Contacts of the helix formed by residues 850 - 854 (chain A) in PDB entry 4N78
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 ASP 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791A ASP* 3.6 13.7 - - - +
792A LEU* 4.9 2.8 + - + +
846A GLU* 2.8 25.6 + - + +
848A ASN 3.6 1.2 - - - -
849A TYR* 1.3 80.7 - - + +
851A PHE* 1.3 66.4 + - - +
853A PRO* 3.2 2.6 - - - +
854A ASN* 2.9 50.8 + - - +
855A TYR* 3.8 7.0 - - - -
866A ARG* 2.8 37.4 + - - -
873A GLN 5.0 0.2 - - - +
877A ARG* 4.1 9.6 - - - +
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Residues in contact with PHE 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A LEU* 4.5 12.6 - - + -
846A GLU 3.0 10.7 + - - +
847A LEU* 3.7 33.9 - - + +
850A ASP* 1.3 72.3 + - - +
852A LEU* 1.3 75.7 + - + +
855A TYR* 3.1 47.8 + + + +
864A PHE* 3.5 56.8 - + + -
909A VAL* 4.0 22.9 - - + -
914A PHE* 4.6 1.8 - + - -
1002A ASN* 3.8 22.6 + - + -
1006A PHE* 4.0 20.0 - + + -
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Residues in contact with LEU 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847A LEU* 3.1 22.5 + - + +
848A ASN* 4.7 7.4 - - - +
851A PHE* 1.3 87.0 - - + +
853A PRO* 1.3 68.2 - - + +
933A LEU* 4.2 20.2 - - + -
936A VAL* 4.2 25.4 - - + -
998A ARG* 3.2 9.7 - - - -
999A GLU* 3.7 27.5 - - + +
1002A ASN* 2.8 32.7 + - + +
1003A ALA* 3.4 36.6 - - + +
1006A PHE* 5.5 1.1 - - + -
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Residues in contact with PRO 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847A LEU 4.0 2.0 - - - +
848A ASN 4.0 8.3 - - - +
849A TYR* 3.7 19.5 - - - +
850A ASP* 3.2 19.1 - - - +
852A LEU* 1.3 98.5 - - + +
854A ASN* 1.3 67.2 + - - +
871A PHE 4.4 2.4 - - - +
873A GLN* 4.1 15.9 + - + +
995A GLN* 3.0 28.1 + - - +
998A ARG* 3.3 14.9 + - - -
999A GLU* 3.6 20.2 - - + +
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Residues in contact with ASN 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A TYR 4.0 2.4 + - - -
850A ASP* 2.9 44.4 + - - +
853A PRO* 1.3 86.8 - - - +
855A TYR* 1.3 58.9 + - + +
866A ARG* 3.4 17.5 - - + +
867A THR* 2.7 40.9 + - + +
871A PHE 3.5 6.4 - - - +
872A SER* 4.5 5.5 + - - +
873A GLN* 3.0 49.5 + - - +
874A GLU* 5.7 0.8 + - - -
998A ARG* 4.1 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