Contacts of the helix formed by residues 803 - 811 (chain B) in PDB entry 2R4B
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 CYS 803 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B GW7 1.6 64.8 - - + -
801B HIS 4.4 0.2 - - - +
802B GLY* 1.3 73.6 - - - -
804B LEU* 1.3 62.4 + - - +
805B LEU* 3.4 4.5 - - + +
806B GLU* 3.0 33.6 + - + +
807B TYR* 3.1 11.8 + - - +
847B ARG* 4.0 17.9 - - - +
849B VAL 3.5 8.7 - - - +
850B LEU* 3.7 7.6 - - - -
851B VAL* 4.3 0.4 - - - -
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Residues in contact with LEU 804 (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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802B GLY 4.0 0.8 + - - -
803B CYS* 1.3 69.2 - - - +
805B LEU* 1.3 60.4 + - - +
807B TYR* 3.0 3.3 + - + +
808B VAL* 2.9 35.5 + - + +
823B TRP* 3.8 35.9 - - + -
827B ILE* 4.1 6.7 - - + -
846B ALA* 3.9 4.7 - - + +
849B VAL* 2.6 46.8 + - + +
851B VAL* 3.7 24.4 - - + +
857B VAL* 4.0 10.3 - - + -
913B LEU* 3.5 37.7 - - + -
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Residues in contact with LEU 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B CYS* 3.4 2.0 - - + -
804B LEU* 1.3 76.2 - - - +
806B GLU* 1.3 60.7 + - - +
808B VAL* 3.4 19.0 - - + +
809B HIS* 3.5 11.8 + - - +
846B ALA* 3.5 13.9 + - + +
847B ARG* 4.0 33.2 - - + +
886B TRP* 6.2 0.2 - - + -
912B GLU* 3.6 25.8 - - + +
917B GLY* 3.7 29.6 - - - +
918B GLY 5.0 1.3 - - - +
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Residues in contact with GLU 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GW7 3.7 12.4 - - - +
801B HIS 4.8 1.1 - - - +
802B GLY* 3.8 7.3 - - - -
803B CYS* 3.0 44.3 + - + +
805B LEU* 1.3 77.5 - - - +
807B TYR* 1.3 59.9 + - + +
809B HIS* 3.5 4.9 + - - +
810B GLU* 3.0 50.3 + - + +
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Residues in contact with TYR 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B HIS* 3.7 43.2 + - + +
803B CYS 3.1 17.3 + - - +
804B LEU* 3.0 5.7 + - + +
806B GLU* 1.3 77.4 - - - +
808B VAL* 1.3 57.6 + - - +
810B GLU* 4.8 1.8 - - - -
811B HIS* 3.0 70.4 + + + +
815B ILE* 4.3 11.9 - - + +
823B TRP* 4.1 31.0 - + - -
851B VAL* 4.0 17.3 - - + -
854B PRO* 3.5 34.4 - - + +
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Residues in contact with VAL 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B LEU* 2.9 27.8 + - + +
805B LEU* 3.4 16.4 - - + +
807B TYR* 1.3 72.9 - - - +
809B HIS* 1.3 59.2 + - - +
812B LYS* 3.1 28.9 + - - +
815B ILE* 4.8 7.2 - - + -
820B LEU* 4.7 7.4 - - + -
823B TRP* 3.3 37.0 - - + -
912B GLU 4.8 0.2 - - - +
913B LEU* 4.2 17.5 - - + +
916B PHE* 3.9 16.1 - - + +
917B GLY* 3.6 21.1 - - - +
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Residues in contact with HIS 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B LEU 3.5 13.2 + - - +
806B GLU* 3.5 7.0 + - - +
807B TYR 3.4 0.4 - - - -
808B VAL* 1.3 79.8 - - - +
810B GLU* 1.3 68.0 + - + +
812B LYS* 3.9 13.0 - - - +
916B PHE 3.8 19.2 + - - +
917B GLY* 4.2 12.1 + - - -
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Residues in contact with GLU 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B GLU* 3.0 39.4 + - + +
807B TYR* 4.8 0.9 - - - -
809B HIS* 1.3 85.6 - - + +
811B HIS* 1.3 75.1 + - + +
812B LYS* 3.3 2.2 + - - +
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Residues in contact with HIS 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B TYR* 3.0 63.6 + + + +
808B VAL 3.9 0.4 - - - -
810B GLU* 1.3 91.7 - - + +
812B LYS* 1.3 62.9 + - - +
813B ASP 3.3 2.9 - - - -
814B ASN* 2.8 38.2 + - + +
815B ILE* 3.2 29.2 + - + +
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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
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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