Contacts of the strand formed by residues 125 - 135 (chain A) in PDB entry 1XU2
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 THR 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.4 30.7 - - + -
117A THR 3.3 5.2 - - - +
118A SER* 3.4 2.4 + - - -
124A VAL* 1.3 70.8 - - - +
126A GLU* 1.3 68.9 + - - +
219A LYS* 3.7 0.3 - - - -
220A ILE* 2.8 37.7 + - - +
222A ARG 2.6 20.7 + - - -
224A ASN 3.0 9.9 + - - -
225A ALA* 3.0 35.9 + - + +
227A LEU* 4.0 12.6 - - + -
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Residues in contact with GLU 126 (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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116A ILE* 3.5 7.1 - - - +
117A THR* 2.8 38.9 + - + +
124A VAL* 3.8 13.8 - - + +
125A THR* 1.3 78.2 - - - +
127A VAL* 1.3 66.7 + - - +
144A ASP* 3.7 41.8 - - + +
145A ILE* 4.9 5.4 - - - +
217A THR* 5.0 1.9 - - - +
218A VAL 3.5 19.1 - - - +
219A LYS* 3.7 30.8 - - + +
220A ILE* 4.9 0.4 - - - -
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.6 37.0 - - + -
115A ASN 3.5 7.0 - - - +
116A ILE* 4.0 16.6 - - + -
126A GLU* 1.3 78.8 - - - +
128A MET* 1.3 68.5 + - - +
129A TRP* 3.3 40.9 + - + +
144A ASP* 3.1 22.6 - - - +
160A VAL* 5.9 1.3 - - + -
218A VAL* 4.6 5.4 + - + +
220A ILE* 4.6 13.5 - - + -
227A LEU* 4.0 12.8 - - + -
234A THR* 4.8 3.6 - - + -
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Residues in contact with MET 128 (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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113A PRO* 3.4 6.2 - - - +
114A VAL* 2.9 43.1 + - + -
115A ASN* 2.9 33.3 + - + +
116A ILE 5.0 1.8 - - - +
117A THR* 4.5 19.5 - - + -
127A VAL* 1.3 69.9 - - - +
129A TRP* 1.3 59.2 + - - +
143A GLY* 3.4 17.3 - - - +
144A ASP* 3.9 24.5 - - - +
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Residues in contact with TRP 129 (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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111A LEU* 3.9 19.7 - - + -
112A VAL 3.5 20.2 - - - -
113A PRO* 3.9 13.5 - - + -
114A VAL* 4.1 5.0 - - - +
127A VAL* 3.3 46.4 + - + +
128A MET* 1.3 74.8 - - - +
130A GLN* 1.3 62.0 + - - +
131A PRO* 4.8 0.2 - - - +
141A ALA* 4.1 20.3 - - + +
143A GLY* 2.9 24.0 + - - +
144A ASP 4.1 13.3 + - - -
145A ILE* 4.7 5.2 - - - -
146A VAL* 4.8 2.7 - - + -
158A SER* 6.0 0.7 - - - -
159A GLN 5.1 0.4 - - - -
160A VAL* 5.8 2.0 - - + -
218A VAL* 4.5 24.1 + - + +
234A THR* 4.1 12.8 - - + -
235A PHE* 3.8 30.1 - - - -
236A LEU* 3.6 40.0 - - + +
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Residues in contact with GLN 130 (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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111A LEU* 3.3 5.0 - - - -
112A VAL* 2.8 49.7 + - + +
113A PRO 3.3 22.4 + - - -
114A VAL* 4.1 19.2 - - + +
129A TRP* 1.3 75.0 - - - +
131A PRO* 1.3 77.7 - - + +
132A VAL* 5.0 2.5 - - + -
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Residues in contact with PRO 131 (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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109A LEU* 4.0 23.6 - - + -
110A HIS 3.6 6.7 - - - +
111A LEU* 3.7 8.3 - - + -
129A TRP 4.8 0.4 - - - +
130A GLN* 1.3 93.5 - - + +
132A VAL* 1.3 63.2 + - - +
133A LEU 4.6 4.3 - - - +
134A ARG* 4.9 15.3 - - + +
141A ALA* 5.0 5.8 - - + -
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Residues in contact with VAL 132 (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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110A HIS* 3.0 37.7 + - + +
112A VAL* 3.6 35.9 - - + -
130A GLN* 3.6 3.5 + - + -
131A PRO* 1.3 77.2 - - - +
133A LEU* 1.3 65.0 + - + +
134A ARG* 6.0 0.2 - - - -
231A PRO* 5.7 2.2 - - + -
208D PHE* 6.3 0.2 - - + -
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Residues in contact with LEU 133 (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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108A VAL* 4.1 12.6 - - + -
109A LEU* 3.4 4.6 - - - +
110A HIS* 2.8 43.7 + - + +
131A PRO* 3.7 0.8 - - - -
132A VAL* 1.3 83.0 - - + +
134A ARG* 1.3 69.4 + - - +
153D ILE* 4.2 15.0 - - + -
207D VAL* 3.5 45.3 - - + +
208D PHE* 4.0 8.5 - - - -
209D HIS* 3.9 30.5 - - + +
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Residues in contact with ARG 134 (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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108A VAL* 3.3 10.8 - - - +
109A LEU* 3.8 22.1 - - + +
131A PRO* 4.9 13.6 - - + +
133A LEU* 1.3 84.7 - - - +
135A ARG* 1.3 63.1 + - - +
136A GLY 3.4 22.6 + - - +
137A ARG* 4.6 6.7 + - - +
139A LEU 3.0 27.5 + - - -
140A GLU* 4.6 7.7 - - - +
153D ILE* 5.3 0.9 - - - +
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Residues in contact with ARG 135 (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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105A LYS* 3.6 29.7 - - - +
106A HIS 2.9 31.9 + - - +
107A SER* 3.1 5.0 - - - -
108A VAL* 2.9 43.0 + - + +
134A ARG* 1.3 75.6 - - - +
136A GLY* 1.3 69.2 + - - +
152D GLY* 5.6 1.2 - - - -
153D ILE* 3.4 44.1 - - + +
241D LEU* 3.1 30.3 + - - +
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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