Contacts of the strand formed by residues 135 - 140 (chain D) in PDB entry 3MX0
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 GLU 135 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D PHE* 5.5 3.1 - - - -
134D ARG* 1.3 81.9 - - - +
136D TYR* 1.3 68.0 + - - +
137D PHE* 3.3 31.4 - - + -
155D LYS* 3.9 34.5 + - + +
156D VAL 3.4 9.0 - - - +
157D PHE* 4.5 18.5 - - + +
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D MET* 4.6 12.1 - - + -
118D PHE* 5.8 3.8 - + + -
128D PHE* 3.5 32.7 - + - -
129D GLU 4.1 1.4 + - - -
130D PHE* 3.6 28.1 - + + -
131D ARG* 2.8 39.2 + - - +
134D ARG* 3.7 19.2 - - + +
135D GLU* 1.3 77.8 - - - +
137D PHE* 1.3 67.1 + + - +
138D TYR* 4.3 10.0 + - + +
154D LEU 3.8 0.9 - - - +
155D LYS* 3.4 4.9 - - - -
156D VAL* 3.0 35.2 + - + +
158D VAL* 3.5 31.9 - - + -
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Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D MET* 3.3 6.1 - - - +
82D VAL* 2.7 45.5 + - + +
83D ASN* 3.1 6.7 - - - +
84D PHE* 3.0 56.1 - + + -
87D TYR* 3.1 42.4 - + + -
135D GLU* 3.3 33.2 - - + -
136D TYR* 1.3 78.3 - - - +
138D TYR* 1.3 59.7 + - - +
154D LEU 3.5 2.7 - - - -
155D LYS* 3.7 27.8 - - + -
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Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TRP* 4.3 16.2 - + + -
58D LEU* 4.0 24.7 - - + -
79D LEU* 5.3 7.0 - - + -
80D TYR 3.3 13.0 - - - +
81D MET* 3.0 39.8 - - + -
87D TYR* 4.3 1.5 - - - -
99D ARG* 4.5 7.0 - - + -
100D TRP* 4.6 15.5 - + - -
116D GLU* 3.2 24.3 + - - +
118D PHE* 3.8 19.3 - + - -
130D PHE* 4.1 1.4 - - - -
136D TYR* 4.9 7.9 - - + +
137D PHE* 1.3 73.9 - - - +
139D ILE* 1.3 64.9 + - - +
153D LYS* 3.0 8.0 - - - +
154D LEU* 2.8 52.2 + - + +
156D VAL* 4.4 14.8 - - + -
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TRP* 3.8 6.3 - - - -
79D LEU* 3.2 8.1 - - - +
80D TYR* 3.0 37.5 + - + +
82D VAL* 3.1 40.4 - - + -
86D GLY 4.3 1.1 - - - +
87D TYR* 4.4 14.4 - - - +
90D CYS* 4.5 2.5 - - - -
91D ASP 3.1 35.0 - - - +
92D HIS* 4.4 2.9 - - + +
138D TYR* 1.3 76.3 - - - +
140D SER* 1.3 62.5 + - - +
151D CYS* 3.9 15.3 - - - -
152D LEU 3.4 20.6 - - - +
153D LYS* 3.7 9.2 - - + -
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Residues in contact with SER 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TRP* 3.2 31.1 + - - -
77D TYR* 3.0 37.9 - - - -
78D VAL 3.5 7.0 - - - -
79D LEU* 4.3 2.0 - - - -
80D TYR* 4.8 0.2 - - - -
139D ILE* 1.3 76.5 - - - +
141D SER* 1.3 61.2 + - - +
142D ALA 3.6 2.8 + - - -
151D CYS* 3.1 22.7 - - - +
152D LEU* 3.6 11.9 + - - +
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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