Contacts of the strand formed by residues 1023 - 1027 (chain B) in PDB entry 5DGY
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 VAL1023 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017B VAL* 4.4 0.2 - - - +
1018B SER* 3.2 35.4 + - - -
1020B ASP* 4.6 0.6 + - - +
1022B SER* 1.3 83.7 + - - +
1024B THR* 1.3 73.3 + - - +
1025B ILE* 4.8 2.5 - - + +
1046B VAL* 4.8 12.1 - - + -
1047B LEU 3.6 8.1 - - - +
1048B VAL* 5.0 2.9 - - + -
1053B VAL* 4.7 11.7 - - + -
1058B VAL* 4.5 28.7 - - + -
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Residues in contact with THR1024 (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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1015B LYS* 4.0 13.2 - - + +
1016B LYS 3.6 15.5 - - - +
1017B VAL* 3.6 31.9 - - + +
1021B LYS 5.3 1.2 - - - -
1022B SER 4.6 3.6 + - - -
1023B VAL* 1.3 79.6 + - - +
1025B ILE* 1.3 59.8 + - - +
1026B TYR* 3.3 29.0 - - + +
1046B VAL* 3.5 1.4 - - - -
1047B LEU* 2.9 49.5 + - + +
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Residues in contact with ILE1025 (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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1015B LYS* 3.2 6.7 - - - +
1016B LYS* 3.0 55.7 + - + +
1023B VAL* 4.3 3.4 - - + +
1024B THR* 1.3 74.0 - - - +
1026B TYR* 1.3 70.4 + - - +
1027B LEU* 4.8 18.8 - - + -
1045B VAL 4.1 1.3 - - - +
1046B VAL* 3.8 23.8 - - + -
1060B VAL* 4.8 15.0 - - + -
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Residues in contact with TYR1026 (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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1013B ILE* 5.1 2.7 - - + -
1014B PHE 3.7 7.4 - - - +
1015B LYS* 3.6 40.2 + - + +
1024B THR* 3.3 31.5 - - + +
1025B ILE* 1.3 75.9 - - - +
1027B LEU* 1.3 74.4 + - - +
1044B GLY* 3.4 1.0 - - - -
1045B VAL* 2.8 54.2 + - + +
1047B LEU* 3.8 25.3 - - + +
1108B LEU* 4.2 22.2 - - + -
1112B LEU* 3.5 30.9 - - + +
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Residues in contact with LEU1027 (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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1013B ILE* 3.5 4.9 - - - +
1014B PHE* 3.0 44.1 + - + +
1025B ILE* 4.8 20.6 - - + -
1026B TYR* 1.3 80.8 - - - +
1028B GLY* 1.3 64.1 + - - +
1029B LYS 3.4 13.0 - - - +
1030B ARG* 6.3 0.7 - - + -
1032B TYR* 3.8 7.9 - - + +
1042B VAL* 3.6 26.5 - - + -
1043B ASP 3.4 22.4 - - - +
1044B GLY* 4.2 2.2 - - - -
1104B LEU* 4.7 0.4 - - - -
1108B LEU* 5.9 0.2 - - - -
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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