Contacts of the strand formed by residues 1043 - 1048 (chain A) in PDB entry 1D0H
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 SER1043 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A THR* 3.9 1.7 + - - +
1038A ASN* 3.8 0.5 - - - -
1039A ASP* 2.8 33.2 + - - +
1042A SER* 1.3 87.8 + - - +
1044A ALA* 1.3 60.6 + - - +
1045A ASN* 3.4 21.1 + - - -
1055A SER* 3.9 11.3 + - - -
1056A ALA 3.1 18.6 - - - -
1057A GLU* 4.0 3.4 - - - -
1058A ILE* 4.1 4.0 - - - +
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Residues in contact with ALA1044 (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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1002A TRP* 4.3 8.7 - - + +
1004A LEU* 4.6 0.9 - - + -
1014A ILE* 3.3 16.0 - - + +
1036A ILE* 5.0 0.2 - - + -
1037A THR 3.0 6.7 - - - +
1038A ASN* 3.4 24.0 - - - +
1043A SER* 1.3 74.1 - - - +
1045A ASN* 1.3 61.2 + - - +
1055A SER* 3.2 3.3 - - - -
1056A ALA* 2.7 32.3 + - + +
1058A ILE* 3.8 19.6 - - + +
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Residues in contact with ASN1045 (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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1014A ILE* 4.0 2.7 - - - -
1036A ILE* 3.2 5.7 - - - +
1037A THR* 2.9 39.0 + - - +
1043A SER* 3.4 21.3 + - - -
1044A ALA* 1.3 75.3 - - - +
1046A LEU* 1.3 60.7 + - - +
1047A TYR* 3.5 28.9 + - + -
1052A LEU* 3.7 15.1 - - + +
1054A GLY 3.4 2.6 - - - +
1055A SER* 2.4 33.8 + - - -
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Residues in contact with LEU1046 (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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1000A LEU* 4.6 12.8 - - + +
1002A TRP* 5.7 2.9 - - + -
1014A ILE* 3.8 25.0 - - + +
1016A PHE* 3.4 39.7 - - + -
1034A ILE* 3.9 12.3 - - + -
1035A THR 3.6 1.3 - - - -
1036A ILE* 3.6 26.2 - - + -
1045A ASN* 1.3 74.0 - - - +
1047A TYR* 1.3 72.6 - - - +
1048A ILE* 4.5 10.8 - - + -
1052A LEU* 3.7 1.4 - - - +
1053A MET* 2.8 30.8 + - + -
1054A GLY 2.7 21.6 + - - +
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Residues in contact with TYR1047 (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 PHE 4.3 0.4 - - - -
1034A ILE* 3.7 2.3 - - - -
1035A THR* 2.7 51.1 + - - +
1037A THR* 4.1 8.1 + - + -
1045A ASN* 3.5 33.8 + - + +
1046A LEU* 1.3 79.8 - - - +
1048A ILE* 1.3 65.7 + - - +
1049A ASN 4.3 0.4 - - - -
1050A GLY* 3.9 14.8 - - - -
1051A VAL 3.1 12.1 - - - +
1052A LEU* 3.5 39.6 - - + +
1096A LEU 4.9 2.4 + - - -
1098A PRO* 3.9 30.5 - - + +
1101A ILE* 3.5 35.1 - - + +
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Residues in contact with ILE1048 (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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1000A LEU* 4.6 7.9 - - + -
1016A PHE* 3.7 41.3 - - + -
1026A TYR* 3.5 37.5 - - + -
1027A LEU* 5.9 1.1 - - + -
1032A VAL* 4.1 17.7 - - + -
1033A PHE 3.4 5.2 - - - +
1034A ILE* 4.1 17.0 - - + -
1046A LEU* 4.5 8.7 - - + -
1047A TYR* 1.3 77.1 - - - +
1049A ASN* 1.3 73.8 + - - +
1050A GLY 3.1 0.7 - - - -
1051A VAL* 2.8 24.2 + - - +
1053A MET* 4.2 17.9 - - + +
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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