Contacts of the helix formed by residues 822 - 829 (chain B) in PDB entry 4YZ9
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 SER 822 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B HIS* 6.1 0.2 - - - -
753B TYR* 3.8 31.9 + - - -
757B ILE* 4.0 0.9 - - - -
820B ARG 3.8 1.2 + - - -
821B PRO* 1.3 76.5 - - - +
823B ALA* 1.3 61.6 + - - +
824B LYS* 3.9 5.9 + - - +
825B HIS* 2.8 54.2 + - - +
826B VAL* 2.9 11.5 + - - +
962B PHE* 5.6 0.3 - - - -
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Residues in contact with ALA 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B THR* 3.4 24.7 - - + +
676B LEU* 4.3 6.7 - - + -
677B ALA* 3.6 36.6 - - + +
680B HIS* 4.3 13.2 + - + +
757B ILE* 3.6 17.1 - - + +
822B SER* 1.3 73.6 - - - +
824B LYS* 1.3 61.1 + - - +
826B VAL* 3.2 4.0 + - - -
827B LEU* 3.2 19.2 + - - +
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Residues in contact with LYS 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A HIS* 4.9 8.5 + - - -
677B ALA* 4.0 28.9 - - + -
681B SER* 4.7 14.4 - - - -
822B SER* 3.1 7.1 + - - +
823B ALA* 1.3 74.0 - - - +
825B HIS* 1.3 66.3 + - - +
827B LEU* 3.5 20.4 + - + +
828B LYS* 3.6 16.3 + - - +
962B PHE* 3.9 36.0 - - + -
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Residues in contact with HIS 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B PRO* 3.7 20.6 - - + -
822B SER* 2.8 33.4 + - - +
824B LYS* 1.3 75.1 - - - +
826B VAL* 1.3 64.8 + - - +
828B LYS* 3.2 14.1 + - - +
829B HIS* 3.5 9.0 + - - +
945B TYR* 5.6 0.3 + - - -
962B PHE* 3.2 56.0 + + + -
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Residues in contact with VAL 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B THR* 3.9 13.5 - - + -
757B ILE* 4.9 4.0 - - + -
764B PHE* 3.9 11.9 - - + -
808B LEU* 3.9 24.2 - - + -
812B MET* 3.9 21.1 - - + -
821B PRO* 4.0 21.8 - - + +
822B SER 2.9 19.0 + - - +
823B ALA* 3.2 11.4 + - - +
825B HIS* 1.3 75.5 - - - +
827B LEU* 1.3 62.6 + - - +
829B HIS* 3.1 15.2 + - - +
832B PHE* 3.2 24.9 - - + -
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Residues in contact with LEU 827 (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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670B GLN* 3.8 42.2 - - + +
673B THR* 3.8 13.0 - - + -
674B SER* 4.1 24.0 - - - +
677B ALA* 4.4 8.7 - - + -
823B ALA 3.2 15.2 + - - +
824B LYS* 3.8 16.8 - - + +
825B HIS 3.2 0.8 - - - -
826B VAL* 1.3 77.1 - - - +
828B LYS* 1.3 63.3 + - + +
829B HIS 3.5 1.6 + - - +
832B PHE* 3.8 20.9 - - + +
833B TRP* 5.2 1.9 + - - -
837B LYS* 5.8 1.0 + - - -
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Residues in contact with LYS 828 (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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824B LYS 3.6 12.1 + - - +
825B HIS 3.2 10.3 + - - +
827B LEU* 1.3 76.0 - - + +
829B HIS* 1.3 65.5 + - - +
833B TRP* 3.0 16.5 + - - +
837B LYS* 5.7 3.0 - - - +
945B TYR* 3.6 4.6 + - - +
958B GLN 3.8 8.8 + - - -
959B PRO* 3.3 31.7 + - - +
960B TYR 3.4 19.4 - - - +
961B TYR* 3.3 28.5 - - - +
962B PHE* 4.2 15.9 - - + +
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Residues in contact with HIS 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B ILE* 3.5 24.2 - - + -
807B GLU* 3.4 25.0 - - + +
808B LEU* 3.5 48.1 + - + +
825B HIS 3.5 5.9 + - - +
826B VAL 3.1 18.9 + - - +
828B LYS* 1.3 80.8 - - - +
830B PRO* 1.3 89.7 - - + +
831B PHE* 3.0 15.5 + - + +
832B PHE* 3.3 10.6 + - - +
833B TRP* 3.2 9.5 + - - -
945B TYR* 4.2 6.4 - + - -
946B ARG* 3.5 21.9 + - - -
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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
------------------------------------------------------------
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