Contacts of the strand formed by residues 110 - 118 (chain A) in PDB entry 1MPU
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 CYS 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PRO 3.5 8.1 - - - -
99A CYS* 2.0 54.7 - - + -
100A PRO* 3.8 6.1 - - + -
103A TRP* 3.5 17.5 - - + -
104A ILE 3.2 4.7 - - - +
109A ASN* 1.3 75.5 - - - +
111A TYR* 1.3 63.0 + - - +
212A MET* 3.1 10.1 - - - +
213A GLN* 2.8 48.0 + - + +
215A THR* 4.1 6.1 - - - -
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Residues in contact with TYR 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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103A TRP* 3.5 4.4 - - - +
104A ILE* 2.7 62.4 + - + +
106A TYR* 4.3 14.4 - - + -
109A ASN* 3.4 37.7 + - + +
110A CYS* 1.3 78.7 - - - +
112A GLN* 1.3 63.6 + - - +
113A PHE* 4.8 0.4 - - + -
135A LEU* 4.3 12.8 - - + -
142A ASP 4.0 3.6 + - - -
143A GLN* 3.4 29.7 + - - +
145A LEU* 4.4 22.8 - - + +
146A LEU* 4.8 11.9 - - + -
210A ILE* 4.5 14.4 - - + -
211A CYS 3.4 5.2 - - - +
212A MET* 3.6 28.0 - - + -
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Residues in contact with GLN 112 (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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101A LYS 4.9 0.8 + - - -
102A ASN* 3.8 17.4 + - - +
103A TRP* 3.4 45.1 - - + +
111A TYR* 1.3 79.3 - - - +
113A PHE* 1.3 97.0 + - - +
114A PHE* 3.3 35.2 - - + -
210A ILE* 3.2 8.3 - - - +
211A CYS 2.8 34.4 + - - +
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Residues in contact with PHE 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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102A ASN 5.3 3.4 - - - -
104A ILE* 3.8 34.1 - - + -
111A TYR* 5.9 0.2 - - + -
112A GLN* 1.3 96.7 - - - +
114A PHE* 1.3 64.1 + - - +
115A ASP* 3.8 2.6 + - - +
153A HIS* 6.3 2.5 - - + -
209A TYR 3.7 5.4 - - - -
210A ILE* 4.6 11.0 - - + -
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Residues in contact with PHE 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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103A TRP* 4.7 2.0 - + - -
112A GLN* 3.3 43.5 - - + -
113A PHE* 1.3 71.5 - - - +
115A ASP* 1.3 61.6 + - - +
116A GLU* 3.3 12.9 + - + +
126A SER* 5.5 0.2 - - - -
130A GLN* 3.3 37.5 - - - -
208A THR* 3.3 8.0 - - - -
209A TYR* 2.8 79.3 + + + +
211A CYS* 3.7 16.8 - - + -
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Residues in contact with ASP 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 PHE 3.8 3.2 + - - +
114A PHE* 1.3 72.7 - - - +
116A GLU* 1.3 82.8 + - - +
117A SER* 3.0 9.7 + - - -
208A THR* 3.7 17.9 - - + +
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Residues in contact with GLU 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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114A PHE* 3.3 14.0 - - + +
115A ASP* 1.3 95.6 + - - +
117A SER* 1.3 66.0 - - - +
118A LYS* 2.9 32.7 + - - +
209A TYR* 3.9 8.5 - - - +
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Residues in contact with SER 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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115A ASP 3.0 12.6 + - - -
116A GLU* 1.3 73.4 - - - +
118A LYS* 1.3 60.6 + - - +
206A PRO* 3.1 24.8 - - - +
207A ASN* 3.2 24.0 + - - -
208A THR* 4.2 5.1 - - - +
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Residues in contact with LYS 118 (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 GLU* 2.9 36.0 + - - +
117A SER* 1.3 74.4 + - - +
119A ASN* 1.3 69.3 + - - +
122A GLU* 3.7 33.7 - - + +
123A SER 4.2 2.2 - - - +
126A SER* 2.9 28.6 + - - +
154A TRP* 3.1 8.1 + - - -
206A PRO* 3.5 8.7 - - - -
207A ASN 3.0 22.0 + - - +
209A TYR* 3.2 21.4 + - + -
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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