Contacts of the helix formed by residues 850 - 856 (chain i) in PDB entry 5JPQ
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 i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844i TYR* 5.4 0.4 - - - +
848i LEU 3.3 4.7 + - - +
849i LEU* 1.4 78.4 - - - +
851i TYR* 1.3 68.4 + - - +
852i HIS* 3.5 5.2 - - + +
853i VAL* 3.4 22.8 + - + +
854i VAL* 3.4 8.1 + - - +
22r LYS* 4.6 27.1 - - + +
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Residues in contact with TYR 851 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844i TYR* 6.2 1.8 - - - -
849i LEU 3.9 0.4 + - - -
850i ASP* 1.3 72.2 - - - +
852i HIS* 1.3 55.3 + - - +
854i VAL* 3.0 6.3 + - - +
855i LEU* 2.6 44.8 + - + +
879i LEU* 5.5 12.3 - - + -
880i GLN 6.0 0.9 - - - +
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Residues in contact with HIS 852 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749i GLN* 4.0 26.5 - - + -
850i ASP* 3.5 3.1 - - + +
851i TYR* 1.3 77.2 - - - +
853i VAL* 1.3 64.0 + - - +
855i LEU* 3.2 14.4 + - - -
856i ASP* 3.4 16.0 + - - +
859i PRO* 5.4 0.3 - - - +
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Residues in contact with VAL 853 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620i GLN 4.9 13.2 - - - +
621i GLN* 4.9 18.6 - - + +
849i LEU* 5.1 4.9 - - + -
850i ASP* 3.4 21.8 + - + +
851i TYR 3.1 0.4 - - - -
852i HIS* 1.3 81.2 - - - +
854i VAL* 1.3 59.0 + - - +
859i PRO* 4.4 7.6 - - - +
22r LYS* 6.1 2.2 - - - +
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Residues in contact with VAL 854 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840i ARG* 5.2 13.2 - - + +
841i LEU* 5.8 1.8 - - - -
844i TYR* 4.7 18.4 - - + -
849i LEU* 6.1 1.8 - - + -
850i ASP 3.4 6.4 + - - +
851i TYR* 3.0 6.7 + - - +
853i VAL* 1.3 80.1 - - - +
855i LEU* 1.3 57.8 + - - +
859i PRO* 3.0 16.7 - - - +
860i THR* 3.1 9.3 + - - +
861i ILE* 2.9 33.3 + - + +
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Residues in contact with LEU 855 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851i TYR* 2.6 33.5 + - + +
852i HIS* 3.2 3.2 + - - -
854i VAL* 1.3 72.9 - - - +
856i ASP* 1.4 74.5 + - - +
857i LEU 3.5 2.6 - - - +
858i MET* 3.4 3.8 + - - -
859i PRO 3.1 15.5 - - - -
861i ILE* 3.5 14.4 - - + -
862i ALA* 4.0 5.4 + - - +
878i GLY 5.2 8.1 - - - +
879i LEU* 5.5 5.4 - - + -
888i GLY* 6.2 1.6 - - - -
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Residues in contact with ASP 856 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785i ARG* 6.1 1.3 - - + -
788i SER* 3.5 27.4 - - - +
789i LEU* 3.8 9.4 - - + +
792i TYR* 4.0 14.8 - - + -
852i HIS* 3.4 15.0 + - - +
854i VAL 4.1 0.4 - - - -
855i LEU* 1.4 87.1 - - - +
857i LEU* 1.3 65.1 + - - +
859i PRO* 4.4 5.4 - - + +
888i GLY* 4.9 8.5 - - - +
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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