Contacts of the strand formed by residues 1042 - 1047 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997A PHE* 3.3 46.2 - + + -
999A ILE* 3.5 7.8 - - + +
1011A GLU* 2.5 45.4 + - + +
1014A LEU* 4.1 5.4 - - + -
1033A LEU* 3.9 26.2 - - + -
1036A LEU* 3.7 16.4 + - + -
1037A GLU* 3.2 50.8 - - + +
1040A GLY* 3.7 1.5 - - - -
1041A ARG* 1.3 79.8 - - - +
1043A ALA* 1.3 60.7 + - - +
1044A LYS* 3.4 23.2 - - + +
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Residues in contact with ALA1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A SER* 5.0 5.2 - - - +
888A GLU 3.6 23.6 - - - +
889A PHE* 3.8 13.0 - - + -
997A PHE 2.9 7.5 + - - +
998A TYR* 3.2 22.2 - - + -
999A ILE* 2.9 26.3 + - - +
1040A GLY 5.8 3.1 - - - +
1041A ARG 5.5 0.4 - - - -
1042A TYR* 1.3 77.0 - - - +
1044A LYS* 1.3 63.9 + - - +
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Residues in contact with LYS1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A SER* 4.4 18.9 + - - +
889A PHE* 3.6 7.8 - - - -
999A ILE* 3.3 21.1 - - + +
1007A ALA* 5.1 10.9 + - - +
1008A PRO* 6.0 0.8 - - - +
1011A GLU* 2.5 33.7 + - - +
1037A GLU* 5.0 6.3 + - - +
1042A TYR* 3.4 23.5 - - + +
1043A ALA* 1.3 80.6 - - - +
1045A ASP* 1.3 59.5 + - - +
1046A VAL* 3.7 24.0 + - + -
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Residues in contact with ASP1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A GLY* 5.5 1.8 - - - +
700A HIS* 2.8 29.5 + - - -
831A SER* 2.7 31.8 + - - -
885A PRO* 6.3 0.7 - - - -
889A PHE* 3.5 29.2 - - + -
910A PRO* 3.7 13.9 - - - +
999A ILE 2.8 8.5 + - - -
1000A CYS* 3.3 4.7 - - + +
1001A GLY 3.2 18.0 + - - -
1044A LYS* 1.3 72.6 - - - +
1046A VAL* 1.3 58.0 + - - +
1047A TRP* 3.5 5.7 - - - -
1101A FAD 3.9 9.4 - - - +
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Residues in contact with VAL1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999A ILE* 4.0 16.4 - - + +
1000A CYS* 4.2 2.7 - - - -
1001A GLY 3.1 19.5 - - - +
1003A GLY* 3.7 15.3 - - - -
1007A ALA* 3.9 23.8 - - + -
1044A LYS* 3.7 22.3 - - + -
1045A ASP* 1.3 82.1 + - - +
1047A TRP* 1.3 66.2 + - - +
1101A FAD 4.7 9.3 - - - +
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Residues in contact with TRP1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A SER* 3.9 8.7 - - - -
906A THR* 3.6 29.6 - - + +
907A GLY* 4.3 1.1 - - - -
909A ALA* 5.5 0.7 - - + -
910A PRO* 5.7 0.9 - - + -
1000A CYS* 4.9 0.9 - - + -
1001A GLY* 2.9 35.1 + - - +
1002A ASP* 3.6 6.3 - - - +
1003A GLY* 2.9 20.4 + - - -
1045A ASP* 3.5 23.6 - - - -
1046A VAL* 1.3 77.7 - - - +
1048A ALA* 1.3 72.3 + - - +
1049A GLY* 5.3 2.5 - - - -
1101A FAD 3.3 104.3 + + + -
1102A NAP 6.4 0.4 - - - -
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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