Contacts of the strand formed by residues 1018 - 1024 (chain A) in PDB entry 3DOX
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 GLN1018 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013A ILE 3.7 0.3 - - - +
1014A LYS* 3.2 4.9 - - - -
1015A ILE* 2.9 31.5 + - - +
1016A GLY 3.2 16.6 + - - +
1017A GLY* 1.3 82.2 - - - +
1019A LEU* 1.3 64.7 + - - +
1020A LYS* 3.9 25.6 + - - +
1036A MET* 3.7 12.2 - - - +
1037A SER* 2.7 44.0 + - - +
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Residues in contact with LEU1019 (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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1012A THR* 5.0 14.1 - - + -
1013A ILE 3.4 4.9 - - - +
1014A LYS* 3.8 36.3 - - + -
1017A GLY 5.5 1.1 - - - +
1018A GLN* 1.3 73.1 - - - +
1020A LYS* 1.3 70.6 + - - +
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Residues in contact with LYS1020 (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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1012A THR* 3.4 7.3 - - - +
1013A ILE* 2.8 49.7 + - + -
1015A ILE* 4.5 8.1 - - + -
1018A GLN* 3.9 18.7 + - + +
1019A LEU* 1.3 81.8 - - - +
1021A GLU* 1.3 62.5 + - - +
1033A LEU* 5.3 1.3 - - + -
1034A GLU* 5.5 1.9 + - - +
1035A GLU 5.0 3.0 + - - -
1036A MET* 3.5 51.6 - - + +
1083A ASN* 4.2 20.3 - - - +
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Residues in contact with GLU1021 (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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1010A LEU* 4.7 24.8 - - + +
1011A VAL 3.2 10.6 - - - +
1012A THR* 4.9 9.4 + - + +
1020A LYS* 1.3 77.1 - - - +
1022A ALA* 1.3 62.0 + - - +
1082A VAL* 5.9 0.7 - - - +
1083A ASN* 2.8 25.5 + - - +
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Residues in contact with ALA1022 (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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1010A LEU* 3.3 9.5 - - - +
1011A VAL* 2.8 35.1 + - + +
1013A ILE* 4.0 16.2 - - + -
1020A LYS 4.3 0.2 + - - -
1021A GLU* 1.3 76.8 - - - +
1023A LEU* 1.3 61.4 + - - +
1082A VAL* 5.7 0.9 - - - -
1083A ASN* 3.4 19.7 - - + +
1085A ILE* 3.7 31.4 - - + -
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Residues in contact with LEU1023 (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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26A THR 4.6 0.9 - - - +
27A GLY* 3.4 39.0 - - - +
1008A ARG* 3.7 24.9 - - + +
1009A PRO* 3.6 34.1 - - + +
1010A LEU* 3.7 21.1 - - + -
1022A ALA* 1.3 72.1 - - - +
1024A LEU* 1.3 62.0 + - - +
1025A ASP* 3.0 4.5 + - - +
1082A VAL* 4.5 14.3 - - + +
1083A ASN 2.7 17.5 + - - +
1084A ILE* 3.4 16.5 - - + -
1085A ILE 2.8 27.6 + - - -
1Q PRO* 5.2 1.3 - - + -
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Residues in contact with LEU1024 (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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26A THR* 2.6 25.2 + - - -
27A GLY 4.0 0.3 + - - -
97A LEU* 3.7 28.7 - - + -
99A PHE* 4.0 23.6 - - + -
1003A VAL* 5.7 3.6 - - + -
1009A PRO* 2.9 32.1 + - + +
1011A VAL* 3.5 44.6 - - + -
1022A ALA 3.9 0.2 + - - -
1023A LEU* 1.3 68.3 - - - +
1025A ASP* 1.3 54.0 + - - +
1026A THR 4.0 0.2 - - - -
1066A ILE* 4.2 9.9 - - + -
1085A ILE* 4.1 11.4 - - + -
1090A LEU* 3.7 27.4 - - + -
1093A ILE* 4.7 2.0 - - + -
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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