Contacts of the strand formed by residues 1085 - 1089 (chain A) in PDB entry 1TXD
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 VAL1085 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1080A ILE* 3.5 25.4 - - + -
1081A LYS 3.4 18.2 - - - +
1082A LEU* 3.3 25.5 + - + +
1083A SER 3.7 0.4 - - - -
1084A THR* 1.3 79.0 - - - +
1086A LEU* 1.3 67.2 + - - +
1087A VAL* 3.6 27.6 - - + -
1099A VAL* 3.8 15.3 - - + -
1100A ILE 3.3 5.8 - - - +
1101A SER* 4.5 0.2 - - - +
1127A ILE* 4.2 9.6 - - + -
1131A ALA* 4.5 7.5 - - + +
1135A LYS* 2.4 29.6 + - - -
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Residues in contact with LEU1086 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1084A THR 5.1 2.5 - - - +
1085A VAL* 1.3 80.0 - - - +
1087A VAL* 1.3 65.6 + - - +
1088A ARG* 4.1 26.7 - - - +
1100A ILE* 3.0 51.4 + - + +
1102A MET* 5.2 12.3 - - + -
1135A LYS* 4.4 8.5 - - - +
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Residues in contact with VAL1087 (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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1085A VAL* 3.6 19.3 - - + -
1086A LEU* 1.3 78.5 - - - +
1088A ARG* 1.3 90.9 + - - +
1097A LEU* 4.2 24.9 - - + -
1098A PHE 3.3 11.0 - - - +
1099A VAL* 4.7 8.3 - - + -
1124A GLN* 4.2 27.1 + - + -
1127A ILE* 3.7 22.9 - - + -
1128A CYS* 4.0 20.2 - - - -
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Residues in contact with ARG1088 (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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1086A LEU* 4.1 30.5 - - + +
1087A VAL* 1.3 106.1 + - - +
1089A GLN* 1.3 71.5 + - - +
1097A LEU* 3.5 2.1 - - - -
1098A PHE* 3.0 41.1 + - + +
1100A ILE* 5.2 10.8 - - + -
1124A GLN* 4.4 5.2 - - - +
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Residues in contact with GLN1089 (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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1088A ARG* 1.3 82.5 - - - +
1090A VAL* 1.3 74.4 + - - +
1091A ALA* 4.1 5.0 + - - +
1095A LYS* 4.7 15.8 - - + +
1096A ALA 4.0 8.5 - - - +
1097A LEU* 4.1 3.6 - - - +
1098A PHE* 4.5 3.8 - - - -
1120A LYS* 2.5 42.2 + - + +
1124A GLN* 4.1 18.6 - - - +
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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