Contacts of the strand formed by residues 108 - 117 (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 VAL 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A HIS* 3.7 10.5 + - + +
107A SER* 1.3 80.4 - - - +
109A LEU* 1.3 64.3 + - - +
133A LEU* 4.1 27.8 - - + -
134A ARG* 3.3 3.8 - - - +
135A ARG* 2.9 47.2 + - + +
139A LEU* 5.6 2.9 - - - -
238A PHE* 3.3 10.8 - - - +
239A VAL* 4.2 21.3 - - + -
153D ILE* 4.2 14.1 - - + -
207D VAL* 4.2 15.7 - - + -
241D LEU* 4.3 6.7 - - + -
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Residues in contact with LEU 109 (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* 1.3 78.1 - - - +
110A HIS* 1.3 60.1 + - - +
111A LEU* 3.8 41.1 - - + -
131A PRO* 4.0 10.3 - - + -
133A LEU 3.4 15.3 - - - +
134A ARG* 3.8 24.9 - - + +
139A LEU* 3.7 38.1 - - + -
140A GLU* 4.5 1.3 - - - +
141A ALA 4.7 3.8 - - - +
146A VAL* 4.5 5.2 - - + -
157A TYR* 4.3 1.6 + - - -
237A GLY* 3.1 5.2 - - - -
238A PHE* 2.9 44.9 + - + +
207D VAL* 6.1 0.7 - - - -
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Residues in contact with HIS 110 (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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109A LEU* 1.3 73.3 - - - +
111A LEU* 1.3 62.7 + - - +
112A VAL* 4.5 6.2 - - + +
131A PRO* 3.6 2.8 - - - +
132A VAL* 3.0 44.7 + - + +
133A LEU* 2.8 30.2 + - + +
157A TYR* 2.6 30.5 + + - +
231A PRO 4.9 1.6 + - - -
235A PHE* 3.7 43.4 - + + +
236A LEU 3.8 1.3 + - - -
184D LEU 5.4 0.4 + - - -
207D VAL* 3.8 15.3 + - + +
208D PHE* 3.9 30.3 - + - -
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Residues in contact with LEU 111 (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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109A LEU* 3.8 24.0 - - + -
110A HIS* 1.3 73.8 - - - +
112A VAL* 1.3 63.9 + - - +
129A TRP* 3.9 20.3 - - + -
130A GLN 3.3 6.1 - - - +
131A PRO* 3.7 27.1 - - + -
141A ALA* 3.8 19.7 - - + -
146A VAL* 3.8 29.6 - - + -
235A PHE* 3.2 9.7 - - - +
236A LEU* 2.7 52.2 + - + +
238A PHE* 3.9 11.0 - - + -
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Residues in contact with VAL 112 (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* 4.5 4.0 + - + -
111A LEU* 1.3 78.0 - - - +
113A PRO* 1.3 75.0 - - + +
129A TRP* 3.5 8.1 - - - -
130A GLN* 2.8 52.7 + - + +
132A VAL* 3.6 39.3 - - + -
231A PRO* 3.6 41.1 - - + +
234A THR 4.3 0.4 - - - -
235A PHE* 4.3 3.8 - - + -
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Residues in contact with PRO 113 (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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112A VAL* 1.3 90.4 - - + +
114A VAL* 1.3 58.9 + - - +
115A ASN 4.4 0.2 - - - +
127A VAL* 3.6 19.7 - - + -
128A MET 3.4 8.1 - - - +
129A TRP* 3.9 2.2 - - + -
130A GLN* 3.3 15.2 + - - -
227A LEU* 5.7 0.2 - - + -
228A SER 4.3 0.4 - - - +
229A LEU* 3.8 50.8 - - + +
230A SER 4.2 0.9 - - - +
234A THR* 3.2 40.4 - - + +
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Residues in contact with VAL 114 (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* 1.3 76.5 - - - +
115A ASN* 1.3 79.9 + - + +
128A MET* 2.9 30.8 + - + +
129A TRP 4.1 13.2 - - - +
130A GLN* 4.1 20.0 - - + +
229A LEU* 4.3 11.1 - - - +
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Residues in contact with ASN 115 (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* 3.7 1.6 - - - +
114A VAL* 1.3 97.0 + - + +
116A ILE* 1.3 69.4 + - - +
127A VAL* 3.5 8.7 - - - +
128A MET* 2.9 44.8 + - + +
229A LEU* 4.1 13.5 - - - +
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Residues in contact with ILE 116 (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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115A ASN* 1.3 85.6 + - - +
117A THR* 1.3 68.4 + - - +
118A SER* 4.8 2.2 - - - +
125A THR* 3.4 24.2 - - + -
126A GLU 3.5 2.0 - - - +
127A VAL* 4.0 13.5 - - + -
128A MET* 5.0 2.3 - - - +
224A ASN* 6.0 1.3 - - - -
225A ALA 4.8 6.5 - - - +
227A LEU* 3.3 46.4 - - + +
229A LEU* 3.6 23.2 - - + +
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Residues in contact with THR 117 (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* 1.3 77.6 - - - +
118A SER* 1.3 67.4 + - - +
119A LYS* 4.7 11.8 + - - +
124A VAL* 5.7 0.2 - - - +
125A THR* 3.3 2.1 - - - +
126A GLU* 2.8 55.7 + - + +
128A MET* 4.5 18.2 - - + -
144A ASP* 3.5 29.2 - - + +
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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