Contacts of the strand formed by residues 153 - 158 (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 LYS 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 4.4 2.6 - - - -
43B PHE* 4.0 6.8 - - - -
46B GLY* 3.7 26.7 - - - +
48B TYR* 3.7 22.7 + - - +
87B TYR* 3.1 50.9 + - + +
88B SER* 3.6 11.5 + - - +
90B CYS* 3.5 28.9 - - - -
138B TYR 3.3 9.2 - - - +
139B ILE* 4.0 2.0 - - + -
151B CYS 4.3 8.7 - - - +
152B LEU* 1.3 82.2 - - + +
154B LEU* 1.3 58.3 + - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 4.9 15.7 - - + -
36B TRP* 4.4 13.9 - - + -
43B PHE* 4.4 9.0 - - + -
48B TYR* 3.7 16.4 - - + +
49B HIS* 3.8 16.8 - - - +
50B ILE* 3.8 26.7 - - + -
58B LEU* 4.4 18.2 - - + -
60B VAL* 5.9 2.5 - - + -
87B TYR* 3.6 8.5 - - - -
137B PHE* 3.6 1.4 - - - -
138B TYR* 3.0 40.6 + - + +
153B LYS* 1.3 73.9 - - - +
155B LYS* 1.3 81.7 + - - +
156B VAL* 4.0 9.9 - - + -
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Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP 5.7 0.9 - - - -
48B TYR 3.2 7.1 + - - -
49B HIS* 3.7 26.1 - - + -
50B ILE 3.0 23.3 + - - -
84B PHE* 6.0 2.4 - - + -
87B TYR* 3.4 23.1 - - + +
135B GLU* 3.6 28.8 + - + +
136B TYR 3.6 1.8 - - - -
137B PHE* 3.4 37.2 - - + -
154B LEU* 1.3 75.1 - - - +
156B VAL* 1.3 70.3 + - - +
157B PHE* 4.3 0.7 - - + -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.7 21.3 - - + -
52B VAL* 3.6 33.9 - - + -
58B LEU* 4.7 0.4 - - + -
118B PHE* 4.2 15.7 - - + -
135B GLU* 3.1 5.9 - - - -
136B TYR* 2.7 50.8 + - + +
138B TYR* 4.3 18.2 - - + -
154B LEU* 4.0 12.3 - - + -
155B LYS* 1.3 82.7 - - - +
157B PHE* 1.3 67.8 + - - +
158B VAL* 4.0 3.5 + - + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B HIS* 6.3 1.1 - - + -
50B ILE 2.9 12.8 + - - +
51B ASP* 3.5 26.7 - - - +
52B VAL* 3.2 25.6 + - - +
133B GLY* 4.3 14.8 - - - -
134B ARG 3.8 11.0 - - - -
135B GLU* 4.0 24.5 - - + +
155B LYS* 6.0 0.9 - - + +
156B VAL* 1.3 77.9 - - - +
158B VAL* 1.3 82.4 + - - +
159B ARG* 3.7 9.6 + - + -
160B PRO* 4.9 7.2 - - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 3.7 12.8 - - + +
53B CYS 4.7 1.3 - - - -
54B ILE* 4.1 26.2 - - + +
118B PHE* 5.7 2.9 - - + -
130B PHE* 5.3 5.6 - - + -
131B ARG 3.3 14.4 - - - +
132B PRO* 3.4 22.4 - - + -
133B GLY* 2.9 26.6 + - - +
134B ARG 3.2 14.1 + - - +
136B TYR* 3.9 19.1 - - + -
156B VAL* 4.5 3.1 - - + +
157B PHE* 1.3 82.7 - - - +
159B ARG* 1.3 73.3 + - - +
160B PRO 3.3 0.3 - - - -
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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
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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