Contacts of the helix formed by residues 928 - 937 (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 GLY 928 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921B PRO 5.0 6.3 + - - -
923B ALA 5.6 0.4 + - - -
926B MET 3.4 1.2 + - - -
927B PRO* 1.3 70.5 - - - +
929B GLN* 1.3 64.8 + - - +
930B LEU 3.3 2.7 - - - -
931B ASN* 3.1 22.3 + - - +
932B VAL* 2.9 29.8 + - - +
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Residues in contact with GLN 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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890B TYR* 4.7 4.6 - - - -
893B CYS* 3.7 31.1 - - - +
923B ALA 5.0 1.0 + - - -
924B GLY* 3.2 6.6 - - - -
925B ARG* 2.6 35.5 + - - +
926B MET* 3.1 52.1 + - + +
927B PRO 3.0 5.5 + - - -
928B GLY* 1.3 76.6 - - - +
930B LEU* 1.3 66.9 + - + +
932B VAL* 3.3 6.0 + - - +
933B LEU* 3.0 33.1 + - + +
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Residues in contact with LEU 930 (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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888B PRO* 3.7 39.0 - - + +
889B GLY 4.1 7.0 - - - +
892B LEU* 3.8 14.6 - - + -
893B CYS* 3.6 31.2 - - - -
919B ILE* 4.2 24.9 - - + +
923B ALA* 3.8 10.1 + - + -
924B GLY* 3.7 29.4 - - - +
928B GLY 3.3 0.6 - - - -
929B GLN* 1.3 75.1 - - - +
931B ASN* 1.3 64.2 + - - +
933B LEU* 4.6 2.2 - - + +
934B LEU* 2.9 34.2 + - + +
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Residues in contact with ASN 931 (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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919B ILE* 3.6 24.2 - - - +
928B GLY* 3.1 23.3 + - - +
930B LEU* 1.3 75.2 - - - +
932B VAL* 1.3 59.8 + - + +
934B LEU* 4.0 4.0 - - - +
935B ALA* 3.0 30.4 + - - +
941B TYR* 5.4 3.6 - - + -
944B VAL* 3.8 28.2 - - + +
945B LEU 6.2 0.6 - - - -
946B GLU* 6.4 0.2 - - - +
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Residues in contact with VAL 932 (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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927B PRO 5.5 1.1 - - - +
928B GLY* 2.9 21.9 + - - +
929B GLN* 3.7 6.3 - - - +
931B ASN* 1.3 77.3 - - + +
933B LEU* 1.3 73.0 + - + +
935B ALA* 3.3 6.3 + - - +
936B GLU* 3.0 26.7 + - + +
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Residues in contact with LEU 933 (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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892B LEU* 5.2 2.0 - - + -
893B CYS* 3.5 45.1 - - + +
896B LYS* 6.3 0.9 - - - +
898B GLN* 3.5 37.4 + - + +
899B TYR* 5.4 0.5 + - - -
929B GLN* 3.0 28.5 + - + +
930B LEU* 4.1 2.9 - - - +
932B VAL* 1.3 84.4 - - + +
934B LEU* 1.3 62.3 + - - +
936B GLU* 3.5 20.4 + - - +
937B ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 934 (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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888B PRO* 4.3 4.9 - - + -
892B LEU* 4.5 14.8 - - + -
898B GLN* 4.6 7.2 - - + -
901B ILE* 4.3 18.2 - - + -
917B PHE* 3.6 45.3 - - + -
919B ILE* 4.1 18.4 - - + -
930B LEU* 2.9 25.1 + - + +
931B ASN* 4.0 2.2 - - - +
933B LEU* 1.3 72.8 - - - +
935B ALA* 1.3 69.7 + - - +
937B ALA* 3.0 13.7 + - - +
938B GLY 3.1 0.3 + - - -
939B VAL* 3.0 32.9 + - + +
944B VAL* 4.4 12.1 - - + -
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Residues in contact with ALA 935 (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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931B ASN 3.0 19.9 + - - +
932B VAL* 3.5 6.7 - - - +
934B LEU* 1.3 75.8 - - - +
936B GLU* 1.3 53.8 + - - +
938B GLY* 2.5 30.5 + - - -
939B VAL 4.2 12.3 - - - +
941B TYR* 3.4 37.2 - - + +
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Residues in contact with GLU 936 (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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898B GLN* 5.2 0.2 + - - -
899B TYR* 3.5 26.1 + - + +
932B VAL* 3.0 21.0 + - + +
933B LEU* 3.7 23.9 - - - +
935B ALA* 1.3 74.8 - - - +
937B ALA* 1.3 58.8 + - - +
938B GLY 3.1 1.0 + - - -
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Residues in contact with ALA 937 (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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898B GLN* 3.6 35.9 - - + +
899B TYR* 3.9 21.1 - - + -
902B ALA* 3.3 18.7 - - + +
903B ASP* 5.3 2.3 - - - +
933B LEU 3.1 12.0 + - - +
934B LEU* 3.0 10.0 + - - +
935B ALA 3.0 1.2 - - - -
936B GLU* 1.3 76.9 - - - +
938B GLY* 1.3 58.2 + - - +
939B VAL* 3.6 0.7 - - + -
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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