Contacts of the helix formed by residues 722 - 728 (chain A) in PDB entry 2IVF
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 GLU 722 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A ARG* 4.8 3.3 - - - +
719A ARG* 3.6 49.3 + - + +
720A TYR 3.2 0.4 - - - -
721A ASP* 1.3 82.3 + - - +
723A LEU* 1.3 66.3 + - + +
724A TYR 3.3 2.7 - - - -
725A LYS* 3.4 31.7 + - - +
726A LYS* 3.0 46.2 + - + +
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Residues in contact with LEU 723 (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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178A PHE* 5.6 0.9 - - + -
209A LEU* 3.7 44.4 - - + +
210A MET* 4.1 18.6 - - + -
695A LEU* 4.1 20.3 - - + +
698A VAL* 3.7 29.8 - - + -
710A PHE* 4.2 16.4 - - + -
718A ARG* 5.9 1.1 - - + -
719A ARG 3.8 10.3 - - - +
720A TYR* 3.3 19.8 + - + +
722A GLU* 1.3 79.6 - - + +
724A TYR* 1.3 57.7 + - - +
726A LYS* 4.6 5.6 - - - -
727A PHE* 2.9 30.7 + - - +
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Residues in contact with TYR 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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692A ALA* 3.2 36.3 - - + +
693A LEU* 5.3 0.2 - - - -
695A LEU* 4.1 7.9 + - - +
696A LYS* 3.5 46.9 - - + +
699A GLY* 6.3 0.4 - - - -
720A TYR 4.8 0.8 + - - -
721A ASP 4.9 3.9 + - - +
722A GLU 3.3 0.6 - - - -
723A LEU* 1.3 75.3 - - - +
725A LYS* 1.3 71.9 + - + +
727A PHE* 3.4 1.9 + - - +
728A THR* 3.0 51.9 + - + +
731A GLY* 6.0 1.8 - - - -
734A LEU* 3.7 19.5 - - + +
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Residues in contact with LYS 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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721A ASP 5.1 4.2 + - - +
722A GLU* 3.4 39.6 + - + +
723A LEU 3.4 0.2 - - - -
724A TYR* 1.3 84.7 - - + +
726A LYS* 1.3 69.4 + - + +
728A THR* 3.9 5.4 - - - -
729A MET* 3.0 3.3 + - - -
730A ASP* 2.7 52.7 + - + +
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Residues in contact with LYS 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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205A ARG* 2.9 19.6 + - - -
209A LEU* 3.5 34.7 - - + +
495A SER* 5.3 7.0 - - - +
722A GLU* 3.0 46.2 + - + +
723A LEU* 3.8 7.0 - - + +
725A LYS* 1.3 81.1 - - + +
727A PHE* 1.3 65.6 + - - +
729A MET* 3.1 9.0 + - - +
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Residues in contact with PHE 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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202A ALA* 3.3 31.0 - - + -
205A ARG* 2.8 43.1 + - + +
206A MET 3.8 4.7 - - - -
209A LEU* 3.3 9.5 - - + +
688A TRP* 3.4 62.5 - + - -
691A ILE* 3.6 18.4 - - + -
692A ALA* 3.9 17.9 - - + -
695A LEU* 3.5 22.2 - - + -
723A LEU 2.9 18.5 + - - +
724A TYR* 3.4 5.4 + - - +
726A LYS* 1.3 76.7 - - - +
728A THR* 1.3 68.0 + - + +
729A MET 3.4 0.2 + - - -
733A LEU* 4.7 0.3 - - - +
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Residues in contact with THR 728 (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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692A ALA* 4.1 4.5 - - + -
724A TYR* 3.0 46.8 + - + +
725A LYS* 3.5 6.2 + - - -
727A PHE* 1.3 88.7 - - + +
729A MET* 1.3 65.5 + - - +
730A ASP 3.6 0.2 + - - -
731A GLY* 3.0 18.5 + - - -
732A HIS 2.9 5.4 + - - -
733A LEU* 2.8 50.0 + - - +
734A LEU* 3.8 13.2 - - + -
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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