Contacts of the helix formed by residues 1089 - 1096 (chain F) in PDB entry 3DLS
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 ASP1089 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F ADP 2.8 35.8 + - - +
1006F GLY* 5.0 6.8 - - - -
1007F SER* 5.3 1.7 + - - -
1087F GLY 3.8 2.3 + - - +
1088F LEU* 1.3 78.0 - - - +
1090F LEU* 1.3 58.5 + - - +
1091F PHE* 3.2 15.1 + - - +
1092F ALA* 3.2 26.5 + - - +
1093F PHE* 2.9 26.0 + - - +
1131F ASP 3.9 0.4 - - - +
1132F GLU* 3.8 20.3 - - - +
1134F ILE 3.1 15.7 - - - +
1135F VAL* 4.0 1.8 - - + +
1136F ILE* 4.4 1.3 - - - -
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Residues in contact with LEU1090 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089F ASP* 1.3 69.2 - - - +
1091F PHE* 1.3 58.7 + - - +
1093F PHE* 3.5 21.5 - - + +
1094F ILE* 2.8 35.6 + - + +
1108F ILE* 4.0 26.9 - - + -
1112F LEU* 6.0 0.7 - - + -
1131F ASP* 3.0 26.9 + - + +
1134F ILE* 2.8 38.6 + - + +
1136F ILE* 4.1 21.8 - - + -
1192F THR* 5.1 6.1 - - + -
1196F LEU* 3.9 29.2 - - + -
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Residues in contact with PHE1091 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007F SER* 5.8 3.4 - - - -
1089F ASP* 3.2 11.1 + - - +
1090F LEU* 1.3 78.4 - - - +
1092F ALA* 1.3 60.2 + - + +
1094F ILE* 3.8 5.4 - - + +
1095F ASP* 3.0 43.7 + - + +
1131F ASP* 3.4 42.0 + - - +
1132F GLU* 3.7 29.4 - - + +
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Residues in contact with ALA1092 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088F LEU* 3.5 24.2 - - + +
1089F ASP* 3.2 17.2 + - - +
1091F PHE* 1.3 80.9 - - + +
1093F PHE* 1.3 64.9 + - - +
1095F ASP* 3.5 16.8 + - - +
1096F ARG* 3.7 14.4 + - - +
1266F PHE* 4.0 2.9 - - - -
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Residues in contact with PHE1093 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088F LEU* 4.3 2.8 - - + +
1089F ASP 2.9 14.2 + - - +
1090F LEU* 3.5 25.4 - - + +
1092F ALA* 1.3 76.4 - - - +
1094F ILE* 1.3 62.6 + - - +
1095F ASP 3.4 0.5 + - - -
1096F ARG* 3.5 9.4 + - - +
1098F PRO* 3.3 42.5 - - + +
1100F LEU* 4.2 12.3 - - + -
1108F ILE* 3.9 27.4 - - + -
1136F ILE* 3.9 16.4 - - + -
1140F PHE* 4.7 2.2 - + - -
1196F LEU* 4.3 10.8 - - + -
1262F TRP* 4.0 28.0 - + - -
1265F VAL* 4.0 21.1 - - + -
1266F PHE* 3.8 25.0 - + - -
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Residues in contact with ILE1094 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090F LEU* 2.8 26.5 + - + +
1091F PHE* 3.8 6.3 - - + +
1093F PHE* 1.3 72.7 - - + +
1095F ASP* 1.3 66.9 + - - +
1097F HIS* 3.1 15.8 + - - -
1098F PRO* 3.7 10.1 - - + +
1131F ASP* 4.0 12.6 - - + +
1195F THR* 3.4 35.7 - - + +
1196F LEU* 3.6 34.5 - - + +
1199F GLU* 3.7 39.3 - - + +
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Residues in contact with ASP1095 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091F PHE* 3.0 38.3 + - + +
1092F ALA* 3.7 13.0 - - - +
1093F PHE 3.3 0.6 - - - -
1094F ILE* 1.3 78.1 - - - +
1096F ARG* 1.3 56.9 + - + +
1097F HIS* 3.2 19.7 + - - -
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Residues in contact with ARG1096 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092F ALA 3.7 5.8 + - - +
1093F PHE 3.5 3.5 + - - +
1094F ILE 3.2 1.4 - - - -
1095F ASP* 1.3 76.4 - - + +
1097F HIS* 1.3 72.2 + - - +
1098F PRO* 4.4 2.3 - - + +
1266F PHE* 3.4 80.6 + - + -
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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