Contacts of the helix formed by residues 814 - 826 (chain B) in PDB entry 4HPF
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 814 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801B SER* 3.4 15.8 + - - -
813B VAL* 1.3 80.4 - - - +
815B THR* 1.3 67.1 + - - +
816B GLU 3.2 2.5 - - - -
817B ALA* 3.1 9.6 + - + +
818B ILE* 2.9 31.0 + - + +
864B GLU 4.0 1.3 - - - +
865B LEU* 3.7 12.7 - - + +
866B LYS* 3.2 22.4 + - - +
867B ASN* 3.1 28.5 + - - +
870B ASN* 3.1 27.8 + - + +
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Residues in contact with THR 815 (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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812B LEU* 3.8 36.6 + - + +
813B VAL 3.5 1.7 + - - +
814B ASP* 1.3 75.8 - - - +
816B GLU* 1.3 71.4 + - - +
818B ILE* 3.0 12.8 + - + +
819B MET* 2.8 40.2 + - - +
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Residues in contact with GLU 816 (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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721B PHE* 4.2 37.3 - - + +
781B LEU* 4.0 13.2 - - + +
802B PRO* 3.6 27.3 - - + +
813B VAL 5.4 3.5 - - - +
814B ASP 3.2 0.6 - - - -
815B THR* 1.3 87.6 + - - +
817B ALA* 1.3 63.7 + - - +
819B MET* 3.1 7.9 + - - +
820B ALA* 3.0 24.8 + - - +
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Residues in contact with ALA 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B PHE* 4.7 3.5 - - + -
799B VAL* 4.1 14.5 - - + +
801B SER* 4.0 13.9 - - - +
802B PRO* 6.1 0.4 - - + -
814B ASP* 3.1 16.8 + - + +
816B GLU* 1.3 78.6 - - - +
818B ILE* 1.3 59.4 + - - +
820B ALA* 3.7 1.9 + - - +
821B THR* 2.9 29.3 + - - -
863B THR* 3.7 11.9 - - + +
864B GLU 3.6 23.6 - - - +
865B LEU* 4.9 2.0 - - + -
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Residues in contact with ILE 818 (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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814B ASP* 2.9 34.0 + - + +
815B THR* 3.4 11.2 - - + +
817B ALA* 1.3 75.4 - - + +
819B MET* 1.3 66.4 + - + +
821B THR* 3.4 7.2 + - - -
822B LEU* 3.0 25.2 + - + +
863B THR* 5.5 0.2 - - - -
865B LEU* 5.7 2.5 - - + -
870B ASN* 4.6 9.0 - - + +
873B PHE* 3.8 41.3 - - + -
874B ILE* 4.8 14.8 - - + -
877B LEU* 3.8 20.1 - - + +
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Residues in contact with MET 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B LEU* 3.4 23.7 - - + +
815B THR* 2.8 30.5 + - - +
816B GLU* 3.7 2.9 - - - +
818B ILE* 1.3 75.6 - - + +
820B ALA* 1.3 66.2 + - - +
822B LEU* 3.2 23.8 + - + +
823B THR* 3.1 29.2 + - + +
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Residues in contact with ALA 820 (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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721B PHE* 4.2 11.2 - - + -
780B ALA* 4.8 9.6 - - + -
781B LEU* 3.4 9.9 - - + +
799B VAL* 3.5 31.4 - - + -
816B GLU 3.0 13.2 + - - +
819B MET* 1.3 76.7 - - - +
821B THR* 1.3 64.9 + - - +
822B LEU 2.9 0.7 + - - -
823B THR* 3.0 8.0 + - - -
824B ILE* 2.9 33.3 + - + +
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Residues in contact with THR 821 (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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799B VAL* 4.5 1.9 - - - +
817B ALA 2.9 16.3 + - - -
818B ILE* 3.7 7.4 - - - -
820B ALA* 1.3 77.1 - - - +
822B LEU* 1.3 61.5 + - - +
824B ILE* 4.9 0.4 - - - +
825B GLY* 3.1 20.0 + - - -
861B ILE* 4.0 23.1 - - + +
863B THR* 2.7 33.1 + - - +
874B ILE* 4.6 22.0 - - + -
877B LEU* 4.6 10.2 - - + +
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Residues in contact with LEU 822 (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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818B ILE* 3.0 14.6 + - + +
819B MET* 3.3 31.2 - - + +
820B ALA 3.0 0.8 - - - -
821B THR* 1.3 76.8 - - - +
823B THR* 1.3 61.0 + - + +
825B GLY 3.9 0.2 - - - -
826B SER* 2.7 43.0 + - - +
877B LEU* 3.7 35.9 - - + +
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Residues in contact with THR 823 (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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780B ALA 3.8 13.5 + - - -
781B LEU* 3.6 23.5 + - + +
783B SER* 5.1 8.2 - - - -
786B LEU* 4.3 7.3 - - - +
819B MET* 3.1 13.4 + - + +
820B ALA* 3.0 15.3 + - - -
822B LEU* 1.3 84.9 - - + +
824B ILE* 1.3 59.4 + - - +
826B SER* 2.9 26.6 - - - +
827B LEU* 3.5 9.8 - - - +
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Residues in contact with ILE 824 (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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719B CYS* 4.5 7.0 - - - -
780B ALA* 5.3 0.9 - - + +
786B LEU* 3.8 21.1 - - + -
791B ILE* 4.2 6.7 - - + -
797B CYS* 3.5 29.6 - - - -
799B VAL* 4.1 11.7 - - + -
820B ALA* 2.9 22.2 + - + +
823B THR* 1.3 79.9 + - - +
825B GLY* 1.3 64.8 + - - +
826B SER 3.2 1.2 + - - -
827B LEU* 3.3 24.7 - - + +
859B VAL* 4.1 32.8 + - + +
861B ILE* 3.5 29.8 - - + -
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Residues in contact with GLY 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B THR* 3.1 17.8 + - - -
822B LEU 3.9 0.4 - - - -
824B ILE* 1.3 81.6 - - - +
826B SER* 1.3 56.8 + - - +
827B LEU 3.6 2.5 + - - -
858B LYS* 5.3 11.3 - - - +
859B VAL 5.8 4.7 - - - -
861B ILE* 4.7 3.3 - - - +
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Residues in contact with SER 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B LEU* 2.7 34.3 + - - +
823B THR* 2.9 14.8 + - - +
825B GLY* 1.3 76.9 - - - +
827B LEU* 1.3 59.6 + - - +
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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