Contacts of the strand formed by residues 96 - 106 (chain A) in PDB entry 1XTD
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 LYS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 4.1 5.5 - - + -
95A VAL* 1.3 74.9 - - - +
97A THR* 1.3 67.7 + - - +
98A PHE* 3.7 34.5 - - + -
156A VAL 4.5 0.4 - - - -
157A VAL* 3.4 7.4 - - - +
158A SER* 3.1 40.6 + - - -
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Residues in contact with THR 97 (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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95A VAL* 4.5 9.2 + - - +
96A LYS* 1.3 82.1 + - - +
98A PHE* 1.3 71.0 + - - +
99A THR* 5.3 2.9 - - - +
155A VAL* 3.4 33.4 - - + -
156A VAL 3.4 4.3 - - - +
157A VAL* 4.4 7.8 - - + +
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Residues in contact with PHE 98 (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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96A LYS* 3.7 40.2 - - + -
97A THR* 1.3 83.0 - - - +
99A THR* 1.3 60.6 + - - +
100A TYR* 3.8 28.0 - - + +
154A VAL 4.0 0.2 - - - +
155A VAL* 3.7 1.1 - - - -
156A VAL* 2.8 44.2 + - + +
158A SER* 5.5 6.7 - - - -
163A GLU* 5.7 4.9 - - - -
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Residues in contact with THR 99 (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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97A THR* 5.3 2.4 + - - +
98A PHE* 1.3 74.9 + - - +
100A TYR* 1.3 69.6 + - - +
121A ASP* 4.3 10.7 - - - +
122A ASP* 4.8 6.8 + - - +
153A LEU* 4.2 20.9 - - + -
154A VAL 3.5 10.8 - - - +
155A VAL* 4.2 10.6 - - + +
169A LYS* 3.4 29.6 + - - +
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Residues in contact with TYR 100 (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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98A PHE* 3.8 31.9 - + + +
99A THR* 1.3 75.9 - - - +
101A SER* 1.3 59.1 + - - +
119A LEU* 3.7 27.6 - - + -
120A MSE 3.1 27.4 - - - +
121A ASP* 3.5 27.4 + - + +
125A GLU 5.1 1.3 - - - -
127A ARG* 3.2 41.5 + - + -
153A LEU* 3.2 12.4 - - - +
154A VAL* 2.9 34.8 + - + +
156A VAL* 3.7 30.1 - - + -
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Residues in contact with SER 101 (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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100A TYR* 1.3 72.4 - - - +
102A VAL* 1.3 67.2 + - - +
103A LEU* 3.7 5.5 + - - +
119A LEU* 3.3 5.4 - - - -
120A MSE 2.7 48.8 + - - +
151A GLU* 3.3 29.0 + - - +
152A VAL 3.5 6.7 - - - -
153A LEU* 3.8 10.3 - - - +
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Residues in contact with VAL 102 (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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101A SER* 1.3 78.0 + - - +
103A LEU* 1.3 61.7 + - - +
104A ASP 3.6 21.8 - - - +
105A ILE* 4.1 7.2 - - + -
117A LEU* 4.0 14.1 - - + -
118A SER 3.6 5.4 - - - +
119A LEU* 3.8 11.7 - - + -
142A ILE* 4.6 4.9 - - + -
146A PHE* 3.6 28.8 - - + -
151A GLU* 5.6 1.9 - - - +
152A VAL* 3.0 31.0 + - + +
154A VAL* 3.7 28.0 - - + -
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Residues in contact with LEU 103 (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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101A SER* 4.5 5.8 - - - +
102A VAL* 1.3 75.1 - - - +
104A ASP* 1.3 60.3 + - + +
118A SER* 2.7 29.5 + - - +
119A LEU 4.0 17.7 - - - +
120A MSE 3.8 41.5 - - + -
126A SER* 4.0 16.4 - - - -
146A PHE* 3.6 13.0 - - - -
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Residues in contact with ASP 104 (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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102A VAL* 3.6 11.9 - - - +
103A LEU* 1.3 80.8 - - + +
105A ILE* 1.3 76.4 + - - +
106A GLN* 3.4 32.7 + - + +
117A LEU* 3.9 0.5 - - - -
118A SER* 3.0 36.4 + - - -
146A PHE* 3.7 11.9 - - - -
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Residues in contact with ILE 105 (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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102A VAL* 4.1 5.6 - - + -
104A ASP* 1.3 81.3 + - - +
106A GLN* 1.3 76.4 + - - +
107A PRO* 4.0 5.0 - - + +
115A SER* 4.1 22.4 - - - +
116A HIS 3.6 5.8 - - - +
117A LEU* 3.8 18.2 - - + -
132A MSE 4.8 8.1 - - - -
142A ILE* 4.5 8.5 - - + -
143A LYS* 4.3 37.7 - - + +
146A PHE* 3.6 47.2 - - + -
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Residues in contact with GLN 106 (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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104A ASP* 3.4 30.1 + - + +
105A ILE* 1.3 85.7 + - - +
107A PRO* 1.3 76.8 - - - +
115A SER* 4.2 2.9 - - - -
116A HIS* 2.8 52.1 + - + +
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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