Contacts of the helix formed by residues 971 - 976 (chain B) 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 SER 971 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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969B VAL 3.4 4.9 + - - -
970B ASN* 1.3 68.5 + - - +
972B ALA* 1.3 55.3 + - - +
973B ALA 3.0 5.8 - - - -
974B GLN* 2.9 6.5 + - - +
975B GLU* 2.8 58.5 + - - +
990B TRP* 3.6 37.2 - - - -
1011B ASN* 3.8 2.8 + - - -
1012B PRO* 3.4 16.6 - - - +
1013B ILE* 3.5 10.6 - - - +
1016B LYS* 3.6 2.8 - - - -
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Residues in contact with ALA 972 (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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970B ASN* 2.8 19.8 + - - +
971B SER* 1.3 79.4 + - - +
973B ALA* 1.3 61.0 + - - +
974B GLN 3.1 0.2 - - - -
975B GLU* 3.7 4.9 - - - +
976B ASP* 3.1 40.6 + - + +
979B SER* 3.8 15.8 - - - +
981B ILE* 4.3 3.4 - - + -
1009B VAL* 6.1 1.3 - - + -
1010B ASP 4.4 5.6 - - - +
1012B PRO* 3.8 18.5 - - + +
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Residues in contact with ALA 973 (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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970B ASN 3.2 14.6 + - - +
971B SER 3.0 0.6 - - - -
972B ALA* 1.3 79.9 - - - +
974B GLN* 1.3 60.1 + - + +
976B ASP 5.1 0.3 - - - +
981B ILE* 3.4 35.5 - - + +
982B ALA* 3.5 3.3 - - - +
983B GLY* 2.8 27.0 + - - -
984B MET* 3.4 20.9 - - + +
986B VAL* 3.8 11.7 - - + -
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Residues in contact with GLN 974 (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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971B SER 2.9 7.6 + - - +
973B ALA* 1.3 82.9 - - + +
975B GLU* 1.3 63.9 + - + +
976B ASP 3.7 1.1 - - - -
984B MET 5.4 2.2 - - - +
985B PRO* 6.2 0.4 - - - +
986B VAL* 4.4 12.1 + - + +
988B GLU* 2.6 36.4 + - - +
990B TRP* 3.4 25.7 - - + -
991B LYS* 3.6 10.9 + - - -
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Residues in contact with GLU 975 (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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971B SER* 2.8 39.4 + - - +
972B ALA* 4.6 1.6 - - - -
974B GLN* 1.3 85.3 - - + +
976B ASP* 1.3 58.3 + - + +
977B PRO* 3.5 11.1 - - - +
990B TRP* 4.5 6.7 + - + -
1012B PRO* 3.7 15.3 - - + +
1016B LYS* 2.7 27.3 + - - -
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Residues in contact with ASP 976 (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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972B ALA* 3.1 24.3 + - + +
973B ALA 5.6 0.4 - - - -
974B GLN 3.7 1.3 - - - -
975B GLU* 1.3 79.1 - - + +
977B PRO* 1.3 60.2 - - - +
978B ASN* 3.0 21.7 + - - +
979B SER* 2.9 41.7 + - - -
982B ALA* 3.6 5.4 - - - +
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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