Contacts of the helix formed by residues 705 - 718 (chain V) in PDB entry 5IY8
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 705 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703V PHE 2.9 2.9 + - - +
704V SER* 1.4 86.0 - - - +
706V LYS* 1.3 63.8 + - - +
707V GLU* 3.3 20.0 + - + +
708V GLU* 2.8 36.4 + - - +
709V GLN* 3.2 32.5 + - - +
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Residues in contact with LYS 706 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151 ALA* 4.3 1.1 - - - -
516V PRO* 2.2 62.0 - - + +
517V GLU* 3.4 14.4 + - - +
705V THR* 1.3 72.9 - - - +
707V GLU* 1.3 70.2 + - - +
709V GLN* 3.0 26.0 + - - +
710V GLN* 2.9 29.7 + - - +
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Residues in contact with GLU 707 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705V THR* 3.3 22.4 - - - +
706V LYS* 1.3 81.5 + - - +
708V GLU* 1.3 66.2 - - + +
710V GLN* 3.2 9.2 + - - +
711V GLN* 3.1 22.6 + - - +
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Residues in contact with GLU 708 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703V PHE* 3.6 27.9 + - + -
704V SER* 2.5 40.7 + - - -
705V THR* 2.8 26.1 + - - +
707V GLU* 1.3 73.2 - - + +
709V GLN* 1.3 67.4 + - - +
711V GLN* 3.5 21.4 + - - +
712V LEU 3.3 15.8 + - - -
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Residues in contact with GLN 709 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515V SER* 3.4 17.7 + - - -
516V PRO 4.2 1.2 - - - +
517V GLU* 4.4 7.2 - - - +
518V PHE* 3.7 12.6 - - + -
538V PRO* 3.8 22.2 - - + +
539V ASN* 5.6 1.8 + - - -
703V PHE* 3.0 36.7 + - + +
705V THR* 3.2 18.5 + - - +
706V LYS* 3.0 40.4 + - - +
708V GLU* 1.3 79.8 - - - +
710V GLN* 1.3 54.2 + - - +
712V LEU* 3.2 5.4 + - - +
713V LEU* 2.9 28.4 + - - +
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Residues in contact with GLN 710 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517V GLU* 2.7 36.0 + - - +
520V ARG* 5.1 5.4 + - - +
706V LYS 2.9 17.1 + - - +
707V GLU* 3.2 10.7 + - - +
709V GLN* 1.3 72.7 - - - +
711V GLN* 1.3 57.6 + - - +
713V LEU* 3.6 15.8 - - - +
714V GLN* 3.0 43.1 + - - +
717V LEU* 6.0 2.6 - - - +
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Residues in contact with GLN 711 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703V PHE* 6.2 0.8 - - - -
707V GLU 3.1 12.2 + - - +
708V GLU* 3.5 25.4 + - - +
710V GLN* 1.3 74.0 - - - +
712V LEU* 1.3 61.3 + - - +
714V GLN* 3.8 5.2 + - - +
715V LYS* 3.5 18.4 + - - +
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Residues in contact with LEU 712 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518V PHE* 4.2 14.8 - - + -
536V MET* 3.9 38.4 - - + +
538V PRO* 5.2 1.3 - - + -
541V PHE* 5.8 0.2 - - + -
570V GLU* 4.6 4.5 - - + +
574V ARG* 4.0 25.6 - - - +
703V PHE* 3.6 39.5 - - + -
708V GLU 3.3 2.8 + - - -
709V GLN 3.2 9.1 + - - +
711V GLN* 1.3 77.4 - - - +
713V LEU* 1.3 65.5 + - - +
715V LYS* 3.0 10.3 + - + +
716V VAL* 2.9 42.0 + - + +
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Residues in contact with LEU 713 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517V GLU* 3.0 41.3 - - + +
518V PHE* 3.5 48.6 - - + -
520V ARG* 4.0 14.1 - - - +
521V GLU* 4.5 6.1 - - + -
533V LEU* 4.0 13.2 - - + -
709V GLN 2.9 19.8 + - - +
710V GLN* 3.4 18.6 + - - +
712V LEU* 1.3 73.1 - - - +
714V GLN* 1.3 55.9 - - - +
716V VAL* 3.6 3.4 + - - +
717V LEU* 3.0 43.6 + - + +
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Residues in contact with GLN 714 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710V GLN* 3.0 29.1 + - - +
711V GLN* 3.9 6.5 - - - +
713V LEU* 1.3 75.0 - - - +
715V LYS* 1.3 60.6 + - - +
717V LEU* 3.5 11.1 + - - +
718V ALA* 3.5 21.0 + - - +
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Residues in contact with LYS 715 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529V LYS* 5.3 0.2 + - - -
566V PHE* 4.8 18.0 - - + -
570V GLU* 3.2 37.6 + - - +
574V ARG* 4.3 10.7 - - - +
711V GLN 3.5 11.0 + - - +
712V LEU* 3.0 14.6 + - + +
714V GLN* 1.3 76.4 - - - +
716V VAL* 1.3 61.6 + - + +
718V ALA* 3.5 18.6 + - - +
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Residues in contact with VAL 716 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518V PHE* 5.2 2.7 - - + -
529V LYS* 2.8 30.0 + - + +
532V LEU* 3.8 41.2 - - + +
533V LEU* 3.7 31.9 - - + -
536V MET* 4.4 11.2 - - + -
566V PHE* 5.3 6.3 - - + -
570V GLU* 6.5 0.4 - - + -
712V LEU* 2.9 40.1 + - + +
713V LEU* 3.9 4.3 - - - +
715V LYS* 1.3 76.1 - - + +
717V LEU* 1.3 58.0 + - - +
718V ALA 3.2 0.3 + - - -
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Residues in contact with LEU 717 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520V ARG* 5.3 2.5 - - - +
521V GLU* 3.9 35.7 - - + +
525V ILE* 3.8 28.4 - - + +
529V LYS* 3.3 17.4 - - + +
533V LEU* 5.0 5.8 - - + -
710V GLN* 6.0 2.2 - - - +
713V LEU* 3.0 34.2 + - + +
714V GLN* 3.5 10.3 + - - +
716V VAL* 1.3 75.9 - - - +
718V ALA* 1.4 60.0 + - - +
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Residues in contact with ALA 718 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529V LYS* 3.6 18.3 - - - -
714V GLN 3.5 9.6 + - - +
715V LYS* 3.5 16.6 - - - +
716V VAL 3.2 2.8 + - - -
717V LEU* 1.4 80.1 - - - +
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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