -
738B LYS* 3.5 35.4 - - - +
752B LYS* 4.4 9.4 - - + +
753B THR* 1.3 77.1 - - - +
755B SER* 1.3 67.8 + - - +
756B PHE* 4.2 11.2 - - + -
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Residues in contact with SER 755 (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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541A MET 3.2 12.1 - - - -
542A LYS* 3.9 23.4 + - - +
753B THR* 5.2 2.6 + - - +
754B MET* 1.3 82.6 - - - +
756B PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 756 (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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541A MET* 2.8 51.7 + - + +
543A ILE* 3.8 35.4 - - + -
733B TRP* 3.7 37.7 - + - -
734B LEU* 3.9 33.0 - - + -
754B MET* 4.2 15.0 - - + -
755B SER* 1.3 79.4 - - - +
757B TYR* 1.3 69.8 + - - +
758B LEU* 4.4 5.4 - - + -
767B VAL* 5.1 5.4 - - + -
786B ILE* 4.3 16.2 - - + -
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Residues in contact with TYR 757 (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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538A GLY* 3.4 22.2 - - - +
539A ALA* 3.4 2.5 - - - -
540A ALA* 3.4 35.3 - - + +
733B TRP* 3.8 13.7 - - - -
756B PHE* 1.3 82.8 - - - +
758B LEU* 1.3 69.7 + - - +
759B ARG* 4.6 3.1 - - - -
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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