Contacts of the helix formed by residues 916 - 929 (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 ASN 916 (chain A).
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Specific contacts
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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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Residues in contact with TYR 917 (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* 3.6 13.9 - - - +
466A TRP* 4.1 19.5 + - + -
467A ASP* 4.3 10.4 + - - -
469A GLY* 4.7 10.8 - - - -
470A ASP 5.8 0.7 - - - -
471A ASN* 3.2 31.9 - - - +
567A PHE* 5.1 5.9 + - - -
913A ALA* 3.2 23.6 + - + +
914A PHE 4.5 1.7 + - - -
915A TYR 4.2 0.2 - - - -
916A ASN* 1.3 71.5 + - - +
918A HIS* 1.3 101.7 + + - +
919A VAL 3.1 2.0 - - - -
920A LEU* 3.0 9.1 + - + +
921A GLU* 3.0 22.6 + - + +
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Residues in contact with HIS 918 (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* 4.6 1.8 - - + +
558A GLU* 3.2 23.1 + - - -
567A PHE* 3.4 41.4 - + + -
585A LEU* 3.6 20.0 - - + -
587A PHE* 3.9 22.7 - - + -
916A ASN* 3.3 20.8 - - - +
917A TYR* 1.3 111.3 - + - +
919A VAL* 1.3 61.3 + - - +
921A GLU* 3.1 8.5 + - - +
922A LEU* 3.0 23.6 + - - +
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Residues in contact with VAL 919 (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* 4.0 25.6 - - + -
525A ILE* 4.1 30.5 - - + +
527A THR* 5.0 3.4 - - - +
587A PHE* 4.8 3.1 - - + -
912A THR* 4.5 18.2 - - + -
916A ASN* 2.9 42.2 - - + +
917A TYR 3.1 0.6 - - - -
918A HIS* 1.3 77.7 - - - +
920A LEU* 1.3 56.5 + - - +
922A LEU* 3.4 5.7 + - - +
923A LEU* 2.9 27.5 + - + +
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Residues in contact with LEU 920 (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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471A ASN* 4.1 22.4 - - - +
472A ILE 4.7 7.0 - - - +
473A ILE* 4.0 20.6 - - + -
478A LEU* 5.4 6.7 - - + -
909A LEU* 4.7 19.5 - - + -
912A THR* 5.7 1.9 - - + +
913A ALA* 3.7 31.9 - - + +
916A ASN 4.1 0.8 + - - +
917A TYR* 3.0 14.5 + - + +
919A VAL* 1.3 76.3 - - - +
921A GLU* 1.3 61.8 + - - +
923A LEU* 3.2 10.9 + - + +
924A GLN* 2.7 56.5 + - + +
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Residues in contact with GLU 921 (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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558A GLU* 4.6 6.3 - - - +
570A LEU* 4.3 15.8 - - + +
917A TYR* 3.0 17.1 + - + +
918A HIS* 3.1 15.9 + - - +
920A LEU* 1.3 85.0 - - + +
922A LEU* 1.3 64.0 + - - +
924A GLN* 3.3 11.4 + - - +
925A MET* 3.3 13.0 + - - +
931A VAL* 4.4 7.0 - - + +
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Residues in contact with LEU 922 (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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525A ILE* 3.2 45.3 - - + -
555A ILE* 4.6 6.7 - - + -
556A ALA* 4.4 18.4 - - + -
570A LEU* 4.1 27.5 - - + +
572A LEU* 5.2 2.5 - - + -
587A PHE* 4.1 21.1 - - + -
918A HIS 3.0 11.8 + - - +
919A VAL* 3.7 6.3 - - - +
921A GLU* 1.3 73.6 - - - +
923A LEU* 1.3 68.0 + - - +
925A MET* 2.9 17.5 + - - +
926A LEU* 3.0 41.4 + - + +
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Residues in contact with LEU 923 (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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478A LEU* 4.4 17.3 - - + -
482A PHE* 3.5 16.2 - - + -
496A LEU* 6.2 0.4 - - + -
500A PHE* 3.7 39.2 - - + -
906A LEU* 4.6 9.6 - - + -
909A LEU* 4.0 27.1 - - + -
919A VAL* 2.9 18.7 + - + +
920A LEU* 3.5 8.1 - - + +
922A LEU* 1.3 76.3 - - - +
924A GLN* 1.3 65.7 + - - +
926A LEU* 3.3 6.6 + - + +
927A VAL* 3.0 46.3 + - + +
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Residues in contact with GLN 924 (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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455A LYS* 3.8 22.8 + - - +
472A ILE 5.1 2.8 - - - +
477A GLU* 3.9 16.6 + - - +
478A LEU* 4.7 13.6 - - + +
920A LEU* 2.7 38.1 + - + +
921A GLU* 3.4 7.8 - - - +
922A LEU 3.0 0.2 + - - -
923A LEU* 1.3 77.1 - - - +
925A MET* 1.3 51.8 + - - +
927A VAL* 4.9 0.2 - - - -
928A THR* 2.5 48.7 + - + +
930A GLY 4.3 4.8 + - - -
931A VAL* 3.6 35.5 - - + +
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Residues in contact with MET 925 (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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570A LEU* 3.0 39.0 - - + +
572A LEU* 4.3 28.5 - - + +
921A GLU 3.3 4.4 + - - +
922A LEU* 2.9 15.8 + - - +
924A GLN* 1.3 76.1 - - - +
926A LEU* 1.3 78.4 + - + +
928A THR* 4.0 0.2 - - - -
929A GLY* 2.8 31.5 + - - -
930A GLY* 4.0 15.0 - - - +
931A VAL* 3.9 18.4 - - + +
960A ARG* 6.2 4.5 - - + -
961A CYS 5.6 2.5 - - - +
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Residues in contact with LEU 926 (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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485A GLN* 3.5 19.2 + - - +
496A LEU* 4.1 29.1 - - + +
499A LEU* 5.2 4.5 - - + -
500A PHE* 5.6 2.7 - - + -
525A ILE* 4.6 11.2 - - + -
555A ILE* 5.2 7.2 - - + -
572A LEU* 4.9 12.8 - - + -
922A LEU* 3.0 54.5 + - + +
923A LEU* 3.8 9.6 - - + +
925A MET* 1.3 94.2 - - + +
927A VAL* 1.3 64.5 + - + +
929A GLY* 4.2 0.9 + - - -
963A LEU* 4.7 15.8 - - + +
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Residues in contact with VAL 927 (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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478A LEU* 3.7 15.9 - - + +
481A GLY* 3.2 34.5 - - - +
482A PHE* 3.5 31.9 - - + +
485A GLN* 2.9 29.0 + - - +
496A LEU* 4.5 9.2 - - + -
737A PRO* 3.9 4.0 - - - +
923A LEU* 3.0 37.2 + - + +
924A GLN* 4.1 1.3 - - - +
926A LEU* 1.3 78.8 - - + +
928A THR* 1.3 67.5 + - + +
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Residues in contact with THR 928 (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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477A GLU* 4.1 36.1 - - + +
478A LEU* 4.4 6.7 - - + -
481A GLY* 5.3 0.7 - - - -
485A GLN* 4.9 0.2 - - - -
736A MET* 4.6 9.9 - - - +
737A PRO* 3.8 29.3 - - + +
740A ALA* 5.9 0.2 - - - +
924A GLN* 2.5 35.2 + - + +
927A VAL* 1.3 84.9 - - + +
929A GLY* 1.3 59.5 + - - +
930A GLY 3.0 21.7 + - - -
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Residues in contact with GLY 929 (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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485A GLN* 4.8 4.0 - - - +
688A MET* 4.8 4.5 - - - +
737A PRO* 5.5 0.7 - - - -
740A ALA* 4.9 10.3 - - - +
925A MET* 2.8 27.3 + - - -
926A LEU 4.2 2.1 + - - -
927A VAL 3.5 1.6 - - - -
928A THR* 1.3 73.8 - - - +
930A GLY* 1.3 55.3 + - - +
960A ARG* 3.7 27.3 + - - -
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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