Contacts of the helix formed by residues 133 - 141 (chain D) in PDB entry 4G5S
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 ASP 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D PHE* 3.9 9.5 - - + +
96D GLY* 3.0 24.6 + - - -
97D GLU* 3.4 12.3 + - - +
100D ARG* 3.9 16.8 - - + +
129D ARG 3.2 11.0 + - - +
130D LEU* 2.8 19.6 + - - +
132D ARG* 1.3 78.1 - - - +
134D GLY* 1.3 63.6 + - - +
135D GLY* 2.8 26.3 + - - -
136D VAL* 3.1 21.5 + - + +
137D GLN* 3.3 22.9 + - - +
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Residues in contact with GLY 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLY* 5.0 4.7 - - - -
132D ARG 3.5 3.3 + - - -
133D ASP* 1.3 74.4 + - - +
135D GLY* 1.3 60.1 + - - +
137D GLN* 3.3 8.6 + - - +
138D ALA* 2.9 26.5 + - - +
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Residues in contact with GLY 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D MET* 4.5 4.5 - - - -
93D ILE* 4.1 10.2 - - - +
94D ASP 4.3 18.6 - - - -
95D PHE* 4.7 1.1 - - - -
96D GLY* 4.2 6.3 - - - +
133D ASP* 2.8 15.3 + - - -
134D GLY* 1.3 69.8 - - - +
136D VAL* 1.3 57.5 + - - -
138D ALA* 3.1 9.9 + - - +
139D CYS* 2.9 28.1 + - - +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ILE* 4.5 16.8 - - + -
84D ILE* 3.9 21.5 - - + +
85D ILE* 4.5 2.2 - - + -
88D MET* 3.7 29.7 - - + -
95D PHE* 4.6 6.5 - - + +
130D LEU* 3.4 35.7 - - + +
131D TRP* 4.9 11.2 - - + -
133D ASP* 3.1 17.2 + - + +
135D GLY* 1.3 75.5 - - - +
137D GLN* 1.3 57.2 + - - +
139D CYS* 3.2 4.3 + - - +
140D PHE* 2.9 25.5 + - - +
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D TRP* 2.8 69.8 + - - +
132D ARG 5.1 1.6 - - - +
133D ASP 3.3 14.8 + - - +
134D GLY* 3.6 9.9 - - - +
135D GLY 3.2 0.4 - - - -
136D VAL* 1.3 74.3 - - - +
138D ALA* 1.3 61.4 + - - +
140D PHE* 3.2 16.5 + - - +
141D SER* 2.9 32.3 + - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 5.1 8.5 - - + -
134D GLY 2.9 14.7 + - - +
135D GLY* 3.1 12.8 + - - +
137D GLN* 1.3 76.2 - - - +
139D CYS* 1.3 61.6 + - - +
141D SER* 3.5 11.9 + - - -
142D ARG* 3.3 23.8 - - - +
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Residues in contact with CYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ILE* 3.8 11.4 - - - -
87D ALA* 4.2 1.3 - - - -
88D MET* 3.7 39.9 - - + -
91D LEU* 4.7 5.8 - - - -
93D ILE* 4.2 15.2 - - + +
135D GLY 2.9 9.3 + - - +
136D VAL 3.4 8.7 - - - +
138D ALA* 1.3 75.2 - - - +
140D PHE* 1.3 60.5 + - - +
142D ARG* 2.8 25.5 + - - +
146D TYR* 3.1 38.9 + - - -
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ILE* 4.6 6.3 - - + +
131D TRP* 4.0 28.7 - + + -
136D VAL 2.9 14.4 + - - +
137D GLN* 3.2 25.8 + - - +
139D CYS* 1.3 76.6 - - - +
141D SER* 1.3 66.8 + - - +
142D ARG 3.0 1.4 + - - -
143D SER* 3.1 24.6 + - - -
146D TYR* 3.7 7.9 - - - -
148D LEU* 4.0 25.1 - - + -
152D ALA* 4.8 3.1 - - + -
153D SER* 3.8 31.6 - - - -
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Residues in contact with SER 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN 2.9 15.3 + - - -
138D ALA* 3.6 13.9 - - - -
139D CYS 3.1 0.6 - - - -
140D PHE* 1.3 82.0 - - - +
142D ARG* 1.3 60.8 + - - +
143D SER 3.4 1.5 + - - -
144D ARG* 5.2 4.0 - - - +
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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