Contacts of the helix formed by residues 713 - 717 (chain B) 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 PHE 713 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B PRO* 1.3 77.2 - - + +
714B PRO* 1.3 70.2 - - - +
715B ASP* 3.0 11.7 - - - -
716B HIS* 3.2 36.6 + + + +
717B ASN* 3.6 10.4 + - - -
759B VAL* 4.7 2.0 - - + -
979B GLY* 4.2 11.1 - - - -
982B ILE* 3.8 35.7 - - + -
983B GLU* 4.1 12.6 - - - -
986B GLN* 4.5 12.6 - - + -
998B ASP 4.3 6.5 - - - -
999B ALA* 3.0 44.0 + - + -
1000B THR 5.2 4.0 - - - -
1001B PRO* 5.5 0.9 - - + -
1007B ASN* 4.0 20.9 - - + -
1011B ILE* 4.9 5.6 - - + -
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Residues in contact with PRO 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A PHE* 3.1 17.4 - - + -
704B LEU* 4.1 25.4 - - + -
708B ALA 5.0 0.4 - - - +
711B ILE* 3.4 47.1 - - + +
712B PRO 3.4 0.4 - - - -
713B PHE* 1.3 89.2 - - - +
715B ASP* 1.3 64.3 + - - +
717B ASN* 3.3 6.9 + - - +
722B ASN* 3.0 30.1 + - + +
1001B PRO* 4.1 17.3 - - + -
1002B PHE* 6.3 0.4 - - + -
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Residues in contact with ASP 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 4.9 0.2 - - - -
830A GLY* 3.9 4.7 - - - -
831A LEU* 3.4 51.5 + - - +
836A PHE* 3.6 20.1 - - + -
713B PHE* 3.5 10.9 - - - -
714B PRO* 1.3 76.2 - - - +
716B HIS* 1.3 76.9 + - - -
717B ASN 3.3 2.1 + - - +
1001B PRO* 2.9 43.4 - - - +
1002B PHE* 4.2 9.9 - - + -
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Residues in contact with HIS 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 3.2 42.8 - - - +
828A LEU* 3.0 21.5 + - - -
829A ALA 3.8 2.0 - - - -
830A GLY* 3.6 16.8 + - - -
713B PHE* 3.2 27.4 + + + +
715B ASP* 1.3 88.8 + - - +
717B ASN* 1.3 59.1 + - - +
976B MET 3.9 0.9 - - - +
978B ILE* 3.8 7.1 + - + +
979B GLY* 3.8 23.8 + - - +
982B ILE* 4.1 18.9 - - + +
1007B ASN* 3.0 32.7 + - - -
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Residues in contact with ASN 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 4.5 7.1 - - - -
831A LEU* 5.7 2.3 - - - +
836A PHE* 4.9 2.8 - - - -
839A HIS* 5.3 0.5 - - - -
711B ILE* 3.4 12.3 - - - +
713B PHE 3.6 11.4 + - - -
714B PRO 3.3 4.0 + - - +
715B ASP 3.3 2.0 - - - +
716B HIS* 1.3 79.6 - - - +
718B GLN* 1.3 67.7 + - - +
719B SER* 3.2 2.9 + - - -
721B ARG* 4.5 4.3 - - + -
722B ASN* 2.9 37.7 + - - +
939B HIS* 3.3 25.0 + - - +
976B MET 4.6 1.6 - - - -
977B THR* 3.1 33.5 - - - +
979B GLY* 3.5 10.1 + - - -
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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
------------------------------------------------------------
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