Contacts of the strand formed by residues 1096 - 1102 (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 ALA1096 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089A GLN* 4.0 4.2 - - - +
1090A VAL* 3.6 28.0 + - + -
1094A ASN* 3.0 11.7 + - + +
1095A LYS* 1.3 77.3 - - - +
1097A LEU* 1.3 77.6 + - - +
1111A GLU* 4.6 9.6 - - + +
1112A LEU 3.4 16.2 - - - +
1113A VAL* 3.7 25.4 - - + +
1114A ALA 4.8 0.2 - - - +
1120A LYS* 4.4 0.8 - - - +
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Residues in contact with LEU1097 (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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1026A LEU* 6.4 0.9 - - + -
1087A VAL* 4.2 16.6 - - + -
1088A ARG 3.5 4.9 - - - +
1089A GLN* 4.1 10.8 - - - -
1090A VAL* 3.8 6.5 - - - -
1096A ALA* 1.3 85.2 - - - +
1098A PHE* 1.3 62.0 + - - +
1099A VAL* 3.8 7.8 + - + -
1110A TYR 3.5 0.9 - - - +
1111A GLU* 3.4 6.9 - - - +
1112A LEU* 3.1 35.5 + - + +
1120A LYS* 3.9 32.5 - - + +
1123A TRP* 4.2 11.9 - - + -
1124A GLN* 3.9 42.0 - - + +
1127A ILE* 4.9 7.6 - - + -
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Residues in contact with PHE1098 (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 3.5 0.9 - - - +
1087A VAL* 3.3 8.7 - - - +
1088A ARG* 3.0 39.6 + - + +
1089A GLN 4.5 4.5 - - - -
1090A VAL* 3.5 39.0 - - + -
1097A LEU* 1.3 72.5 - - - +
1099A VAL* 1.3 61.6 + - - +
1100A ILE* 3.8 19.8 - - + +
1109A ILE* 3.8 22.7 - - + -
1110A TYR 3.5 2.2 - - - -
1111A GLU* 3.6 38.1 - - + -
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Residues in contact with VAL1099 (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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1047A LEU* 4.6 11.4 - - + -
1080A ILE* 4.3 20.6 - - + -
1082A LEU* 6.4 0.2 - - + -
1085A VAL* 3.8 29.2 - - + -
1086A LEU 3.8 2.2 - - - -
1087A VAL* 4.7 9.6 - - + -
1097A LEU* 4.8 11.0 - - + -
1098A PHE* 1.3 75.6 - - - +
1100A ILE* 1.3 60.5 + - - +
1101A SER 4.1 0.2 - - - -
1109A ILE* 3.5 2.9 - - - -
1110A TYR* 2.9 46.3 + - + +
1112A LEU* 3.6 26.7 - - + -
1127A ILE* 4.8 10.3 - - + -
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Residues in contact with ILE1100 (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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1084A THR 3.4 3.1 - - - +
1085A VAL* 3.3 5.5 - - - -
1086A LEU* 3.0 51.1 + - + +
1088A ARG* 5.2 11.7 - - + -
1098A PHE* 3.8 24.0 - - + +
1099A VAL* 1.3 83.6 - - - +
1101A SER* 1.3 58.8 + - - +
1102A MET* 4.6 8.0 - - - +
1107A ALA* 4.0 19.3 - - + -
1108A GLN 3.5 11.0 - - - +
1109A ILE* 4.3 15.5 - - + -
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Residues in contact with SER1101 (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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1080A ILE* 3.4 26.4 - - - +
1081A LYS* 4.1 3.1 + - - +
1084A THR* 2.8 22.0 + - - -
1085A VAL* 4.8 0.7 - - - +
1099A VAL 4.1 1.0 - - - -
1100A ILE* 1.3 74.0 - - - +
1102A MET* 1.3 59.6 + - - +
1103A SER* 4.0 1.4 + - - -
1106A GLY 3.8 0.2 - - - +
1107A ALA* 3.3 6.8 - - - -
1108A GLN* 3.2 36.3 + - - +
1110A TYR* 4.5 14.6 - - - -
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Residues in contact with MET1102 (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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1084A THR* 3.2 46.9 + - - +
1086A LEU* 5.2 13.5 - - + -
1100A ILE* 4.6 9.6 - - + +
1101A SER* 1.3 73.1 - - - +
1103A SER* 1.3 68.7 + - - +
1106A GLY* 3.4 23.8 - - - +
1107A ALA* 3.9 18.2 - - - -
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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