Contacts of the helix formed by residues 129 - 135 (chain A) in PDB entry 2GRU
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 THR 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLY 4.3 0.2 + - - -
103A GLY* 3.8 4.9 - - - -
128A THR* 1.3 79.7 + - - +
130A PHE* 1.3 63.6 + - - +
131A LEU* 3.9 3.7 + - - -
132A ALA* 3.1 13.2 + - - +
133A ALA* 3.0 21.7 + - - +
169A LEU* 3.6 3.6 - - - -
172A SER* 5.3 4.3 - - - -
176A GLN* 3.2 31.4 - - - +
603A NAD 2.6 62.6 + - + +
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A THR* 1.3 72.1 - - - +
131A LEU* 1.3 53.5 + - - +
133A ALA* 4.5 1.1 - - + -
134A SER* 2.7 62.4 + - - -
169A LEU* 3.8 20.2 - - + +
172A SER* 4.8 5.5 + - - +
176A GLN* 4.6 3.2 + - - +
177A VAL* 3.6 44.2 - - + -
180A GLY 3.7 17.3 - - - -
181A MET* 3.4 25.8 - - + -
184A LEU* 4.4 4.5 - - + -
214A LEU* 4.0 22.4 - - + -
217A PHE* 3.7 25.8 - + + -
218A ILE* 3.9 20.6 - - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A THR* 3.3 3.6 + - - +
130A PHE* 1.3 74.3 - - - +
132A ALA* 1.3 66.6 + - - +
134A SER* 4.2 0.7 - - - -
135A ASP* 3.0 37.9 + - + +
136A SER* 3.1 8.1 + - - -
176A GLN 4.7 4.6 + - - +
179A ALA* 4.3 11.2 - - + +
180A GLY* 3.9 22.6 - - - +
183A GLU* 3.5 33.9 - - + +
262A HIS* 4.5 24.7 - - + -
603A NAD 3.1 44.9 - - + +
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY 4.3 0.2 - - - +
103A GLY* 3.7 8.3 - - - -
104A GLY* 3.7 17.7 - - - +
127A PRO* 3.8 15.7 - - + -
129A THR* 3.1 23.0 + - - +
131A LEU* 1.3 79.2 - - - +
133A ALA* 1.3 61.5 + - - +
136A SER* 3.4 18.5 + - - +
137A VAL* 3.0 31.7 + - + +
603A NAD 3.9 1.2 + - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.3 28.7 - - - -
127A PRO* 3.5 24.4 - - + +
129A THR 3.0 16.1 + - - +
130A PHE* 4.0 3.1 - - - +
132A ALA* 1.3 76.9 - - - +
134A SER* 1.3 59.4 + - - +
135A ASP 3.5 0.2 - - - -
137A VAL* 3.7 4.0 - - - +
138A LEU* 4.2 1.6 - - - +
164A ALA* 4.0 8.7 - - + -
169A LEU* 3.7 27.1 - - + -
218A ILE* 4.1 10.0 - - + +
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 2.7 55.2 + - - -
131A LEU* 4.2 3.5 + - - -
133A ALA* 1.3 78.3 - - - +
135A ASP* 1.3 62.2 + - - +
138A LEU* 3.5 12.2 - - - +
180A GLY 4.2 6.8 + - - -
183A GLU* 5.8 0.3 - - - +
187A ASN* 4.9 0.9 + - - -
218A ILE* 4.3 8.1 - - - +
221A CYS* 3.2 38.1 - - - +
225A LYS* 4.1 4.2 - - - +
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Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.0 26.4 + - + +
133A ALA 3.5 1.4 - - - -
134A SER* 1.3 84.9 - - - +
136A SER* 1.3 61.8 + - - +
137A VAL 3.5 1.3 - - - -
138A LEU* 2.9 19.5 + - - -
139A SER* 4.4 0.3 - - - -
183A GLU* 3.6 21.1 - - + +
186A LYS* 4.8 0.4 - - - -
225A LYS* 2.8 46.4 + - - +
601A CO 3.9 0.2 + - - -
603A NAD 4.4 2.1 - - - -
607A EXO 2.7 41.1 + - - -
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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