Contacts of the helix formed by residues 609 - 613 (chain B) in PDB entry 5YDJ
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 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B PRO* 5.9 1.4 - - - +
295B ALA* 3.5 19.1 - - - +
605B ASN 3.3 2.8 + - - -
606B TYR 3.5 1.8 + - - -
607B VAL 3.4 4.4 - - - -
608B PHE* 1.3 78.4 - - - +
610B GLU* 1.3 62.6 + - - +
611B PRO* 3.4 2.5 - - - -
612B LEU* 3.4 18.3 + - - +
613B ASN* 4.3 2.3 + - - +
626B SER* 3.5 8.5 - - - -
630B MET* 3.5 23.3 - - - -
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Residues in contact with GLU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B MET* 5.8 1.2 - - - +
289B ASP 5.0 6.3 - - - +
290B VAL* 3.6 30.1 - - - +
292B ASP* 6.5 1.8 - - + -
605B ASN* 2.9 53.5 + - + +
608B PHE 3.5 2.0 - - - -
609B GLY* 1.3 73.8 - - - +
611B PRO* 1.4 66.3 - - + +
612B LEU 3.2 0.9 - - - -
613B ASN* 3.2 21.3 + - + +
616B LEU* 3.6 27.3 - - + +
618B TYR* 3.3 12.7 + - - +
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Residues in contact with PRO 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B ASN 3.3 13.7 - - - +
606B TYR* 3.7 25.6 - - + -
609B GLY 3.5 3.1 - - - -
610B GLU* 1.4 90.2 - - + +
612B LEU* 1.3 58.7 + - - +
613B ASN 3.2 6.9 + - - +
618B TYR* 3.6 44.3 - - + +
622B GLU 3.8 14.1 - - - +
623B LYS* 3.4 28.4 - - - +
626B SER* 3.5 13.7 - - - +
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 4.9 0.7 - - + -
184B SER* 3.9 26.4 - - - +
295B ALA* 5.3 6.7 - - + -
299B GLU* 3.2 42.4 - - + +
609B GLY* 3.6 13.0 - - - +
610B GLU 3.2 1.0 - - - -
611B PRO* 1.3 76.1 - - + +
613B ASN* 1.3 61.0 + - - +
614B PRO* 3.3 9.9 - - - +
623B LYS* 3.8 34.8 + - + +
626B SER* 4.1 17.3 - - - +
627B ARG* 4.2 15.9 - - + +
630B MET* 4.7 7.2 - - + -
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Residues in contact with ASN 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 3.7 28.5 - - + +
609B GLY 4.3 1.2 + - - +
610B GLU* 3.2 19.2 + - - +
611B PRO 3.2 8.0 - - - +
612B LEU* 1.3 75.8 - - - +
614B PRO* 1.4 72.4 - - - +
615B THR* 2.6 30.6 + - - +
616B LEU* 3.3 38.0 + - + +
623B LYS* 5.2 1.3 - - - -
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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