Contacts of the helix formed by residues 131 - 138 (chain A) in PDB entry 1A9N
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 TYR 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.7 23.1 - - + -
106A LEU* 3.9 11.0 - - + -
120A ILE* 3.5 23.2 - - + +
125A VAL* 3.6 34.1 - - + +
126A THR* 3.8 28.6 + - + +
128A LYS 3.2 17.2 + - - +
129A LYS 3.2 1.2 - - - -
130A HIS* 1.3 75.2 - - - +
132A ARG* 1.3 84.7 + - + +
134A TYR* 3.6 1.4 - - - +
135A VAL* 3.1 42.9 + - + +
145A LEU* 3.9 7.1 - - + +
146A ASP* 2.7 29.5 + - - -
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Residues in contact with ARG 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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130A HIS 3.3 1.0 - - - -
131A TYR* 1.3 90.2 - - + +
133A LEU* 1.3 70.5 + - + +
135A VAL* 3.2 5.2 + - - +
136A ILE* 3.1 29.1 + - + +
145A LEU* 3.2 46.6 + - + +
146A ASP* 4.5 5.3 + - - +
148A GLN* 3.4 35.1 + - - +
149A LYS 3.6 9.1 + - - -
150A VAL* 4.2 6.3 - - - +
154A GLU* 2.4 39.3 + - - +
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Residues in contact with LEU 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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130A HIS* 3.2 21.8 + - + +
132A ARG* 1.3 83.3 - - + +
134A TYR* 1.3 63.2 + - - +
136A ILE* 3.2 5.3 + - + -
137A TYR* 3.1 21.3 + - - +
154A GLU* 3.2 43.1 - - + +
157A GLU* 4.1 19.7 - - + +
158A ALA* 3.6 26.1 - - + +
161A MET* 4.8 8.7 - - + -
162A PHE* 4.3 10.1 - - + -
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Residues in contact with TYR 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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103A LEU* 3.3 57.2 + - + -
104A GLY* 3.9 4.0 - - - -
106A LEU* 5.1 4.9 - - + -
107A ASP* 2.3 35.1 + - - -
130A HIS 2.9 18.0 + - - +
131A TYR 3.6 4.3 - - - +
133A LEU* 1.3 75.8 - - - +
135A VAL* 1.3 70.0 + - + +
137A TYR* 4.0 3.7 - + - +
138A LYS* 3.0 37.4 + - + +
162A PHE* 3.6 39.1 - + + -
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Residues in contact with VAL 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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106A LEU* 3.7 20.0 - - + -
109A LEU* 6.3 0.2 - - + -
118A LEU* 4.0 26.0 - - + -
120A ILE* 4.9 2.2 - - + -
131A TYR* 3.1 44.4 + - + +
132A ARG 3.2 5.8 + - - +
134A TYR* 1.3 77.7 - - + +
136A ILE* 1.3 59.6 + - + +
138A LYS* 5.0 0.4 - - - -
139A VAL* 2.7 45.6 + - + +
142A VAL* 5.1 4.0 - - + -
145A LEU* 4.1 17.5 - - + -
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Residues in contact with ILE 136 (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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132A ARG* 3.1 24.4 + - + +
133A LEU* 3.2 11.2 + - + +
135A VAL* 1.3 76.6 - - + +
137A TYR* 1.3 59.0 + - - +
139A VAL 4.7 3.6 - - - -
140A PRO* 3.3 25.5 - - - +
142A VAL* 6.3 0.9 - - - -
145A LEU* 4.4 6.5 - - + -
150A VAL* 3.9 39.3 - - + -
154A GLU* 3.7 38.1 - - + +
155A ARG* 4.0 31.3 + - - +
158A ALA* 4.3 4.9 - - + -
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Residues in contact with TYR 137 (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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133A LEU 3.1 15.3 + - - +
134A TYR* 4.1 5.2 - + - +
136A ILE* 1.3 76.3 - - - +
138A LYS* 1.3 73.1 + - + +
140A PRO* 3.2 18.3 - - - +
158A ALA* 3.3 31.2 - - + +
159A GLU* 3.6 22.7 - - - -
162A PHE* 3.0 46.2 + + + -
163A LYS* 3.6 10.3 + - - -
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Residues in contact with LYS 138 (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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106A LEU 5.5 0.4 - - - +
107A ASP* 3.7 43.9 + - - +
110A ALA* 3.1 35.3 - - + +
134A TYR* 3.0 35.2 + - + +
135A VAL* 4.4 1.1 - - - +
137A TYR* 1.3 88.4 - - + +
139A VAL* 1.3 61.7 + - + +
140A PRO* 3.3 5.3 - - - +
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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