Contacts of the helix formed by residues 796 - 801 (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 LEU 796 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692B CYS 3.6 13.9 - - - +
693B ASN 3.4 26.7 - - - +
694B GLN* 4.2 16.6 - - + +
697B PHE* 4.1 11.2 - - + -
795B SER* 1.3 67.6 - - - +
797B LYS* 1.3 63.1 + - - +
799B SER* 2.6 20.4 + - - -
800B GLN* 3.2 8.0 + - - +
1046B LYS* 4.1 22.9 - - + +
1047B GLN* 4.1 28.0 - - + +
1050B LEU* 3.1 21.6 - - + +
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Residues in contact with LYS 797 (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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691B GLN* 3.8 34.7 + - - +
692B CYS* 4.2 8.5 - - - +
693B ASN* 3.4 36.9 - - - +
727B LYS* 3.4 27.1 + - - +
731B LEU* 3.6 16.9 - - - +
736B PHE* 4.6 7.0 - - - -
791B LEU* 3.9 18.2 - - + -
795B SER* 3.0 2.7 + - - +
796B LEU* 1.3 78.5 - - - +
798B GLY* 1.3 64.3 + - - +
800B GLN 3.1 10.7 + - - -
801B PHE* 3.5 15.1 + - + -
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Residues in contact with GLY 798 (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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791B LEU* 3.5 24.5 - - - +
792B PRO 3.5 5.6 - - - -
793B ARG 3.3 6.7 - - - -
795B SER* 2.8 26.5 + - - -
797B LYS* 1.3 74.4 - - - +
799B SER* 1.3 58.7 + - - -
801B PHE* 3.0 14.8 + - - +
802B GLN* 3.3 18.9 + - - -
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Residues in contact with SER 799 (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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697B PHE* 3.3 13.5 - - - -
793B ARG 3.0 15.8 + - - -
795B SER 2.5 16.1 + - - -
796B LEU* 2.6 15.6 + - - -
798B GLY* 1.3 67.4 - - - +
800B GLN* 1.3 84.5 + - - +
801B PHE 3.0 9.4 + - - -
802B GLN* 3.1 24.0 + - - +
823B VAL* 5.5 0.7 - - - -
826B GLN* 3.3 11.8 - - - +
827B LEU* 4.2 18.8 - - - -
1050B LEU* 4.5 4.0 - - - -
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Residues in contact with GLN 800 (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* 3.0 50.9 - - + +
696B ALA* 4.0 4.1 - - + +
697B PHE* 2.7 31.2 + - + +
706B PRO* 2.8 33.7 - - + +
796B LEU 3.9 2.0 - - - +
797B LYS 3.1 3.7 + - - +
799B SER* 1.3 108.8 + - - +
801B PHE* 1.3 56.0 + - - +
802B GLN 3.2 7.4 + - - +
822B ARG* 3.0 21.3 + - - -
826B GLN* 2.8 24.6 + - - +
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Residues in contact with PHE 801 (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* 3.7 9.2 - - - -
706B PRO* 3.3 37.7 - - + -
708B LEU* 3.6 35.0 - - + -
731B LEU* 4.5 4.3 - - + -
736B PHE* 3.3 34.3 - + - -
786B VAL* 3.0 20.9 - - + +
787B LYS* 3.1 32.8 - - + +
788B SER* 3.4 2.4 + - - -
790B VAL* 4.7 9.9 - - + -
791B LEU* 4.6 13.0 - - + -
797B LYS* 3.5 24.4 + - + -
798B GLY* 3.0 14.5 + - - +
799B SER 3.0 2.0 - - - -
800B GLN* 1.3 80.3 - - - +
802B GLN* 1.3 56.9 + - - +
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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