Contacts of the strand formed by residues 135 - 140 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE* 4.9 8.0 - - - -
134B ARG* 1.3 77.7 - - - +
136B TYR* 1.3 72.9 + - - +
137B PHE* 3.3 33.6 - - + -
155B LYS* 3.6 35.8 + - + +
156B VAL 3.1 13.5 - - - +
157B PHE* 4.0 24.9 - - + +
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 4.7 9.9 - - + -
82B VAL 5.7 1.8 - - - -
118B PHE* 5.8 1.6 - + + -
128B PHE* 4.1 27.1 - + - -
129B GLU 4.3 0.9 + - - -
130B PHE* 3.6 25.1 - + + -
131B ARG* 2.6 60.7 + - - +
134B ARG* 4.1 13.6 - - + +
135B GLU* 1.3 77.7 - - - +
137B PHE* 1.3 71.5 + + - +
138B TYR* 4.9 10.5 - - + -
155B LYS* 3.5 1.9 - - - -
156B VAL* 2.7 48.9 + - + +
158B VAL* 3.9 18.2 - - + -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 3.7 5.7 - - - +
82B VAL* 2.9 33.5 + - - +
83B ASN* 3.2 33.7 - - + +
84B PHE* 3.7 31.2 - + + -
87B TYR* 3.1 37.7 - + + -
135B GLU* 3.3 41.5 - - + -
136B TYR* 1.3 78.6 - + - +
138B TYR* 1.3 63.9 + - - +
154B LEU 3.6 3.1 - - - -
155B LYS* 3.4 32.1 - - + -
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 4.6 10.5 - - + -
58B LEU* 4.1 18.8 - - + -
79B LEU* 5.7 4.3 - - + -
80B TYR 3.3 14.4 - - - +
81B MET* 3.1 34.4 - - + -
82B VAL* 4.7 0.4 - - - -
87B TYR* 4.0 0.3 - - - -
99B ARG* 3.9 3.6 - - - -
100B TRP* 3.7 31.9 - + - -
116B GLU* 3.6 27.2 + - - +
118B PHE* 3.9 4.8 - + - -
130B PHE* 3.7 13.3 - - - -
136B TYR* 4.9 4.7 - - + -
137B PHE* 1.3 80.2 - - - +
139B ILE* 1.3 70.5 + - - +
153B LYS* 3.3 2.1 - - - +
154B LEU* 3.0 45.1 + - + +
156B VAL* 4.3 20.9 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 4.2 4.7 - - - -
79B LEU* 3.9 0.7 - - - -
80B TYR* 3.0 38.4 + - + +
82B VAL* 3.5 17.3 - - + -
86B GLY 3.7 15.9 - - - +
87B TYR* 3.8 35.7 - - + +
90B CYS* 4.3 9.0 - - - -
91B ASP 4.2 11.9 - - - +
92B HIS* 4.0 28.7 - - + +
138B TYR* 1.3 82.2 - - - +
140B SER* 1.3 61.9 + - - +
151B CYS* 4.9 4.9 - - - -
152B LEU 3.6 8.3 - - - +
153B LYS* 4.0 7.2 - - + +
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 2.9 42.6 + - - -
77B TYR* 4.2 14.9 - - - -
78B VAL 4.1 3.6 - - - -
79B LEU* 3.9 11.0 - - - -
80B TYR* 5.3 0.9 - - - -
92B HIS* 6.0 0.2 - - - -
139B ILE* 1.3 76.1 - - - +
141B SER* 1.3 62.7 + - - +
151B CYS* 3.4 24.8 - - - +
152B LEU* 3.3 18.3 + - - +
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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
------------------------------------------------------------
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