Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 2J9R
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 GLN 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL 5.3 2.2 + - - +
91A GLN* 4.8 3.8 + - - +
93A PHE 4.3 6.3 + - - +
94A ASP 3.9 11.2 - - - +
95A GLY* 4.5 15.5 - - - +
97A ILE* 3.6 33.4 - - + -
98A VAL* 4.0 16.4 - - + +
125A PHE 3.4 0.2 + - - -
126A GLY* 1.3 79.0 + - - -
128A VAL* 1.3 65.4 + - - +
129A PRO* 3.4 2.9 - - - -
130A GLN* 3.2 22.2 + - - +
131A LEU* 3.1 24.2 + - + +
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Residues in contact with VAL 128 (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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12A VAL* 5.1 3.8 - - + -
14A CYS* 4.3 9.2 - - + -
90A VAL* 4.0 18.6 - - + -
91A GLN* 3.7 26.0 - - + +
115A GLY 4.5 1.6 - - - -
116A LEU 3.2 28.0 - - - +
117A ASP* 3.9 13.2 - - - -
125A PHE 3.1 14.7 + - - +
127A GLN* 1.3 79.1 - - - +
129A PRO* 1.4 67.7 - - + +
131A LEU* 3.1 8.8 + - + +
132A MET* 2.9 42.8 + - + +
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Residues in contact with PRO 129 (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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117A ASP 5.0 1.6 - - - +
124A PRO* 3.9 22.4 - - + -
125A PHE 3.5 18.2 - - - +
126A GLY 3.5 6.7 - - - +
127A GLN 3.5 1.8 - - - -
128A VAL* 1.4 90.9 - - + +
130A GLN* 1.3 78.8 + - - +
132A MET* 3.2 15.2 + - + +
133A ALA* 3.0 22.2 + - - +
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Residues in contact with GLN 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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98A VAL* 3.7 22.7 - - + -
126A GLY 3.8 2.3 - - - +
127A GLN* 3.2 35.2 + - - +
129A PRO* 1.3 90.2 - - - +
131A LEU* 1.3 61.9 + - - +
133A ALA* 3.2 9.4 + - - +
134A ILE* 3.1 28.3 + - + +
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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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10A ILE* 4.9 2.3 - - + +
12A VAL* 3.5 16.2 - - + +
90A VAL* 4.1 19.3 - - + +
97A ILE* 4.2 13.9 - - + +
98A VAL* 4.1 21.3 - - + +
101A VAL* 3.5 34.8 - - + -
113A VAL* 3.8 24.0 - - + -
127A GLN* 3.1 21.4 + - + +
128A VAL* 3.1 12.8 + - + +
130A GLN* 1.3 72.7 - - - +
132A MET* 1.3 65.2 + - - +
134A ILE* 3.6 7.0 - - + +
135A ALA* 3.1 28.9 + - - +
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Residues in contact with MET 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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12A VAL* 3.9 18.4 - - + -
14A CYS* 3.5 27.8 - - - -
117A ASP* 4.6 7.4 - - - -
128A VAL* 2.9 33.4 + - + +
129A PRO* 3.2 14.1 + - - +
131A LEU* 1.3 78.4 - - - +
133A ALA* 1.3 61.2 + - - +
135A ALA* 3.8 4.5 + - - +
138A VAL* 3.3 45.0 - - + +
140A LYS* 4.2 17.5 - - - +
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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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129A PRO 3.0 13.4 + - - +
130A GLN* 3.2 11.9 + - - +
132A MET* 1.3 79.1 - - - +
134A ILE* 1.3 62.5 + - + +
135A ALA 3.6 3.1 + - - +
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Residues in contact with ILE 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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10A ILE* 3.8 20.0 - - + +
98A VAL* 3.9 24.5 - - + -
101A VAL* 4.0 12.1 - - + -
102A GLN* 3.7 46.4 + - + +
130A GLN* 3.1 16.1 + - + +
131A LEU* 3.6 10.3 - - + +
133A ALA* 1.3 78.1 - - + +
135A ALA* 1.3 65.2 + - - +
136A GLU* 3.6 8.5 + - - +
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Residues in contact with ALA 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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10A ILE* 3.8 18.6 - - + +
12A VAL* 3.7 14.4 - - + -
131A LEU 3.1 20.0 + - - +
132A MET 4.1 10.2 - - - +
133A ALA 3.4 4.3 - - - +
134A ILE* 1.3 79.7 - - - +
136A GLU* 1.3 63.6 + - - +
137A HIS* 3.6 20.7 - - - +
138A VAL* 4.1 3.0 - - + +
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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