Contacts of the helix formed by residues 892 - 898 (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 SER 892 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514B LYS* 4.1 0.5 + - - -
517B PHE* 5.0 0.2 - - - -
871B ILE* 3.8 19.2 - - - +
875B GLU* 3.3 18.8 - - - -
886B GLU* 4.4 8.7 - - - -
888B ASN 3.4 5.5 + - - -
889B LEU 2.7 22.1 + - - -
890B HIS 4.1 1.7 - - - +
891B LEU* 1.3 82.9 - - - +
893B THR* 1.3 62.5 + - - +
894B ALA* 3.4 3.7 + - - +
895B PHE* 2.9 21.1 + - - +
896B SER* 3.4 17.7 + - - -
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Residues in contact with THR 893 (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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513B TRP* 3.3 25.7 - - - -
514B LYS* 3.9 10.2 - - - +
875B GLU* 3.5 13.2 + - + +
880B LEU* 4.3 18.4 - - + -
891B LEU 3.7 1.2 + - - -
892B SER* 1.3 74.1 - - - +
894B ALA* 1.3 68.5 + - + +
896B SER* 2.9 19.5 + - - -
897B THR* 3.1 14.9 + - - +
1004B ILE* 4.5 5.2 - - - +
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Residues in contact with ALA 894 (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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871B ILE* 4.2 8.1 - - + -
874B ILE* 5.1 6.1 - - + -
875B GLU* 4.5 12.8 - - + +
892B SER* 3.2 6.1 - - - +
893B THR* 1.3 85.5 - - + +
895B PHE* 1.3 57.1 + - - +
897B THR* 3.0 13.5 - - - +
898B GLY 3.0 0.5 + - - -
899B THR* 3.0 39.8 + - - +
900B VAL* 3.7 18.8 + - + -
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Residues in contact with PHE 895 (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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494B THR* 2.8 64.1 - - + +
497B THR* 4.1 26.9 - - + -
498B SER* 4.9 2.5 - - - -
501B VAL* 5.4 0.7 - - + -
517B PHE* 4.2 4.7 - + - -
521B MET* 4.1 24.2 - - + -
889B LEU* 3.2 22.0 - - + +
890B HIS* 3.4 50.0 - - + -
892B SER* 2.9 19.9 + - - +
894B ALA* 1.3 76.5 - - - +
896B SER* 1.3 61.6 + - - +
898B GLY* 3.1 0.6 + - - -
900B VAL* 4.1 17.4 - - + +
901B PHE* 5.6 4.5 - + - -
902B SER 6.3 0.4 - - - -
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Residues in contact with SER 896 (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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494B THR* 5.1 0.4 - - - -
513B TRP* 3.6 19.8 - - - -
514B LYS* 4.3 0.6 + - - -
517B PHE* 3.2 46.7 - - - -
892B SER 3.4 4.4 + - - -
893B THR* 2.9 26.3 + - - -
895B PHE* 1.3 80.2 - - - +
897B THR* 1.3 60.7 + - - +
1004B ILE* 5.6 0.2 - - - +
1016B PHE* 3.5 3.0 - - - +
1017B VAL* 3.2 31.9 + - - +
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Residues in contact with THR 897 (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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491B GLY* 4.3 5.4 + - - -
494B THR* 4.7 0.6 + - - -
893B THR 3.1 15.7 + - - +
894B ALA* 3.0 27.4 - - - +
896B SER* 1.3 80.2 + - - +
898B GLY* 1.3 56.4 + - - +
899B THR* 3.3 24.6 - - + +
1001B TYR* 2.9 27.9 + - - -
1004B ILE* 5.7 4.3 - - - -
1014B LYS* 4.4 16.0 - - - +
1015B ARG 3.4 21.1 + - - -
1016B PHE* 4.5 1.5 - - - +
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Residues in contact with GLY 898 (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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491B GLY* 5.2 7.2 + - - -
493B CYS* 5.8 2.0 - - - +
494B THR* 3.2 29.6 - - - -
796B MET* 5.2 5.7 - - - +
861B ILE 4.3 2.4 - - - +
862B LEU* 3.7 16.1 - - - +
894B ALA 3.0 5.0 + - - -
895B PHE 3.1 3.7 + - - -
897B THR* 1.3 80.0 - - - +
899B THR* 1.3 64.1 + - - +
900B VAL 3.4 2.2 - - - -
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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
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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