Contacts of the helix formed by residues 916 - 929 (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 ASN 916 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527B THR* 2.9 35.6 - - - +
912B THR* 2.8 20.7 + - + +
915B TYR* 1.3 80.6 - - + +
917B TYR* 1.3 65.3 + - - +
918B HIS* 3.4 24.9 + - - +
919B VAL* 3.0 40.5 + - + +
920B LEU 4.1 1.4 + - - -
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Residues in contact with TYR 917 (chain B).
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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444B ARG* 3.6 14.6 - - - +
466B TRP* 4.1 20.0 + - + -
467B ASP* 4.3 10.3 + - - -
469B GLY* 4.7 11.0 - - - -
470B ASP 5.8 0.4 - - - -
471B ASN* 3.2 32.1 - - - +
567B PHE* 5.0 5.9 + - - +
913B ALA* 3.3 23.2 + - - +
914B PHE 4.5 1.5 + - - -
915B TYR 4.2 0.2 - - - -
916B ASN* 1.3 72.0 + - - +
918B HIS* 1.3 87.6 + + - +
920B LEU* 3.0 7.8 + - - +
921B GLU* 3.0 54.7 + - + +
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Residues in contact with HIS 918 (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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527B THR* 4.6 2.0 - - + +
558B GLU* 3.3 11.3 + - - -
567B PHE* 3.4 41.3 - + + -
585B LEU* 3.6 19.0 - - + +
587B PHE* 3.8 22.4 - - + -
916B ASN* 3.2 21.2 - - - +
917B TYR* 1.3 104.6 + + - +
919B VAL* 1.3 64.3 + - - +
921B GLU* 2.6 31.5 + - - +
922B LEU* 3.0 23.2 + - - +
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Residues in contact with VAL 919 (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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500B PHE* 4.1 24.3 - - + -
525B ILE* 4.1 31.0 - - + +
527B THR* 5.0 4.0 - - + +
587B PHE* 5.2 2.5 - - + -
912B THR* 4.6 18.6 - - + -
916B ASN* 3.0 38.4 - - + +
917B TYR 3.1 0.4 - - - -
918B HIS* 1.3 79.0 - - - +
920B LEU* 1.3 57.3 + - - +
922B LEU* 3.4 5.2 + - - +
923B LEU* 3.0 27.0 + - + +
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Residues in contact with LEU 920 (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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471B ASN* 4.0 22.2 - - - +
472B ILE 4.7 7.9 - - - +
473B ILE* 4.0 20.6 - - + -
478B LEU* 5.4 6.7 - - + -
909B LEU* 4.7 19.7 - - + -
912B THR* 5.7 1.5 - - + +
913B ALA* 3.7 32.3 - - + +
916B ASN 4.1 0.8 + - - -
917B TYR* 3.0 13.9 + - - +
919B VAL* 1.3 76.5 - - - +
921B GLU* 1.3 65.0 + - + +
923B LEU* 3.2 10.0 + - + +
924B GLN* 2.7 56.6 + - + +
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Residues in contact with GLU 921 (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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471B ASN* 5.7 1.1 - - - +
558B GLU* 2.6 29.9 - - - +
567B PHE 5.2 2.9 - - - +
570B LEU* 4.4 11.3 - - + +
917B TYR* 3.0 37.4 + - + +
918B HIS* 2.6 30.4 + - - +
920B LEU* 1.3 85.1 - - + +
922B LEU* 1.3 63.5 + - - +
924B GLN* 3.2 12.6 + - - +
925B MET* 3.3 13.5 + - - +
931B VAL* 4.4 7.7 - - + +
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Residues in contact with LEU 922 (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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525B ILE* 3.2 46.0 - - + -
555B ILE* 4.6 6.1 - - + -
556B ALA* 4.4 18.4 - - + -
570B LEU* 4.1 25.5 - - + +
572B LEU* 5.3 2.7 - - + -
587B PHE* 4.2 21.3 - - + -
918B HIS 3.0 8.6 + - - +
919B VAL* 3.7 6.5 - - - +
921B GLU* 1.3 77.1 - - - +
923B LEU* 1.3 66.3 + - - +
925B MET* 2.9 16.3 + - - +
926B LEU* 3.0 46.8 + - + +
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Residues in contact with LEU 923 (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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478B LEU* 4.4 15.7 - - + -
482B PHE* 3.5 15.7 - - + -
496B LEU* 6.3 0.4 - - + -
500B PHE* 3.6 38.6 - - + -
906B LEU* 4.6 10.5 - - + -
909B LEU* 4.0 27.1 - - + -
919B VAL* 3.0 17.7 + - + +
920B LEU* 3.5 8.5 - - + +
922B LEU* 1.3 77.0 - - - +
924B GLN* 1.3 66.9 + - - +
926B LEU* 3.3 6.0 + - + +
927B VAL* 3.0 46.7 + - + +
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Residues in contact with GLN 924 (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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455B LYS* 3.8 23.1 + - - +
472B ILE 5.1 2.9 - - - +
477B GLU* 3.9 16.0 + - - +
478B LEU* 4.7 13.2 - - + -
920B LEU* 2.7 39.8 + - + +
921B GLU* 3.3 7.6 - - - +
923B LEU* 1.3 76.2 - - - +
925B MET* 1.3 52.6 + - - +
928B THR* 2.5 49.1 + - + +
930B GLY 4.3 4.4 + - - -
931B VAL* 3.6 37.3 - - + +
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Residues in contact with MET 925 (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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570B LEU* 3.0 39.3 - - + +
572B LEU* 4.2 29.6 - - + +
921B GLU 3.3 3.9 + - - +
922B LEU* 2.9 15.4 + - - +
924B GLN* 1.3 77.2 - - - +
926B LEU* 1.3 77.4 + - + +
928B THR* 4.0 0.2 - - - -
929B GLY* 2.7 31.0 + - - -
930B GLY* 3.9 15.9 - - - +
931B VAL* 4.0 18.2 - - + -
960B ARG* 6.2 4.7 - - + -
961B CYS 5.6 2.5 - - - +
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Residues in contact with LEU 926 (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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485B GLN* 3.6 18.8 + - - +
496B LEU* 4.0 29.3 - - + +
499B LEU* 5.2 4.5 - - + -
500B PHE* 5.6 2.9 - - + -
525B ILE* 4.6 10.8 - - + -
555B ILE* 5.2 7.9 - - + -
572B LEU* 4.9 13.7 - - + -
922B LEU* 3.0 56.0 + - + +
923B LEU* 3.8 7.0 - - + +
925B MET* 1.3 93.8 - - + +
927B VAL* 1.3 64.1 + - + +
929B GLY* 4.2 1.0 + - - -
963B LEU* 4.7 17.2 - - + +
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Residues in contact with VAL 927 (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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478B LEU* 3.7 15.7 - - + +
481B GLY* 3.2 34.7 - - - +
482B PHE* 3.5 30.3 - - + +
485B GLN* 3.0 29.1 + - - +
496B LEU* 4.5 8.7 - - + -
737B PRO* 3.9 4.2 - - - +
923B LEU* 3.0 38.9 + - + +
924B GLN* 4.1 0.7 - - - +
926B LEU* 1.3 79.7 - - + +
928B THR* 1.3 67.7 + - + +
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Residues in contact with THR 928 (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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477B GLU* 4.1 36.3 - - + +
478B LEU* 4.4 6.7 - - + -
481B GLY* 5.3 0.4 - - - -
485B GLN* 4.9 0.2 - - - -
733B ASN 6.0 0.2 - - - +
736B MET* 4.6 10.2 - - - +
737B PRO* 3.9 29.2 - - + +
740B ALA* 6.0 0.2 - - - +
924B GLN* 2.5 36.2 + - + +
927B VAL* 1.3 83.7 - - + +
929B GLY* 1.3 58.3 + - - +
930B GLY 3.0 22.2 + - - -
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Residues in contact with GLY 929 (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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485B GLN* 4.8 4.0 - - - +
688B MET* 4.9 4.3 - - - +
737B PRO* 5.6 1.1 - - - -
740B ALA* 5.0 10.2 - - - +
925B MET* 2.7 27.6 + - - -
926B LEU 4.2 2.4 + - - -
927B VAL 3.5 1.6 + - - -
928B THR* 1.3 72.5 - - - +
930B GLY* 1.3 56.1 + - - +
960B ARG* 3.8 27.5 + - - -
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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