Contacts of the strand formed by residues 1042 - 1047 (chain B) in PDB entry 4DQL
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 TYR1042 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997B PHE* 3.3 37.5 - + + -
999B ILE* 4.0 18.1 - - + +
1007B ALA* 5.2 2.3 + - - +
1011B GLU* 2.5 31.4 + - + +
1033B LEU* 3.5 28.9 - - + -
1036B LEU* 3.5 14.9 + - + -
1037B GLU* 3.6 53.6 - - + +
1040B GLY 5.1 1.4 - - - -
1041B ARG* 1.3 80.6 + - - +
1043B ALA* 1.3 60.1 + - - +
1044B LYS* 3.4 40.4 - - + +
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Residues in contact with ALA1043 (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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887B SER* 6.3 1.3 - - - -
888B GLU 3.6 24.5 - - - +
889B PHE* 3.6 16.7 - - + -
997B PHE 2.9 6.7 + - - +
998B TYR* 3.2 23.7 - - + -
999B ILE 3.0 24.1 + - - -
1037B GLU* 5.9 0.2 - - - -
1040B GLY 5.8 2.9 - - - +
1041B ARG 4.0 0.6 - - - -
1042B TYR* 1.3 75.3 - - - +
1044B LYS* 1.4 64.0 + - - +
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Residues in contact with LYS1044 (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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885B PRO* 6.1 1.2 - - - +
887B SER 5.8 0.3 - - - +
889B PHE* 3.6 10.8 - - - +
999B ILE* 3.2 9.0 - - + +
1007B ALA* 6.0 2.7 - - + -
1011B GLU* 4.7 3.6 + - - +
1037B GLU* 3.0 39.4 + - - -
1042B TYR* 3.4 35.3 - - + +
1043B ALA* 1.4 76.3 - - - +
1045B ASP* 1.3 62.2 + - - +
1046B VAL* 3.8 25.4 - - + -
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Residues in contact with ASP1045 (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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698B GLY 5.2 3.1 - - - +
700B HIS* 2.9 29.8 + - + -
831B SER* 2.7 30.2 + - - -
889B PHE* 3.6 23.4 - - + -
910B PRO* 3.8 12.1 - - - +
999B ILE 2.8 8.5 + - - -
1000B CYS* 3.1 5.8 - - + -
1001B GLY 3.0 20.3 + - - -
1044B LYS* 1.3 73.9 - - - +
1046B VAL* 1.3 59.3 + - - +
1047B TRP* 3.3 5.6 - - - -
1101B FAD 3.8 13.3 - - - +
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Residues in contact with VAL1046 (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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999B ILE* 3.7 23.3 - - + +
1000B CYS* 4.1 2.7 - - - -
1001B GLY 3.1 12.8 - - - +
1003B GLY* 3.9 15.9 - - - -
1007B ALA* 3.9 23.3 - - + -
1044B LYS* 3.8 23.5 - - + -
1045B ASP* 1.3 81.1 - - - +
1047B TRP* 1.3 64.1 + - - +
1101B FAD 4.7 9.9 - - - +
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Residues in contact with TRP1047 (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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831B SER* 3.9 10.3 - - - -
906B THR* 3.4 36.9 + - - -
907B GLY* 4.2 1.1 - - - -
909B ALA* 5.4 0.4 - - + -
910B PRO* 5.6 0.7 - - + -
1000B CYS* 4.7 2.0 - - + -
1001B GLY* 2.9 33.0 + - - +
1002B ASP* 3.6 4.8 - - - +
1003B GLY* 2.9 22.9 + - - +
1045B ASP* 3.3 27.1 - - - -
1046B VAL* 1.3 76.9 - - - +
1048B ALA* 1.3 72.3 + - - +
1049B GLY* 3.8 4.4 + - - -
1101B FAD 3.4 100.4 + + + -
1102B NAP 5.9 1.4 + - - -
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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