Contacts of the strand formed by residues 1014 - 1019 (chain B) in PDB entry 4DJH
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 ARG1014 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013B LEU* 1.3 82.0 - - - +
1015B LEU* 1.3 63.0 + - - +
1016B LYS 3.3 7.7 + - - +
1018B TYR* 3.6 35.9 - - + -
1027B ILE* 3.8 0.7 - - - +
1028B GLY* 2.8 37.3 + - - -
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Residues in contact with LEU1015 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013B LEU* 4.2 15.5 - - + -
1014B ARG* 1.3 71.3 - - - +
1016B LYS* 1.3 58.4 + - - +
1027B ILE* 3.6 4.5 - - - +
1057B VAL* 3.5 7.0 - - + +
1058B ILE* 3.0 49.4 + - + +
1059B THR* 3.5 24.5 - - - +
1060B LYS* 3.6 26.9 - - + +
1063B ALA* 4.1 14.1 - - + -
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Residues in contact with LYS1016 (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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1014B ARG* 3.9 6.5 - - - +
1015B LEU* 1.3 77.8 - - - +
1017B ILE* 1.3 68.2 + - - +
1018B TYR* 3.5 16.6 + - - +
1027B ILE* 3.4 6.0 - - - +
1056B GLY 3.2 10.8 - - - +
1057B VAL* 4.4 12.3 - - + -
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Residues in contact with ILE1017 (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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1016B LYS* 1.3 75.1 - - - +
1018B TYR* 1.3 64.1 + - - +
1025B TYR* 3.5 37.6 - - + -
1026B THR 3.3 11.9 - - - +
1027B ILE* 3.6 15.9 - - + -
1033B LEU* 3.9 20.6 - - + -
1039B LEU* 4.9 10.1 - - + +
1042B ALA* 4.4 2.0 - - + -
1043B LYS* 4.3 20.4 - - + +
1046B LEU* 4.1 6.3 - - + -
1056B GLY* 3.2 30.8 + - - +
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Residues in contact with TYR1018 (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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1011B GLU 4.5 8.3 + - - -
1012B GLY 5.8 0.5 - - - -
1013B LEU 6.0 0.2 - - - -
1014B ARG* 3.6 32.5 - - + -
1016B LYS 3.6 12.6 - - - +
1017B ILE* 1.3 77.1 - - - +
1019B LYS* 1.3 71.2 + - - +
1020B ASP* 4.2 12.9 - - + +
1025B TYR* 3.4 4.6 - - - -
1026B THR* 2.7 79.2 + - + +
1027B ILE* 4.1 6.5 - - - -
1028B GLY 4.3 8.1 + - - -
1030B GLY* 4.4 6.9 + - - -
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Residues in contact with LYS1019 (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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1018B TYR* 1.3 81.1 - - - +
1020B ASP* 1.3 67.0 + - - +
1023B GLY* 3.6 28.9 - - - +
1024B TYR 3.5 4.7 - - - -
1025B TYR* 3.9 36.7 + - + -
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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