Contacts of the helix formed by residues 153 - 160 (chain H) in PDB entry 5MGX
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 ILE 153 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H LEU* 5.8 1.8 - - + -
150H CYS* 5.4 3.1 - - - -
152H VAL* 1.3 88.8 - - + +
154H GLN* 1.3 64.5 + - - +
155H ALA* 3.9 20.6 - - + -
156H LEU* 3.3 32.0 + - + +
157H ASP* 3.2 17.8 + - - +
177H TYR 3.7 5.2 - - - +
178H CYS* 3.4 33.7 - - - +
179H TYR* 3.6 35.9 - - + +
194H LEU* 4.8 0.2 - - + -
196H LEU* 3.9 24.5 - - + -
231H HIS* 5.3 1.3 - - - -
234H ARG* 5.1 1.3 - - - +
239H LEU* 5.3 3.6 - - - -
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Residues in contact with GLN 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H CYS* 4.4 18.4 - - - -
153H ILE* 1.3 71.2 - - - +
155H ALA* 1.3 60.8 + - - +
157H ASP* 3.1 8.0 + - - +
158H LEU* 2.7 46.6 + - + +
176H LYS 5.2 2.2 - - - +
177H TYR* 3.2 27.6 + - + +
178H CYS 5.3 0.4 + - - -
239H LEU* 5.0 19.6 - - + +
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Residues in contact with ALA 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LEU* 4.2 9.7 - - + +
153H ILE* 3.2 16.4 - - + -
154H GLN* 1.3 71.2 - - - +
156H LEU* 1.3 52.9 + - - +
158H LEU* 3.5 3.2 + - - +
159H SER* 2.7 39.3 + - - -
171H VAL* 5.3 0.2 - - + -
173H ALA* 3.9 27.8 - - + -
177H TYR* 2.8 26.2 + - + +
178H CYS* 4.1 1.3 - - - -
196H LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H VAL* 5.2 1.3 - - + -
127H LEU* 4.1 28.0 - - + -
143H LEU* 3.8 28.0 - - + -
145H PHE* 3.9 23.3 - - + -
152H VAL* 4.1 13.5 - - + -
153H ILE* 3.3 31.3 + - + +
154H GLN 3.2 0.8 - - - -
155H ALA* 1.3 75.1 - - - +
157H ASP* 1.3 58.5 + - - +
159H SER* 3.9 3.4 - - - +
160H VAL* 3.0 49.6 + - + +
196H LEU* 4.3 9.9 - - + -
198H VAL* 4.4 10.1 - - + -
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Residues in contact with ASP 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H PHE* 4.7 9.9 - - - -
146H THR 3.9 4.1 - - - +
147H LEU* 3.9 7.7 - - - +
148H GLY* 2.8 32.2 + - - +
149H ASP 3.3 0.7 + - - -
150H CYS* 3.1 44.7 + - - -
151H ASP 4.4 2.0 + - - -
152H VAL 5.0 1.0 + - - -
153H ILE 3.2 15.1 + - - +
154H GLN 3.1 7.2 + - - +
156H LEU* 1.3 78.4 - - - +
158H LEU* 1.3 63.1 + - + +
161H PRO* 3.2 23.2 - - - +
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H ILE* 4.1 7.4 - - + +
97H LEU* 4.5 19.7 - - + -
102H LEU* 3.6 26.0 - - + -
150H CYS* 6.1 0.4 - - - -
154H GLN* 2.7 50.8 + - + +
155H ALA* 3.9 0.9 - - - +
157H ASP* 1.3 85.5 - - + +
159H SER* 1.3 58.4 + - - +
161H PRO* 3.8 6.6 - - - +
162H LEU* 4.0 15.4 - - - +
177H TYR* 5.1 7.6 - - + -
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Residues in contact with SER 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H ILE* 4.1 16.4 - - - -
102H LEU* 4.8 1.6 - - - -
104H LYS* 4.3 2.8 - - - +
155H ALA 2.7 23.7 + - - -
156H LEU* 3.7 6.9 + - - +
158H LEU* 1.3 77.0 - - - +
160H VAL* 1.3 68.8 + - - +
161H PRO* 3.4 2.9 - - - -
162H LEU* 3.1 23.1 + - - +
163H MET* 3.9 7.6 + - - +
171H VAL* 3.8 37.3 - - - +
196H LEU* 5.6 0.9 - - - +
198H VAL* 5.4 2.1 - - - +
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H PRO* 3.7 5.6 - - + +
123H VAL* 4.4 6.1 - - + -
125H VAL* 4.6 1.8 - - + -
145H PHE* 4.0 15.7 - - + -
147H LEU* 3.6 21.5 - - + -
156H LEU* 3.0 34.7 + - + +
159H SER* 1.3 72.5 - - - +
161H PRO* 1.4 58.9 - - + +
162H LEU 3.0 5.2 - - - -
163H MET* 3.0 35.8 + - - +
198H VAL* 4.4 17.7 - - + -
200H LEU* 4.0 28.9 - - + -
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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