Contacts of the strand formed by residues 921 - 926 (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 LYS 921 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A ILE* 3.4 31.9 + - + +
894A ASP* 2.7 35.3 + - - +
914A LEU* 4.0 26.7 - - + +
915A VAL* 3.2 15.0 - - - +
916A PRO* 5.1 2.0 - - + -
917A GLY 4.0 0.2 - - - +
920A GLY* 1.3 75.6 - - - -
922A ALA* 1.3 61.5 + - - +
1087A ASP* 3.5 11.6 - - - +
1088A LYS* 5.1 2.8 + - - -
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Residues in contact with ALA 922 (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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891A ILE* 3.8 7.2 - - - -
914A LEU* 3.2 8.3 - - - +
915A VAL* 2.7 37.4 + - + +
916A PRO 4.3 0.2 - - - +
917A GLY* 3.8 5.4 - - - -
921A LYS* 1.3 74.6 - - - +
923A ILE* 1.3 61.3 + - - +
1031A TRP* 3.5 38.4 - - + -
1087A ASP* 3.5 20.0 - - + +
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Residues in contact with ILE 923 (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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889A LEU* 4.7 10.8 - - + -
891A ILE* 4.0 9.4 - - + -
896A ILE* 3.8 37.2 - - + -
912A ALA* 4.8 2.9 - - + -
913A GLN 3.5 6.5 - - - +
914A LEU* 4.4 0.2 - - - -
915A VAL* 4.8 0.4 - - - -
922A ALA* 1.3 73.3 - - - +
924A HIS* 1.3 62.2 + - - +
925A LEU* 3.9 29.6 - - + -
933A VAL* 4.1 15.3 - - + -
1072A LEU* 4.0 24.9 - - + -
1085A SER* 3.1 7.3 - - - -
1086A ILE* 2.8 48.0 + - + +
1087A ASP* 4.8 2.7 - - - +
1088A LYS 6.2 0.2 - - - +
1089A PHE* 5.9 1.1 - - + +
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Residues in contact with HIS 924 (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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911A ASP 4.3 0.2 - - - +
912A ALA* 3.8 2.8 - - - -
913A GLN* 2.8 59.0 + - + +
915A VAL* 3.6 31.1 - - + +
923A ILE* 1.3 75.0 - - - +
925A LEU* 1.3 65.3 + - - +
926A VAL* 4.0 11.6 + - + +
931A SER* 4.0 1.0 + - - -
1083A TYR* 3.2 43.8 - + + -
1084A VAL 3.4 8.3 - - - -
1085A SER* 2.8 26.9 - - - -
1310A GLU* 4.9 7.5 + - - -
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Residues in contact with LEU 925 (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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912A ALA* 4.3 5.6 - - + -
923A ILE* 3.9 19.7 - - + +
924A HIS* 1.3 79.9 - - - +
926A VAL* 1.3 65.3 + - - +
931A SER* 3.4 31.0 - - - +
932A GLU* 4.0 4.7 - - - +
933A VAL* 4.7 0.7 - - + +
976A ILE 4.5 0.4 - - - +
1072A LEU* 3.7 13.2 - - + +
1073A LYS* 3.6 30.1 - - - +
1074A LEU* 3.9 13.2 - - + +
1083A TYR* 3.1 25.0 - - - +
1084A VAL* 2.9 20.5 + - + +
1086A ILE* 4.0 24.5 - - + -
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Residues in contact with VAL 926 (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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911A ASP* 3.8 10.5 - - - +
913A GLN* 3.9 19.5 - - - +
924A HIS* 4.0 24.2 - - + +
925A LEU* 1.3 80.5 - - - +
927A ASN* 1.3 60.1 + - - +
928A ASN* 3.0 31.4 + - - +
931A SER* 3.0 23.4 + - - +
1074A LEU* 4.3 8.7 + - - +
1082A GLN 3.9 6.1 - - - +
1083A TYR* 4.1 8.1 - - + -
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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