Contacts of the helix formed by residues 694 - 698 (chain B) in PDB entry 2PDA
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 GLN 694 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690B ILE* 6.1 0.2 - - - +
692B CYS* 3.8 26.3 - - + +
693B ASN* 1.3 78.2 - - - +
695B CYS* 1.3 64.7 + - - +
697B PHE* 3.5 6.1 - - - +
698B VAL* 3.0 29.7 + - - +
754B ILE* 4.6 13.7 + - + +
756B PRO* 3.6 24.0 - - + +
796B LEU* 4.3 14.6 - - + +
1046B LYS* 2.7 39.8 + - - +
1047B GLN* 5.6 0.3 - - - +
1240B SF4 4.3 5.1 - - - -
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Residues in contact with CYS 695 (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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693B ASN* 4.8 1.6 - - - -
694B GLN* 1.3 78.1 - - - +
696B ALA* 1.3 71.1 + - - +
698B VAL* 3.3 5.2 + - - +
699B CYS* 3.0 17.8 + - - +
704B ILE* 3.6 30.4 - - + +
738B ILE* 3.4 26.9 - - - -
751B CYS* 3.8 12.8 - - + +
754B ILE* 4.9 0.7 - - - -
762B LEU* 3.6 15.0 - - + -
1240B SF4 2.3 40.1 - - - -
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Residues in contact with ALA 696 (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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693B ASN* 4.2 3.0 + - - +
695B CYS* 1.3 78.3 - - - +
697B PHE* 1.3 52.7 + - - +
698B VAL 2.8 9.9 + - - -
699B CYS* 2.9 12.5 + - - +
702B SER* 5.6 0.2 - - - -
704B ILE* 3.5 33.4 - - + +
706B PRO* 3.8 20.9 - - + -
800B GLN* 4.0 15.9 - - + +
822B ARG* 2.5 32.5 + - - +
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Residues in contact with PHE 697 (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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693B ASN 3.1 18.5 + - - +
694B GLN* 3.5 8.3 - - - +
696B ALA* 1.3 77.1 - - - +
698B VAL* 1.3 56.1 + - - +
796B LEU* 4.1 9.9 - - + -
799B SER* 3.3 17.9 - - - -
800B GLN* 2.7 28.4 - - + +
819B PRO* 4.3 1.9 - - - +
822B ARG* 3.1 16.8 + - - +
823B VAL* 4.2 12.5 - - + +
1042B MET* 3.1 40.7 - - + +
1046B LYS* 3.4 54.1 - - + -
1049B PHE* 4.4 2.9 - + - -
1050B LEU* 4.1 21.5 - - + -
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Residues in contact with VAL 698 (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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694B GLN 3.0 16.9 + - - +
695B CYS 3.6 6.3 - - - +
696B ALA 2.8 1.2 + - - -
697B PHE* 1.3 81.5 - - - +
699B CYS* 1.3 61.2 + - - +
700B PRO* 2.9 16.8 - - - +
750B ASN* 3.8 16.9 - - + +
751B CYS* 3.8 27.4 - - - +
754B ILE* 4.1 8.3 - - + -
819B PRO* 3.5 13.9 - - - +
1042B MET* 4.9 1.1 - - + -
1046B LYS* 4.2 9.0 - - - -
1084B GLN* 3.1 44.8 - - + +
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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