Contacts of the helix formed by residues 908 - 916 (chain A) 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 908 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A ASN* 3.8 31.6 + - - +
905A PHE 3.2 16.6 + - - -
907A ASP* 1.3 78.3 - - - +
909A LEU* 1.3 64.1 + - - +
910A LEU 3.2 0.2 - - - -
911A ALA* 2.9 21.4 + - - +
912A THR* 3.4 14.3 + - - -
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Residues in contact with LEU 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A ILE* 4.0 14.1 - - + -
475A PHE* 3.9 20.4 - - + -
478A LEU* 3.3 31.2 - - + -
500A PHE* 6.2 1.3 - - + -
906A LEU* 3.0 29.7 + - + +
907A ASP 3.1 0.8 - - - -
908A SER* 1.3 78.5 + - - +
910A LEU* 1.3 56.3 + - - +
912A THR* 3.4 17.8 - - + +
913A ALA* 2.8 29.8 + - - +
920A LEU* 4.7 16.4 - - + -
923A LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PHE* 5.2 9.2 - - + -
412A LEU* 4.5 23.0 - - + +
414A ILE* 6.5 1.6 - - + -
446A ILE* 4.9 5.1 - - + +
473A ILE* 3.6 21.6 - - + +
475A PHE* 5.1 7.5 - - + -
907A ASP 4.0 8.1 + - - +
908A SER 2.9 4.2 + - - +
909A LEU* 1.3 75.0 - - - +
911A ALA* 1.3 60.5 + - - +
913A ALA* 3.7 2.6 + - - +
914A PHE* 3.4 18.5 + - - +
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Residues in contact with ALA 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PHE* 4.5 15.2 - - + -
351A ASN* 3.7 19.5 - - + +
352A PHE* 4.2 13.0 - - + -
412A LEU* 5.9 0.2 - - - -
908A SER* 2.9 11.3 + - - +
910A LEU* 1.3 75.0 - - - +
912A THR* 1.3 60.5 + - - +
914A PHE* 3.2 7.4 + - - +
915A TYR* 3.0 47.4 + - + -
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Residues in contact with THR 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A PHE* 6.4 1.1 - - + -
908A SER* 3.4 18.9 + - - -
909A LEU* 3.1 23.8 + - + +
911A ALA* 1.3 77.7 - - - +
913A ALA* 1.3 57.4 + - - +
915A TYR* 4.6 3.8 - - - +
916A ASN* 2.9 39.5 + - + +
919A VAL* 4.5 23.3 - - + -
920A LEU* 5.7 2.2 - - + +
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Residues in contact with ALA 913 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ARG* 2.9 22.3 + - - -
446A ILE* 4.2 9.6 - - + +
471A ASN* 4.8 7.0 - - - +
473A ILE* 4.1 11.4 - - + -
909A LEU 2.8 16.1 + - - +
910A LEU 4.1 4.5 - - - +
911A ALA 3.4 0.2 - - - -
912A THR* 1.3 74.7 - - - +
914A PHE* 1.3 58.6 + - - +
916A ASN 4.3 0.2 - - - -
917A TYR* 3.2 19.6 - - - +
920A LEU* 3.7 32.0 - - + +
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Residues in contact with PHE 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ILE* 3.5 34.8 - - + -
362A THR* 4.8 10.5 - - + -
409A GLU* 4.2 14.6 - - + -
410A ALA* 3.6 27.6 - - + -
412A LEU* 5.2 9.4 - - + -
444A ARG* 3.0 37.8 + - - +
446A ILE* 5.1 6.5 - - + -
910A LEU 3.4 11.9 + - - +
911A ALA* 3.2 10.1 + - - +
912A THR 3.1 0.2 - - - -
913A ALA* 1.3 80.7 - - - +
915A TYR* 1.3 110.8 + + - +
916A ASN* 3.5 0.9 + - - -
917A TYR* 4.5 1.0 + - - -
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Residues in contact with TYR 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ILE* 6.1 0.5 - - - +
352A PHE* 4.8 17.0 + - + +
361A ASN* 5.4 4.3 - - + +
362A THR* 3.9 25.7 + - - -
911A ALA* 3.0 36.2 + - + +
912A THR* 4.3 2.9 - - - +
914A PHE* 1.3 108.6 - + - +
916A ASN* 1.3 63.0 + - + +
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Residues in contact with ASN 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A THR* 2.9 33.4 - - - +
912A THR* 2.9 19.7 + - + +
915A TYR* 1.3 80.4 - - + +
917A TYR* 1.3 65.2 + - - +
918A HIS* 3.5 24.1 + - - +
919A VAL* 2.9 44.1 + - + +
920A LEU 4.1 1.4 + - - -
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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