Contacts of the strand formed by residues 1042 - 1048 (chain A) in PDB entry 5ID6
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 LEU1042 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036A TYR* 3.3 5.0 - - - -
1037A VAL* 2.4 54.8 + - + +
1040A GLU* 3.1 36.8 - - + +
1041A ASP* 1.3 77.4 - - - +
1043A PHE* 1.3 64.0 + - - +
1066A TYR* 4.6 11.2 - - + -
1067A SER* 3.7 4.3 - - - +
1068A TYR* 3.3 63.5 - - + +
1092A THR* 3.7 19.1 - - + -
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Residues in contact with PHE1043 (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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1034A ILE* 5.3 9.0 - - + -
1035A MSE 3.7 2.2 - - - -
1036A TYR* 3.3 39.9 - + + -
1042A LEU* 1.3 76.5 - - - +
1044A GLU* 1.3 58.4 + - - +
1045A PHE* 4.1 18.2 + + + -
1066A TYR* 3.3 26.0 - - - +
1067A SER* 3.5 19.6 + - - +
1092A THR* 4.0 13.7 - - - -
1095A TYR* 3.4 32.1 - + + -
1096A LYS* 3.9 11.4 - - + -
1099A PHE* 3.6 28.3 - + - -
1106A TYR* 3.7 31.9 - + + -
1111A ILE* 5.1 2.7 - - + -
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Residues in contact with GLU1044 (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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1033A ARG* 3.8 13.7 - - - +
1034A ILE* 3.6 4.6 - - - -
1035A MSE 2.9 40.4 + - + +
1037A VAL* 4.3 14.3 - - + +
1042A LEU 3.9 0.2 + - - -
1043A PHE* 1.3 72.2 - - - +
1045A PHE* 1.3 62.7 + - - +
1046A ALA* 3.7 5.7 + - - +
1064A LYS* 2.8 50.5 + - + -
1065A LEU 3.4 4.9 - - - +
1066A TYR* 3.0 37.5 + - + -
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Residues in contact with PHE1045 (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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1031A PHE* 4.1 18.2 - + + -
1033A ARG 3.7 4.5 - - - -
1034A ILE* 3.5 42.2 - - + -
1043A PHE* 4.3 19.7 - + + -
1044A GLU* 1.3 71.2 - - - +
1046A ALA* 1.3 58.0 + - - +
1047A LEU 3.9 0.2 + - - -
1063A TRP 3.8 0.9 - - - +
1065A LEU* 2.6 52.4 + - + +
1067A SER* 4.5 0.2 - - - -
1095A TYR* 3.2 48.7 - + - -
1099A PHE* 5.8 1.1 - + - -
1127A PHE* 4.3 9.4 - + - -
1131A MSE 4.2 15.3 - - - -
1134A MSE 3.3 31.9 - - + -
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Residues in contact with ALA1046 (chain A).
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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1031A PHE* 3.7 2.5 - - - -
1032A ASP* 3.0 33.7 + - + +
1033A ARG* 3.3 22.6 + - + -
1044A GLU* 3.7 7.2 + - - +
1045A PHE* 1.3 71.2 - - - +
1047A LEU* 1.3 60.0 + - - +
1063A TRP 3.7 4.3 - - - -
1064A LYS* 3.4 37.5 - - + -
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Residues in contact with LEU1047 (chain A).
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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1010A PHE* 5.2 1.1 - - + -
1014A LEU* 3.7 35.2 - - + -
1031A PHE* 3.4 24.2 - - + -
1032A ASP* 4.6 7.1 - - - +
1045A PHE 4.7 0.4 - - - +
1046A ALA* 1.3 75.7 - - - +
1048A ASP* 1.3 61.0 + - - +
1049A TYR* 3.9 20.0 - - + +
1052A PHE* 3.8 18.2 - - + -
1061A LYS 5.0 0.2 - - - +
1062A LYS* 3.2 7.1 - - - +
1063A TRP* 2.9 67.4 + - + +
1065A LEU* 3.6 27.8 - - + -
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Residues in contact with ASP1048 (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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1030A SER 5.3 0.6 + - - -
1032A ASP* 4.1 13.4 + - - +
1047A LEU* 1.3 77.9 - - - +
1049A TYR* 1.3 55.1 + - - +
1050A LYS* 2.6 67.3 + - - +
1051A ASN* 2.9 34.9 + - - +
1052A PHE* 3.8 4.5 - - - -
1061A LYS* 3.6 6.3 - - - +
1062A LYS* 3.3 27.4 + - + +
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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