Contacts of the helix formed by residues 824 - 828 (chain F) in PDB entry 5YWB
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 GLY 824 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779F LEU* 5.5 0.5 - - - +
780F LEU 5.2 1.0 - - - +
781F ASN* 4.7 1.7 - - - +
822F GLN* 3.2 6.0 + - - -
823F ILE* 1.3 82.3 - - - +
825F GLU* 1.3 73.9 - - - -
826F ARG 3.1 1.2 + - - -
827F GLY 3.0 13.7 + - - -
828F ILE* 4.6 2.7 - - - -
829F ASN* 3.0 24.4 + - - -
1206F GLU* 5.4 1.0 - - - +
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Residues in contact with GLU 825 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781F ASN* 3.9 22.8 + - - +
824F GLY* 1.3 74.4 - - - -
826F ARG* 1.3 71.1 + - + +
827F GLY 3.0 5.2 + - - -
828F ILE* 3.3 26.7 - - + +
1117F PRO* 3.8 28.3 - - - +
1118F LEU* 5.5 2.5 - - + +
1119F GLY* 5.2 16.2 - - - +
1198F LEU* 5.7 5.0 - - - +
1202F SER* 4.4 14.3 + - - +
1206F GLU* 4.9 8.3 - - - +
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Residues in contact with ARG 826 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504F ARG* 3.7 49.3 + - - +
778F TRP* 5.7 1.9 - - - +
779F LEU* 4.1 21.5 + - - +
824F GLY 3.1 2.6 + - - -
825F GLU* 1.3 77.6 + - + +
827F GLY* 1.3 58.1 + - - +
828F ILE* 4.0 13.5 - - + +
835F ARG* 3.4 19.2 + - - -
1118F LEU* 3.4 32.9 - - - +
1206F GLU* 4.9 9.6 + - + +
1209F GLU* 3.8 23.8 - - - +
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Residues in contact with GLY 827 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779F LEU* 3.7 20.6 - - - +
823F ILE* 3.9 0.2 - - - -
824F GLY 3.0 14.1 + - - -
826F ARG* 1.3 79.6 - - - +
828F ILE* 1.3 62.1 + - - +
829F ASN 3.4 2.5 - - - -
830F LEU* 3.3 15.3 + - - +
835F ARG* 2.4 32.9 + - - -
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Residues in contact with ILE 828 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824F GLY* 4.5 1.5 + - - -
825F GLU* 3.3 24.5 + - + +
826F ARG* 4.0 13.5 - - + +
827F GLY* 1.3 72.9 - - - +
829F ASN* 1.3 60.1 + - - +
830F LEU 3.0 17.7 + - - +
835F ARG* 4.6 1.1 - - - +
1113F PHE 4.9 0.9 - - - +
1114F GLU* 3.3 51.0 - - + +
1116F THR 4.6 4.5 - - - +
1117F PRO* 5.2 2.2 - - + -
1118F LEU* 3.7 45.8 - - + +
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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