Contacts of the strand formed by residues 144 - 150 (chain X) 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 ALA 144 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136X LEU* 3.9 22.4 - - + -
139X PHE* 3.8 19.5 - - + -
142X ARG 2.9 11.2 + - - +
143X GLU* 1.3 75.9 - - - +
145X LYS* 1.3 60.1 + - - +
146X VAL 4.3 0.5 + - - -
161X GLU* 5.4 2.6 - - - +
175X LEU* 4.5 14.4 - - + +
197X THR 3.6 7.9 - - - +
198X HIS* 4.0 8.1 - - + -
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Residues in contact with LYS 145 (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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144X ALA* 1.3 74.6 - - - +
146X VAL* 1.3 71.7 + - - +
147X GLN* 4.1 28.2 + - + +
195X GLU 3.5 1.0 - - - +
196X VAL* 3.4 6.5 - - - +
197X THR* 2.9 59.2 + - + +
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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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134X CYS* 4.6 0.2 - - - -
136X LEU* 3.7 30.7 - - + -
144X ALA 4.3 0.6 + - - +
145X LYS* 1.3 83.8 - - - +
147X GLN* 1.3 67.3 + - - +
148X TRP* 4.2 14.4 + - + +
161X GLU* 3.7 24.9 + - - +
175X LEU* 4.0 15.0 - - + -
177X SER* 4.1 18.8 - - - +
194X CYS* 4.4 21.8 - - - -
195X GLU 3.5 3.8 - - - +
196X VAL* 4.7 1.3 - - + -
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Residues in contact with GLN 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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145X LYS* 4.1 28.5 + - + +
146X VAL* 1.3 77.9 - - - +
148X TRP* 1.3 64.5 + - - +
149X LYS* 3.8 14.1 + - + +
154X LEU* 4.2 26.0 - - + +
194X CYS* 3.6 3.1 - - - -
195X GLU* 2.8 75.7 + - + +
197X THR* 5.4 4.5 + - - +
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Residues in contact with TRP 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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117X ILE* 4.3 4.5 - - + -
132X VAL* 3.6 38.4 - - + -
133X VAL 3.9 1.1 - - - -
134X CYS* 3.4 44.2 - - + -
146X VAL* 4.2 9.7 - - + +
147X GLN* 1.3 74.6 - - - +
149X LYS* 1.3 62.4 + - - +
154X LEU* 3.3 5.6 - - - +
155X GLN* 2.8 50.5 + - + -
159X SER* 3.8 22.8 - - - -
177X SER* 2.9 28.9 + - - -
179X LEU* 3.7 32.9 - - + +
192X TYR* 5.4 1.3 - - + -
193X ALA 3.2 29.6 - - - -
194X CYS* 3.9 10.3 - - + -
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Residues in contact with LYS 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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147X GLN* 4.2 18.7 + - - +
148X TRP* 1.3 78.7 - - - +
150X VAL* 1.3 65.0 + - - +
151X ASP 4.0 1.1 + - - -
152X ASN* 3.8 41.1 - - - +
153X ALA 3.3 6.7 - - - +
154X LEU* 4.2 21.5 - - + +
191X VAL 3.9 0.5 - - - +
192X TYR* 3.8 0.5 - - - -
193X ALA* 2.9 50.9 + - + +
195X GLU* 2.6 40.1 + - + +
206X THR* 5.8 2.5 - - + -
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Residues in contact with VAL 150 (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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149X LYS* 1.3 76.3 - - - +
151X ASP* 1.3 70.0 + - - +
153X ALA* 2.7 22.7 + - - +
155X GLN* 3.4 30.5 - - + +
179X LEU* 4.0 12.3 - - + -
181X LEU* 4.6 4.7 - - + -
189X HIS* 3.6 40.7 - - + +
191X VAL 3.5 4.5 - - - +
192X TYR* 3.9 31.2 - - + -
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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