Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 2PJ7
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 ASN 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLY 3.0 10.5 + - - +
68A PHE* 3.1 29.2 + - - +
70A ALA* 3.9 8.4 - - - +
110A VAL* 4.0 3.6 - - - +
111A LEU* 1.3 74.8 - - + +
113A ILE* 1.3 60.6 + - - +
114A ASP* 4.1 2.8 + - - +
115A GLY* 3.1 16.3 + - - -
116A TYR* 3.0 17.7 + - - +
127A ARG 3.3 10.5 + - - -
128A LYS 3.0 25.8 + - - -
129A THR* 3.5 24.3 - - + +
143A PRO* 4.6 4.4 - - + +
175A GLU* 5.0 7.6 - - - +
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Residues in contact with ILE 113 (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 TRP* 3.5 52.3 - - + +
41A THR* 4.0 18.0 - - + +
45A ASN* 3.6 16.6 - - + +
46A ASN 3.2 33.4 - - - +
47A ILE* 3.9 7.9 - - + -
110A VAL* 3.5 35.4 - - + +
111A LEU 3.1 3.0 + - - +
112A ASN* 1.3 69.1 - - - +
114A ASP* 1.3 66.1 + - - +
116A TYR* 3.1 2.2 + - - +
117A ILE* 2.9 24.9 + - + +
175A GLU* 5.7 0.2 + - - -
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Residues in contact with ASP 114 (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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41A THR* 2.5 27.4 + - - +
42A PHE* 3.2 12.1 + - - +
43A LEU* 2.7 44.2 + - + +
45A ASN* 2.7 21.4 + - - +
112A ASN* 3.4 2.6 - - - +
113A ILE* 1.3 75.9 - - - +
115A GLY* 1.3 62.1 + - - +
117A ILE* 3.5 5.9 + - - +
118A TYR* 3.1 16.3 + - - +
130A ARG* 3.6 30.1 + - + +
175A GLU* 3.8 4.2 + - - +
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Residues in contact with GLY 115 (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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70A ALA* 3.2 22.1 - - - +
112A ASN* 3.1 19.1 + - - -
114A ASP* 1.3 73.8 - - - +
116A TYR* 1.3 66.4 + - - +
118A TYR* 3.0 4.9 + - - +
119A THR* 3.0 18.2 + - - +
126A TRP* 3.9 9.0 - - - -
128A LYS 3.8 11.0 - - - -
130A ARG* 4.0 5.3 - - - +
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Residues in contact with TYR 116 (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 TYR* 4.5 6.4 - - - +
13A ASN 2.6 36.1 + - - -
15A TRP* 4.0 20.0 - + + -
18A ILE* 3.7 18.5 - - + +
70A ALA* 3.5 15.0 - - - +
73A TRP* 3.4 28.8 - + - +
76A HIS* 3.2 41.7 - + - +
110A VAL* 4.3 5.4 - - + -
112A ASN 3.0 14.8 + - - +
113A ILE* 3.4 10.8 - - - +
115A GLY* 1.3 76.1 - - - +
117A ILE* 1.3 61.4 + - - +
119A THR* 2.5 23.5 + - - -
120A TRP* 3.1 31.0 + + - -
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Residues in contact with ILE 117 (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 TRP* 3.8 27.1 - - + +
16A GLU* 5.3 6.3 - - - +
43A LEU* 6.6 0.2 - - + -
45A ASN* 3.4 37.5 - - - +
113A ILE* 2.9 22.2 + - + +
114A ASP* 3.7 6.3 - - - +
116A TYR* 1.3 76.4 - - - +
118A TYR* 1.3 63.7 + - - +
120A TRP* 3.0 16.9 + - - +
121A THR* 3.0 29.8 + - + +
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Residues in contact with TYR 118 (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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114A ASP 3.1 13.7 + - - +
115A GLY* 3.0 11.0 + - - +
117A ILE* 1.3 77.6 - - - +
119A THR* 1.3 56.3 + - - +
121A THR* 3.6 7.6 - - - -
122A LYS* 2.8 57.1 + - + +
123A ASN* 3.0 24.3 + - + -
126A TRP* 3.8 28.3 - + + -
130A ARG* 3.4 52.2 + - + -
42B PHE 4.9 0.3 + - - -
43B LEU 3.7 2.4 + - - -
44B GLY* 3.0 29.9 + - - -
174B LYS* 5.9 0.3 + - - -
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Residues in contact with THR 119 (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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70A ALA* 3.5 24.7 - - + -
73A TRP* 3.0 35.3 + - - -
115A GLY 3.0 16.8 + - - +
116A TYR* 2.5 21.0 + - - -
118A TYR* 1.3 75.9 - - - +
120A TRP* 1.3 58.6 + - - +
122A LYS 4.8 0.3 + - - -
123A ASN 3.1 20.6 + - - +
124A ARG* 3.5 29.4 + - - +
126A TRP* 3.6 15.0 - - + +
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Residues in contact with TRP 120 (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 TYR* 3.3 31.6 - - + -
13A ASN 3.5 2.0 - - - -
14A ASN* 3.4 43.7 - - + -
15A TRP 5.3 0.4 - - - -
73A TRP* 3.5 35.8 - + - -
116A TYR* 3.1 49.3 + + - +
117A ILE* 3.0 11.7 + - + +
119A THR* 1.3 80.8 + - - +
121A THR* 1.3 64.3 + - + +
122A LYS 3.8 0.2 - - - -
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Residues in contact with THR 121 (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 ILE* 3.0 32.2 + - + +
118A TYR* 3.6 10.7 - - - -
120A TRP* 1.3 86.8 - - + +
122A LYS* 1.3 78.8 + - - +
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Residues in contact with LYS 122 (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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118A TYR* 2.8 44.2 + - + +
119A THR 4.8 0.6 + - - -
120A TRP 3.8 0.2 - - - -
121A THR* 1.3 89.6 + - - +
123A ASN* 1.3 59.7 + - + +
124A ARG 4.2 0.9 - - - -
42B PHE* 3.0 53.2 - - + +
43B LEU* 3.5 30.0 - - + +
174B LYS* 6.3 1.1 - - - +
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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