Contacts of the strand formed by residues 145 - 149 (chain X) in PDB entry 4MXW
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 HIS 145 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136X GLN* 3.5 32.3 + - - +
137X LEU 4.2 2.2 - - - -
138X PHE* 3.2 32.1 - + - +
143X PRO* 2.8 14.7 + - - +
144X PHE* 1.3 85.0 - - + +
146X VAL* 1.3 62.0 + - - +
147X PRO* 3.2 12.7 - - - +
182X SER* 5.2 2.6 + - - -
233Z ARG* 5.4 0.3 + - - -
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Residues in contact with VAL 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X GLN* 3.8 1.1 - - - -
137X LEU* 2.6 48.6 + - + +
139X SER* 4.4 9.9 - - - -
143X PRO* 3.6 35.7 - - + -
144X PHE 4.2 4.9 - - - +
145X HIS* 1.3 71.3 - - - +
147X PRO* 1.3 68.9 - - - +
148X LEU* 3.7 2.1 - - - +
109Z GLU* 5.8 1.6 - - + -
110Z GLN* 3.9 25.4 - - + +
233Z ARG* 3.6 20.6 - - - +
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Residues in contact with PRO 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X GLU* 3.6 37.7 - - + +
135X VAL 4.5 2.0 - - - +
136X GLN* 3.6 13.5 - - + +
145X HIS 3.2 11.9 - - - +
146X VAL* 1.3 93.2 - - - +
148X LEU* 1.3 64.2 + - - +
150X SER* 4.8 8.1 - - - +
109Z GLU* 5.8 0.2 - - - +
110Z GLN* 4.8 3.5 - - - +
233Z ARG* 3.5 39.9 + - + +
234Z GLY* 4.4 7.2 + - - +
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Residues in contact with LEU 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X VAL* 4.8 3.1 - - + -
135X VAL* 2.8 17.1 + - + +
136X GLN 4.4 0.4 - - - -
137X LEU* 3.9 25.8 - - + +
146X VAL 3.7 11.4 - - - +
147X PRO* 1.3 81.3 - - - +
149X LEU* 1.3 74.5 + - + +
173X PHE* 3.2 43.6 - - + -
175X LEU* 5.4 1.3 - - + -
181X LEU* 4.1 18.2 - - + -
91Z HIS* 5.2 1.4 + - - -
110Z GLN* 3.6 37.0 - - + +
234Z GLY* 3.3 19.2 - - - +
237Z PHE* 4.3 4.5 - - - -
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Residues in contact with LEU 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X VAL* 3.2 29.8 - - + +
110X TYR* 4.3 0.2 - - - -
134X GLU* 3.1 4.9 - - - +
135X VAL* 2.9 50.5 + - + -
148X LEU* 1.3 93.2 - - + +
150X SER* 1.3 59.5 + - - +
169X HIS* 3.3 44.5 + - + +
170X GLY* 3.8 2.0 - - - -
171X ALA* 3.5 30.5 - - + -
173X PHE* 3.6 7.6 - - + -
234Z GLY 3.6 2.7 - - - -
237Z PHE* 3.8 13.0 - - + -
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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