Contacts of the helix formed by residues 904 - 907 (chain B) in PDB entry 4DQL
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 PRO 904 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902B VAL* 3.8 6.1 - - + -
903B GLY* 1.3 89.0 - - - +
905B GLY* 1.3 67.0 + - - +
906B THR 3.3 0.3 + - - -
907B GLY* 2.9 15.8 + - - -
934B TYR 4.2 1.1 - - - +
936B GLY* 3.4 31.2 - - - +
976B VAL* 4.1 10.8 - - + -
1000B CYS 3.9 1.2 - - - +
1001B GLY* 4.7 2.6 - - - -
1002B ASP 5.3 1.6 + - - -
1006B MET* 3.7 46.2 - - + -
1102B NAP 4.0 19.6 + - - +
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Residues in contact with GLY 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B PRO* 1.3 71.3 - - - +
906B THR* 1.3 62.8 + - - -
907B GLY 3.1 1.4 + - - -
908B VAL* 3.1 14.9 + - - +
935B PHE* 3.4 18.8 - - - -
936B GLY 2.8 16.0 + - - -
937B CYS* 5.4 2.0 - - - -
943B ASP 5.8 0.7 - - - -
945B LEU* 3.6 10.3 - - - +
1102B NAP 3.4 25.7 - - - -
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Residues in contact with THR 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B THR* 3.8 25.6 - - + +
846B THR* 4.3 15.3 - - + -
848B SER* 3.7 27.7 - - - +
905B GLY* 1.3 69.4 - - - -
907B GLY* 1.3 54.9 + - - +
908B VAL 3.0 5.8 - - - -
909B ALA* 3.0 28.7 + - - +
945B LEU* 3.9 10.5 - - + -
1047B TRP* 3.4 25.8 + - - -
1101B FAD 4.2 7.4 + - - -
1102B NAP 2.7 25.8 + - - +
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Residues in contact with GLY 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B GLY* 3.5 7.6 - - - -
904B PRO 2.9 16.1 + - - -
906B THR* 1.3 77.8 + - - +
908B VAL* 1.3 59.9 + - - +
909B ALA 3.1 1.1 + - - -
910B PRO* 3.4 4.0 - - - +
911B PHE* 3.5 7.1 - - - -
1000B CYS* 3.2 39.0 - - - +
1001B GLY* 3.6 15.0 - - - -
1047B TRP* 4.2 2.5 - - - -
1102B NAP 4.5 0.2 + - - -
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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
------------------------------------------------------------
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