Contacts of the strand formed by residues 128 - 138 (chain A) in PDB entry 5IXM
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 TYR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 5.5 0.5 - - - -
126A ASP* 3.5 15.7 - - - +
127A GLY* 1.3 83.1 - - - +
129A ALA* 1.3 71.6 + - - +
130A THR* 3.8 16.9 + - - -
151A PHE* 4.1 8.5 - + + -
152A GLN 3.2 17.0 - - - +
153A VAL* 3.6 13.5 - - + -
154A PHE* 3.6 14.2 - - - -
108B ASP* 3.0 36.3 + - - -
109B ASN 4.4 0.7 - - - -
110B PRO* 3.5 33.2 - - + -
113B ALA* 3.9 25.8 + - + -
116B LYS* 4.5 11.8 - - - +
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Residues in contact with ALA 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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106A THR* 3.4 38.4 - - + +
107A ARG* 4.9 0.4 - - - -
108A VAL* 5.3 1.1 - - + -
114A PHE* 5.2 2.5 - - + -
128A TYR* 1.3 76.3 - - - +
130A THR* 1.3 62.4 + - - +
131A GLN* 4.0 0.7 + - - +
151A PHE* 3.4 7.6 - - - +
152A GLN* 2.9 44.0 + - + +
154A PHE* 4.1 13.5 - - + -
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Residues in contact with THR 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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104A ASN* 2.9 35.9 + - - +
105A TYR 3.6 0.2 - - - -
106A THR* 2.9 27.9 + - - -
128A TYR* 3.8 17.8 - - - -
129A ALA* 1.3 73.3 - - - +
131A GLN* 1.3 64.1 + - - +
132A ILE* 3.7 20.2 - - + -
151A PHE* 3.6 22.2 - - + -
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Residues in contact with GLN 131 (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 ASN 3.4 1.6 - - - -
105A TYR* 3.6 35.8 + - + -
106A THR 3.2 27.8 + - - +
107A ARG* 3.7 23.6 - - - +
129A ALA 4.6 1.1 - - - +
130A THR* 1.3 73.2 - - - +
132A ILE* 1.3 60.0 + - - +
133A PHE* 4.8 3.6 - - + -
148A SER* 3.5 4.2 + - - +
150A GLN* 2.9 71.6 + - + +
151A PHE 4.8 0.3 - - - -
152A GLN* 3.8 21.5 + - - +
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Residues in contact with ILE 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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102A ASN* 5.1 2.5 - - + +
103A ILE* 3.5 4.3 - - - +
104A ASN* 2.9 51.1 + - + +
105A TYR* 4.5 0.8 - - - +
130A THR* 3.7 21.1 - - + -
131A GLN* 1.3 78.1 - - - +
133A PHE* 1.3 68.7 + - - +
134A THR* 4.0 18.8 - - - +
148A SER 3.2 5.4 - - - +
149A LYS* 3.9 23.6 - - + -
151A PHE* 4.5 4.0 - - + -
117B GLU* 3.7 36.8 - - + +
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Residues in contact with PHE 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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89A TRP* 4.3 15.5 - + - -
102A ASN 3.7 2.2 - - - -
103A ILE* 3.6 40.4 - - + -
105A TYR* 3.4 44.0 - + + -
131A GLN* 4.8 2.7 - - + -
132A ILE* 1.3 77.4 - - - +
134A THR* 1.3 67.7 + - - +
146A LEU 4.6 0.2 - - - -
147A SER* 3.1 3.5 - - - -
148A SER* 2.9 50.4 + - - +
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Residues in contact with THR 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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100A ARG* 4.9 3.1 - - + +
101A PHE* 3.4 5.0 - - - +
102A ASN* 2.9 62.4 + - - +
103A ILE* 5.2 0.9 - - - +
132A ILE* 4.0 11.6 - - - +
133A PHE* 1.3 76.6 + - - +
135A ALA* 1.3 65.2 + - - +
136A GLY* 5.0 0.4 - - - +
145A THR* 3.7 24.0 - - + -
146A LEU 3.4 4.5 - - - -
147A SER* 3.0 15.4 + - - -
149A LYS* 5.5 1.0 - - - -
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Residues in contact with ALA 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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100A ARG 3.3 4.0 - - - -
101A PHE* 3.8 23.6 - - + -
134A THR* 1.3 78.6 - - - +
136A GLY* 1.3 58.4 + - - +
146A LEU* 2.9 38.1 + - + +
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Residues in contact with GLY 136 (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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99A TRP* 3.6 10.7 - - - -
100A ARG* 2.9 41.6 + - - +
101A PHE* 5.1 1.4 - - - -
134A THR* 5.0 1.2 - - - +
135A ALA* 1.3 75.9 - - - +
137A TYR* 1.3 60.3 + - - -
144A ALA 3.1 14.4 - - - -
145A THR* 4.0 6.7 - - - -
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Residues in contact with TYR 137 (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 VAL* 3.3 44.2 - - + +
99A TRP* 3.9 34.1 - + + -
100A ARG* 5.1 1.0 - - - -
136A GLY* 1.3 75.2 - - - -
138A ALA* 1.3 76.0 + - - +
139A ASN* 3.4 35.2 + - - +
142A TRP* 3.7 34.3 - + + -
143A ASN* 3.2 1.7 - - - +
144A ALA* 2.9 35.1 + - + +
145A THR* 5.1 0.3 + - - -
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Residues in contact with ALA 138 (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 GLN 5.7 0.4 - - - +
98A VAL* 2.9 31.6 + - - +
100A ARG* 3.9 21.5 - - - -
137A TYR* 1.3 83.4 - - - +
139A ASN* 1.3 60.8 + - - +
142A TRP 3.7 6.5 - - - -
143A ASN* 3.6 14.4 - - + +
25B TYR* 3.5 28.2 - - + +
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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