Contacts of the strand formed by residues 1019 - 1023 (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 THR1019 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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866B HIS* 5.6 0.2 - - - -
867B THR* 4.2 18.2 + - - +
990B TRP* 5.6 0.9 - - - +
994B GLN* 4.1 1.6 - - - -
995B VAL* 3.4 14.8 - - + +
997B VAL* 3.8 16.2 - - + -
1013B ILE* 2.6 31.0 + - + +
1014B PHE 4.5 1.4 - - - +
1016B LYS* 3.0 19.4 + - - +
1017B PRO 3.3 3.0 - - - +
1018B ASN* 1.3 83.9 + - - +
1020B ALA* 1.3 66.7 + - - +
1021B MET* 2.9 32.7 - - + +
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Residues in contact with ALA1020 (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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867B THR* 3.4 8.3 - - + +
869B ILE* 3.8 36.1 - - + -
877B MET* 4.4 6.5 - - + -
994B GLN* 3.9 15.0 - - - +
995B VAL 2.8 8.6 + - - +
996B ILE* 3.4 4.3 - - + -
997B VAL 2.7 30.5 + - - -
1019B THR* 1.3 78.6 - - - +
1021B MET* 1.3 57.8 + - - +
1022B LEU 4.0 0.2 + - - -
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Residues in contact with MET1021 (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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866B HIS* 4.5 11.9 - - + -
867B THR 2.6 18.3 + - - +
868B GLU* 3.3 7.9 - - + +
869B ILE* 2.8 27.9 + - - +
997B VAL* 3.6 16.6 - - - -
999B LYS* 5.7 2.0 - - - -
1002B LEU* 4.2 18.6 - - + -
1014B PHE* 3.0 52.9 - - + +
1019B THR* 2.9 40.6 - - + +
1020B ALA* 1.3 72.6 - - - +
1022B LEU* 1.3 58.8 + - - +
1023B LEU* 3.6 22.1 + - + -
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Residues in contact with LEU1022 (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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869B ILE* 3.8 27.6 - - + +
870B ASN* 4.2 11.9 - - - -
871B LEU* 4.3 15.3 - - + +
874B ALA* 3.8 24.7 - - + -
996B ILE* 3.9 13.5 - - + -
997B VAL 2.8 20.6 + - - +
998B MET* 3.5 28.1 - - + +
999B LYS 3.8 0.7 + - - +
1020B ALA 4.0 0.4 + - - -
1021B MET* 1.3 71.8 - - - +
1023B LEU* 1.3 67.4 + - - +
1024B GLY 3.8 0.9 + - - +
1029B THR* 3.7 29.9 + - + +
1033B LEU* 4.3 7.4 - - + -
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Residues in contact with LEU1023 (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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868B GLU* 3.5 37.5 - - + +
869B ILE 4.9 1.6 + - - -
997B VAL 5.1 0.4 - - - +
999B LYS* 3.1 17.3 - - + +
1000B ARG 4.0 11.0 - - - +
1001B SER* 4.1 24.5 - - - +
1002B LEU* 4.4 13.2 - - + -
1021B MET* 3.6 23.0 + - + -
1022B LEU* 1.3 80.4 - - - +
1024B GLY* 1.3 59.6 + - - +
1029B THR* 4.3 4.7 + - - -
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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