Contacts of the helix formed by residues 140 - 148 (chain X) in PDB entry 5OOM
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 GLY 140 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H TYR* 3.8 14.4 - - - -
117X GLU* 6.1 0.9 - - - -
135X ILE* 3.1 15.6 + - - -
138X ALA* 4.1 1.4 - - - +
139X TYR* 1.3 80.0 - - - +
141X LEU* 1.3 54.6 + - - -
142X ASP* 3.2 2.9 - - - -
143X PHE* 3.1 6.4 + - - +
144X TYR* 2.6 35.2 + - - +
191X TYR* 6.1 0.4 - - - -
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Residues in contact with LEU 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X LEU* 4.5 14.6 - - + -
114X PHE* 3.5 47.1 - - + -
115X TYR 5.3 4.7 - - - +
116X SER* 4.1 17.7 - - - -
117X GLU* 5.6 2.0 + - - +
123X PHE* 5.5 3.6 - - + -
125X VAL* 5.9 1.3 - - + -
135X ILE* 4.0 22.2 - - + +
140X GLY* 1.3 69.9 - - - -
142X ASP* 1.3 61.6 + - - +
144X TYR* 3.9 8.1 - - + -
145X ILE* 3.0 48.7 + - + +
161X LEU* 5.0 6.5 - - + -
165X MET* 4.1 13.2 - - + -
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Residues in contact with ASP 142 (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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116X SER* 3.5 14.7 - - - -
117X GLU* 2.9 34.7 + - - +
118X ILE* 3.3 23.9 + - + -
140X GLY* 3.2 1.4 - - - -
141X LEU* 1.3 78.3 - - - +
143X PHE* 1.3 57.3 + - - +
145X ILE* 3.5 0.7 + - - +
146X LEU* 2.9 35.0 + - - +
165X MET* 3.3 25.1 - - - +
191X TYR* 3.1 32.7 + - + +
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Residues in contact with PHE 143 (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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135H GLU* 5.9 7.2 - - + -
138X ALA* 3.2 23.1 - - - +
139X TYR* 3.2 26.9 - - + -
140X GLY* 3.1 4.3 + - - +
142X ASP* 1.3 75.8 - - - +
144X TYR* 1.3 61.8 + - - +
146X LEU* 4.4 1.8 - - - +
147X LYS* 2.9 52.9 + - - +
190X LYS* 3.9 35.2 - - + -
191X TYR* 3.5 33.4 - + - -
193X GLU* 4.8 7.4 - - + -
194X PHE* 4.0 21.1 - + - -
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Residues in contact with TYR 144 (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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79X LEU* 4.0 12.3 - - + -
80X TRP 4.0 7.8 + - - -
81X GLY* 4.3 4.9 - - - -
131X THR* 3.7 29.4 - - + +
134X LEU* 3.6 46.5 - - + +
135X ILE* 3.8 18.6 - - + -
138X ALA* 3.7 12.8 - - + +
140X GLY 2.6 21.1 + - - +
141X LEU* 3.8 8.5 - - + +
142X ASP 3.3 0.2 - - - -
143X PHE* 1.3 73.1 - - - +
145X ILE* 1.3 66.3 + - + +
148X THR* 2.5 52.4 + - + +
153X LEU* 3.8 29.5 - - + +
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Residues in contact with ILE 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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79X LEU* 4.3 9.2 - - + -
141X LEU* 3.0 37.3 + - + +
142X ASP 4.2 1.3 - - - +
144X TYR* 1.3 91.3 - - + +
146X LEU* 1.3 64.8 + - + +
147X LYS 3.3 0.7 + - - -
148X THR* 3.7 11.8 + - - +
153X LEU* 5.0 5.8 - - + +
158X GLY* 3.7 13.5 - - - +
161X LEU* 3.7 33.4 - - + -
162X LYS* 3.5 47.0 - - + +
165X MET* 4.1 10.3 - - + -
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Residues in contact with LEU 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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118X ILE* 3.8 28.3 - - + -
142X ASP 2.9 21.5 + - - +
145X ILE* 1.3 77.7 - - - +
147X LYS* 1.3 59.1 + - - +
148X THR 4.6 0.6 - - - +
162X LYS* 4.3 17.9 + - + +
165X MET* 4.1 17.7 - - + -
166X LEU* 3.7 36.6 - - + +
169X LEU* 4.0 10.8 - - + -
191X TYR* 4.3 6.1 - - + -
194X PHE* 3.6 48.4 - - + -
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Residues in contact with LYS 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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137X GLU 5.0 1.2 + - - -
138X ALA* 3.5 31.9 + - + +
139X TYR* 5.0 6.5 - - - -
143X PHE* 2.9 41.7 + - + +
144X TYR* 4.7 0.9 - - - +
146X LEU* 1.3 77.5 - - - +
148X THR* 1.3 68.9 + - + +
149X PRO* 3.4 6.6 - - - +
193X GLU* 5.2 5.2 - - - -
194X PHE* 3.7 22.4 - - + -
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Residues in contact with THR 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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134X LEU* 6.0 0.2 - - + -
144X TYR* 2.5 59.3 + - + +
145X ILE 3.7 6.9 + - - +
147X LYS* 1.3 78.5 - - + +
149X PRO* 1.3 71.4 - - - +
152X ASP* 5.2 2.7 - - - -
153X LEU* 3.4 30.6 - - - +
159X MET* 5.7 0.2 - - - +
162X LYS* 3.2 22.0 + - - +
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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