Contacts of the strand formed by residues 723 - 727 (chain A) in PDB entry 2HYE
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 LYS 723 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ASP* 3.2 27.8 - - + +
378A CYS* 3.3 9.7 - - - -
722A ARG* 1.3 86.5 - - + +
724A ILE* 1.3 64.6 + - - +
725A CYS* 5.6 0.2 - - - -
734A GLY 4.2 0.2 - - - -
735A VAL* 3.2 4.7 - - - -
736A LEU* 3.1 47.5 + - + +
814A LEU 3.7 20.4 + - - +
815A SER* 4.1 9.0 + - - +
816A LEU* 3.9 25.0 + - + +
871A TYR 5.2 4.0 + - - -
872A SER* 5.3 7.1 - - - +
873A MET 5.8 1.4 + - - +
31B GLN* 6.3 0.9 - - - +
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Residues in contact with ILE 724 (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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361A ASP* 2.9 17.7 + - - +
362A MET* 3.9 25.6 - - - +
363A CYS* 4.0 14.3 - - - +
376A VAL* 3.6 37.9 - - + +
377A THR 5.1 0.2 - - - +
378A CYS* 3.4 21.3 - - - +
387A LEU* 4.3 5.6 - - + -
723A LYS* 1.3 77.9 - - - +
725A CYS* 1.3 80.5 + - - +
733A PHE* 4.2 9.6 - - + -
734A GLY 2.8 13.9 - - - +
735A VAL* 3.8 14.8 - - + -
816A LEU* 4.2 0.9 - - - +
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Residues in contact with CYS 725 (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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363A CYS* 4.7 5.6 - - - -
723A LYS* 5.6 0.7 - - - -
724A ILE* 1.3 84.1 - - - +
726A TYR* 1.3 61.9 + - - +
733A PHE* 3.0 11.7 - - - -
734A GLY* 2.8 31.7 + - - +
816A LEU* 3.4 40.2 - - + -
817A VAL* 3.5 16.4 - - - -
818A SER* 4.2 16.2 - - - +
829A PHE* 5.0 3.4 - - + -
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Residues in contact with TYR 726 (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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363A CYS* 4.7 9.0 - - + +
364A VAL 5.7 0.9 - - - +
365A VAL* 3.5 23.6 - - + -
367A LEU* 3.8 16.2 + - + +
725A CYS* 1.3 77.3 - - - +
727A GLN* 1.3 71.2 + - - +
728A GLU* 3.5 38.9 + - + +
731A GLN* 4.2 3.1 + - - -
732A CYS 4.0 6.1 - - - -
733A PHE* 3.1 33.0 - + + -
796A GLN* 2.2 42.7 + - + -
818A SER* 3.6 14.8 + - - -
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Residues in contact with GLN 727 (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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725A CYS 4.1 1.0 + - - -
726A TYR* 1.3 74.6 - - - +
728A GLU* 1.3 57.2 + - - +
729A VAL* 3.1 14.6 + - + +
730A SER* 3.5 33.1 + - - +
731A GLN* 3.3 16.1 + - - -
732A CYS 3.2 24.1 + - - +
818A SER* 3.3 28.2 - - - -
827A THR* 2.8 38.9 - - + +
828A TYR 4.1 1.6 + - - -
829A PHE* 2.9 41.5 - - + -
853A TYR* 5.2 2.1 + - - +
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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