Contacts of the helix formed by residues 1089 - 1096 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ADP 2.8 37.3 + - - +
1006D GLY* 4.9 3.6 - - - -
1007D SER 5.1 1.6 + - - -
1087D GLY 3.9 1.6 + - - +
1088D LEU* 1.3 76.3 - - - +
1090D LEU* 1.3 58.8 + - - +
1091D PHE* 3.1 15.6 + - - +
1092D ALA* 3.1 32.6 + - - +
1093D PHE* 2.9 25.5 + - - +
1131D ASP 3.7 1.3 - - - +
1132D GLU* 3.5 21.7 - - - +
1134D ILE 3.0 17.5 - - - +
1135D VAL* 4.1 2.0 - - + +
1136D ILE* 4.4 2.7 - - - -
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Residues in contact with LEU1090 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D ASP* 1.3 70.6 - - - +
1091D PHE* 1.3 59.0 + - - +
1093D PHE* 3.5 11.1 - - + +
1094D ILE* 2.9 37.7 + - + +
1108D ILE* 4.1 27.4 - - + -
1112D LEU* 5.9 0.9 - - + -
1131D ASP* 3.1 23.5 + - + +
1134D ILE* 2.9 45.0 + - + +
1136D ILE* 4.0 31.9 - - + -
1142D ILE* 5.8 0.2 - - + -
1192D THR* 5.0 6.7 - - + -
1196D LEU* 4.2 21.5 - - + -
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Residues in contact with PHE1091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D ASP* 3.1 11.5 + - - +
1090D LEU* 1.3 75.1 - - - +
1092D ALA* 1.3 62.1 + - - +
1094D ILE* 3.6 4.0 + - - +
1095D ASP* 3.0 46.2 + - + +
1131D ASP* 3.4 40.3 + - - +
1132D GLU* 4.1 16.8 - - + +
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Residues in contact with ALA1092 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D LEU* 3.7 24.9 - - + +
1089D ASP* 3.1 25.2 + - - +
1091D PHE* 1.3 79.3 - - - +
1093D PHE* 1.3 62.9 + - - +
1095D ASP* 3.5 11.2 + - - +
1096D ARG* 3.3 22.9 - - - +
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Residues in contact with PHE1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D LEU* 4.5 1.9 - - + +
1089D ASP 2.9 14.3 + - - +
1090D LEU* 3.5 23.1 - - + +
1092D ALA* 1.3 77.2 - - - +
1094D ILE* 1.3 69.4 + - + +
1095D ASP 3.5 0.2 + - - -
1096D ARG* 3.5 4.5 + - - +
1098D PRO* 3.4 35.5 - - + +
1100D LEU* 4.0 19.1 - - + -
1108D ILE* 4.3 14.6 - - + -
1136D ILE* 3.9 22.0 - - + -
1140D PHE* 4.6 1.6 - + - -
1196D LEU* 4.7 2.5 - - + -
1262D TRP* 3.7 32.5 - + - -
1265D VAL* 4.1 24.5 - - + -
1266D PHE* 3.7 36.2 - + - -
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Residues in contact with ILE1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090D LEU* 2.9 28.3 + - + +
1091D PHE* 4.0 3.6 - - - +
1093D PHE* 1.3 75.0 - - + +
1095D ASP* 1.3 65.8 + - - +
1096D ARG 3.1 2.7 - - - -
1097D HIS* 3.1 15.6 + - - -
1098D PRO* 4.0 7.2 - - + -
1100D LEU* 6.2 0.2 - - + -
1131D ASP* 4.3 14.8 - - + +
1195D THR* 3.6 23.1 - - + +
1196D LEU* 3.6 39.0 - - + +
1199D GLU* 3.4 45.5 - - + +
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Residues in contact with ASP1095 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091D PHE* 3.0 37.5 + - + +
1092D ALA* 3.7 9.6 - - - +
1093D PHE 3.3 0.4 - - - -
1094D ILE* 1.3 77.9 - - - +
1096D ARG* 1.3 63.4 + - + +
1097D HIS* 3.2 21.9 + - - -
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Residues in contact with ARG1096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D LEU* 6.1 0.4 - - + -
1092D ALA 3.3 18.2 - - - +
1093D PHE 4.0 5.6 - - - +
1094D ILE 3.1 1.6 - - - -
1095D ASP* 1.3 85.6 - - - +
1097D HIS* 1.3 72.8 + - - +
1098D PRO* 3.6 2.6 - - + +
1266D PHE* 3.4 46.3 - - + +
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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