Contacts of the helix formed by residues 909 - 920 (chain A) in PDB entry 5B16
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 909 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A GLY 4.9 3.6 + - - -
529A GLN 5.1 0.2 + - - -
535A LEU* 3.4 26.5 - - - +
548A ARG* 5.4 9.6 + - - +
660A TYR 5.3 0.2 - - - +
661A ASP* 3.4 46.1 + - + +
908A MET* 1.3 80.7 - - - +
910A PRO* 1.3 70.8 - - + +
911A ASP* 3.1 16.1 + - - +
912A HIS* 3.3 22.0 + - + +
913A ALA* 3.1 19.8 + - - +
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Residues in contact with PRO 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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530A MET* 4.2 17.3 - - + -
535A LEU* 4.3 10.3 - - + -
548A ARG* 4.4 19.1 - - - +
904A LEU* 4.5 32.8 - - + -
906A PHE* 5.5 4.0 - - + -
908A MET 3.4 8.5 - - - +
909A ASN* 1.3 84.2 - - + +
911A ASP* 1.3 61.3 + - - +
913A ALA* 3.3 7.5 + - + +
914A ARG* 2.9 40.8 + - - +
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Residues in contact with ASP 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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529A GLN 3.0 14.9 - - - +
530A MET* 3.3 30.4 - - + +
531A ASN* 3.2 32.5 - - - +
535A LEU* 3.8 1.3 - - - +
909A ASN* 3.1 18.2 + - - +
910A PRO* 1.3 76.9 - - - +
912A HIS* 1.3 93.4 + - - -
914A ARG* 3.9 3.1 - - - +
915A ASN* 2.9 36.5 + - - +
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Residues in contact with HIS 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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525A ASN* 3.3 28.9 + - + +
526A ASP 3.3 28.2 + - - -
529A GLN 3.8 3.1 - - - -
658A GLU* 3.2 23.6 - - + +
659A LEU* 3.9 3.3 - - + +
660A TYR* 3.7 19.6 + - + +
661A ASP* 3.4 19.9 + - - -
908A MET* 4.2 13.9 - - - -
909A ASN* 3.3 20.2 + - + +
911A ASP* 1.3 110.5 + - - +
913A ALA* 1.3 57.5 + - - +
916A SER* 2.9 36.0 + - - -
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Residues in contact with ALA 913 (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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861A MET* 3.6 18.7 - - + +
904A LEU* 6.0 0.9 - - + -
906A PHE* 4.1 31.2 - - + -
908A MET* 4.6 6.4 - - + -
909A ASN 3.1 13.4 + - - +
910A PRO* 3.5 12.6 - - + +
912A HIS* 1.3 78.0 - - - +
914A ARG* 1.3 59.4 + - + +
916A SER* 3.8 0.5 - - - -
917A LEU* 2.9 37.2 + - + +
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Residues in contact with ARG 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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531A ASN* 5.9 1.6 - - - +
622A ARG* 3.6 38.3 + - - +
903A HIS* 3.9 15.6 + - - -
904A LEU* 3.3 40.6 - - + +
910A PRO* 2.9 25.7 + - - +
911A ASP* 4.1 3.4 - - - +
913A ALA* 1.3 74.4 - - + +
915A ASN* 1.3 59.9 + - - +
917A LEU* 3.2 9.3 + - + +
918A SER* 2.9 32.2 + - - -
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Residues in contact with ASN 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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523A TRP* 3.3 36.5 + - - +
524A TYR 4.0 7.3 + - - -
525A ASN* 3.0 29.4 + - - +
531A ASN* 3.7 20.7 + - - +
911A ASP* 2.9 33.4 + - - +
912A HIS 3.9 1.1 - - - +
914A ARG* 1.3 79.1 - - - +
916A SER* 1.3 58.0 + - - +
918A SER* 3.2 3.7 + - - -
919A ASN* 2.8 39.0 + - - +
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Residues in contact with SER 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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525A ASN* 3.7 9.9 + - - -
657A LEU* 4.6 3.7 - - - +
658A GLU* 4.3 8.0 + - - +
659A LEU* 3.4 23.8 - - - +
861A MET* 4.1 13.8 - - - +
912A HIS 2.9 20.3 + - - -
913A ALA 3.9 2.2 - - - -
915A ASN* 1.3 76.1 - - - +
917A LEU* 1.3 59.3 + - - +
919A ASN* 4.7 2.2 - - - +
920A CYS* 3.1 40.3 + - - -
921A GLY* 3.2 6.1 + - - -
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Residues in contact with LEU 917 (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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622A ARG* 3.8 32.1 - - + +
623A PHE* 4.7 13.2 - - + -
858A GLN* 3.3 34.4 - - - +
861A MET* 3.7 28.7 - - + -
862A MET* 6.5 0.4 - - - -
906A PHE* 4.1 22.4 - - + -
913A ALA* 2.9 27.6 + - + +
914A ARG* 3.6 9.0 - - + +
916A SER* 1.3 77.2 - - - +
918A SER* 1.3 58.8 + - - +
921A GLY* 3.3 21.7 + - - -
922A ILE 4.5 3.5 + - - +
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Residues in contact with SER 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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522A LEU* 5.8 0.5 - - - +
523A TRP* 6.5 0.9 - - - -
914A ARG 2.9 16.1 + - - -
915A ASN* 3.2 4.7 + - - -
917A LEU* 1.3 77.6 - - - +
919A ASN* 1.3 68.4 + - - +
921A GLY 4.7 0.7 - - - -
923A ARG* 5.6 3.6 + - - -
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Residues in contact with ASN 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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522A LEU* 3.6 29.8 - - + +
523A TRP* 3.0 36.5 + - - +
524A TYR* 5.3 0.2 - - - +
525A ASN* 5.2 0.2 + - - -
915A ASN* 2.8 28.6 + - - +
916A SER* 4.6 3.3 - - - +
918A SER* 1.3 87.7 + - - +
920A CYS* 1.3 64.7 + - + +
921A GLY 3.8 0.2 - - - -
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Residues in contact with CYS 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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656A ILE* 5.1 6.7 - - + -
657A LEU* 3.7 35.7 - - + -
854A SER* 4.4 6.2 + - - -
857A CYS* 3.2 30.0 - - - +
916A SER* 3.1 22.8 + - - -
919A ASN* 1.3 79.9 - - + +
921A GLY* 1.3 66.4 + - - +
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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