Contacts of the strand formed by residues 146 - 152 (chain A) in PDB entry 4MXV
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 GLN 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A SER* 5.1 2.6 + - - +
64A SER* 4.0 23.5 + - - +
65A LEU 3.4 3.8 - - - -
66A LEU* 3.7 13.0 - - + +
102A GLN 3.7 0.2 - - - +
103A LEU* 3.5 7.2 - - - +
104A PHE* 3.0 67.4 + - + +
144A GLY 3.4 15.9 + - - +
145A ASP* 1.3 74.4 - - - +
147A LEU* 1.3 63.8 + - - +
148A SER* 3.8 1.8 + - - -
50H TYR* 5.0 0.4 - - - -
57H THR 3.8 16.0 + - - +
58H ASN* 3.7 27.9 + - - +
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Residues in contact with LEU 147 (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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58A PHE* 5.3 1.3 - - + -
64A SER* 3.1 5.0 - - - -
65A LEU* 2.6 51.0 + - + +
67A VAL* 4.2 14.4 - - + -
73A TYR* 6.1 0.4 - - + -
75A VAL* 3.8 29.8 - - + -
101A VAL* 5.0 1.1 - - + -
102A GLN 3.5 4.5 - - - +
103A LEU* 3.9 17.3 - - + -
114A LEU* 3.8 28.7 - - + -
141A LEU* 3.9 18.6 - - + -
146A GLN* 1.3 73.4 - - - +
148A SER* 1.3 59.3 + - - +
166A PHE* 3.7 19.1 - - + -
168A ALA* 4.2 14.4 - - + -
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Residues in contact with SER 148 (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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63A ASN 4.3 13.0 - - - -
64A SER* 4.4 9.6 - - - -
101A VAL* 3.6 3.8 - - - +
102A GLN* 2.8 52.9 + - - +
104A PHE* 5.6 1.7 + - - -
111A HIS* 4.3 7.8 + - - -
146A GLN 3.8 2.3 + - - -
147A LEU* 1.3 76.2 - - - +
149A THR* 1.3 71.6 + - - +
166A PHE* 4.1 5.6 - - - -
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Residues in contact with THR 149 (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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43A LEU* 4.5 2.1 - - - +
45A TRP* 3.2 28.2 + - + +
63A ASN* 5.2 4.2 + - - -
77A SER* 4.5 0.2 - - - +
99A HIS* 3.7 22.4 - - + +
100A GLU 3.0 15.5 - - - +
101A VAL* 4.0 17.5 - - + -
102A GLN* 4.5 0.7 - - - +
148A SER* 1.3 86.2 - - - +
150A HIS* 1.3 59.2 + - - +
151A THR* 4.0 5.2 + - - -
166A PHE* 4.0 26.8 - - + -
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Residues in contact with HIS 150 (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 ALA 4.7 0.2 - - - -
99A HIS* 3.5 2.1 + - - -
100A GLU* 3.0 46.9 + - + +
102A GLN* 3.8 29.8 + - - +
149A THR* 1.3 71.4 - - - +
151A THR* 1.3 77.6 + - - +
152A ASP* 3.5 30.5 + - - -
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Residues in contact with THR 151 (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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43A LEU* 3.6 17.2 - - - +
79A VAL* 4.8 0.7 - - + -
81A PHE* 3.9 20.6 - - + -
98A ALA 3.4 11.2 - - - +
99A HIS* 3.2 25.3 + - + +
149A THR* 4.0 5.5 + - - -
150A HIS* 1.3 91.1 + - - +
152A ASP* 1.3 65.8 + - - +
153A GLY 4.2 0.2 - - - -
154A ILE* 3.9 30.2 - - + +
157A LEU* 4.2 17.9 - - + -
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Residues in contact with ASP 152 (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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81A PHE* 3.8 6.2 - - - -
96A TYR* 3.7 36.0 + - + +
97A LEU* 3.5 4.5 - - - -
98A ALA* 2.8 46.4 + - + +
150A HIS* 3.5 26.5 + - - -
151A THR* 1.3 75.5 - - - +
153A GLY* 1.3 61.0 + - - +
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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