Contacts of the helix formed by residues 1011 - 1016 (chain A) in PDB entry 1DJL
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 ASN1011 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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966A ASN* 3.1 44.4 + - - +
969A VAL* 3.5 8.5 + - - +
970A ASN* 3.5 19.6 - - - +
1009A VAL 3.8 0.4 + - - -
1010A ASP* 1.3 79.8 + - - +
1012A PRO* 1.3 70.6 - - - +
1013A ILE* 3.0 38.9 + - - +
1014A PHE* 3.2 32.4 + - + -
1015A TYR* 3.5 8.8 - - - -
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Residues in contact with PRO1012 (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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970A ASN* 3.3 18.6 - - - +
971A SER* 3.4 13.7 - - - +
972A ALA* 3.6 23.6 - - + +
975A GLU* 3.6 12.3 - - + +
976A ASP* 6.2 0.7 - - + -
1010A ASP* 3.7 4.5 - - - +
1011A ASN* 1.3 86.5 - - - +
1013A ILE* 1.3 61.8 + - - +
1014A PHE 3.0 1.2 + - - -
1015A TYR* 3.0 25.4 + - + +
1016A LYS* 3.6 13.2 + - + +
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Residues in contact with ILE1013 (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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962A VAL* 4.9 0.4 - - + -
969A VAL* 3.6 40.4 - - + +
971A SER* 3.5 21.3 - - - +
989A VAL* 4.0 13.2 - - + -
990A TRP* 3.9 15.5 - - + -
995A VAL* 4.8 3.6 - - + -
997A VAL* 4.1 23.1 - - + -
1011A ASN* 3.0 22.7 + - - +
1012A PRO* 1.3 75.2 - - - +
1014A PHE* 1.3 68.5 - - + +
1015A TYR 3.2 0.9 + - - -
1016A LYS* 3.4 17.4 + - + -
1019A THR* 2.8 35.7 + - - +
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Residues in contact with PHE1014 (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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866A HIS* 3.3 21.8 - - - +
867A THR 4.6 1.6 + - - -
966A ASN* 3.7 20.6 - - - -
969A VAL* 6.2 0.4 - - + -
997A VAL* 4.1 9.6 - - + -
999A LYS* 3.8 24.9 - - + -
1002A LEU* 3.8 39.5 - - + -
1003A GLY 4.0 6.3 - - - -
1010A ASP* 4.2 2.9 - - - -
1011A ASN* 3.5 36.1 - - + +
1012A PRO 3.0 1.2 + - - -
1013A ILE* 1.3 87.5 - - + +
1015A TYR* 1.3 79.2 + - + +
1016A LYS 3.6 0.4 + - - -
1019A THR* 4.3 6.5 - - - +
1021A MET* 3.8 33.5 - - + +
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Residues in contact with TYR1015 (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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864A GLY* 4.0 16.8 - - - -
865A THR 3.3 41.4 - - - +
866A HIS* 4.2 2.0 - - + +
1002A LEU* 3.9 28.0 + - + +
1010A ASP* 3.0 36.0 + - - -
1011A ASN 3.5 16.6 - - - -
1012A PRO* 3.0 19.0 + - + +
1014A PHE* 1.3 87.5 - - + +
1016A LYS* 1.3 63.2 + - - +
1017A PRO* 3.8 2.9 - - - +
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Residues in contact with LYS1016 (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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971A SER* 3.5 21.8 - - - -
975A GLU* 2.8 30.2 + - - -
990A TRP* 3.6 37.2 - - + -
1012A PRO* 3.6 11.7 - - + +
1013A ILE* 3.4 19.5 + - + +
1014A PHE 4.9 0.2 - - - +
1015A TYR* 1.3 79.7 - - - +
1017A PRO* 1.3 75.5 - - + +
1018A ASN* 3.6 13.7 - - - +
1019A THR* 3.0 22.4 + - - +
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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