Contacts of the helix formed by residues 126 - 137 (chain N) in PDB entry 2QJK
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 GLY 126 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14N GLU* 5.8 0.4 + - - -
109N GLY* 4.0 6.9 + - - -
110N PHE* 3.6 15.8 - - - -
123N ASN 4.6 0.2 + - - -
124N GLY* 3.4 3.6 - - - -
125N ILE* 1.3 77.1 - - - +
127N GLY* 1.3 64.3 + - - +
128N PRO* 4.2 1.4 - - - +
129N GLU* 3.2 29.9 + - - +
130N TYR* 2.9 22.9 + - - +
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Residues in contact with GLY 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N ALA* 3.8 16.4 + - - -
107N ARG* 3.4 24.6 + - - -
125N ILE* 3.3 6.3 + - - +
126N GLY* 1.3 75.0 - - - +
128N PRO* 1.3 70.1 - - - +
130N TYR* 3.0 6.5 + - - +
131N ILE* 2.8 29.4 + - - +
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Residues in contact with PRO 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N PHE* 3.6 22.4 - - + -
13N PHE* 4.1 25.1 - - + -
14N GLU* 5.7 0.4 - - - +
104N ALA* 4.0 12.9 - - + +
126N GLY* 4.2 1.6 - - - +
127N GLY* 1.3 87.8 - - - +
129N GLU* 1.3 71.2 + - - +
131N ILE* 3.0 16.0 + - + +
132N TYR* 2.7 33.8 + - - +
212N SER* 3.6 11.0 + - - -
216N MET* 4.4 22.4 - - + -
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Residues in contact with GLU 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N VAL* 5.0 4.0 - - + -
7N GLU 3.5 14.1 - - - +
9N VAL 3.9 11.9 - - - +
11N PHE* 3.8 14.8 - - + -
14N GLU* 3.2 11.2 - - - +
110N PHE* 3.0 23.7 - - + -
126N GLY* 3.2 18.7 - - - +
128N PRO* 1.3 103.8 - - - +
130N TYR* 1.3 68.8 + - - +
132N TYR* 2.8 11.1 + - - +
133N SER* 2.6 28.4 + - - +
257N SR 2.9 34.7 - - - -
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Residues in contact with TYR 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N VAL* 4.2 23.8 - - + +
103N MET* 5.7 0.4 - - + -
107N ARG* 3.9 32.7 + - + -
108N ALA 4.7 12.6 - - - +
126N GLY 2.9 14.1 + - - +
127N GLY* 3.2 11.2 - - - +
129N GLU* 1.3 76.1 - - - +
131N ILE* 1.3 72.6 + - + +
133N SER* 3.1 7.2 + - - -
134N VAL* 2.8 49.6 + - + +
159N ALA* 4.0 19.3 - - + -
160N PHE* 3.5 19.6 - - - -
161N GLN* 4.9 3.1 + - + -
162N ASN* 5.0 2.9 + - - -
301N HEM 2.9 37.4 + - + +
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Residues in contact with ILE 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N MET* 4.0 16.2 - - + -
104N ALA* 3.7 37.9 - - + +
107N ARG* 6.0 0.4 - - + -
127N GLY* 2.8 17.3 + - - +
128N PRO* 3.2 9.4 - - + +
130N TYR* 1.3 85.4 - - + +
132N TYR* 1.3 67.4 + - - +
134N VAL* 3.1 6.6 + - - +
135N LEU* 3.0 31.1 + - + +
212N SER* 3.9 13.5 - - - +
215N LEU* 4.4 28.9 - - + -
301N HEM 4.1 21.5 - - + -
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Residues in contact with TYR 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N GLU* 3.9 23.6 - - + -
9N VAL* 3.3 31.9 - - + -
11N PHE* 4.6 2.9 - + + -
128N PRO 2.7 16.1 + - - +
129N GLU* 2.8 14.1 + - - +
131N ILE* 1.3 71.0 - - - +
133N SER* 1.3 76.9 + - - +
135N LEU* 2.9 11.8 + - - +
136N THR* 2.8 45.1 + - + +
205N HIS* 3.1 51.3 + + - +
208N ALA* 3.8 4.5 - - + -
209N GLU* 3.5 30.3 - - + -
212N SER* 3.5 10.7 + - - +
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Residues in contact with SER 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N VAL* 3.5 9.9 - - - +
7N GLU* 3.0 36.1 + - - +
129N GLU 2.6 17.6 + - - -
130N TYR* 3.3 11.2 - - - -
132N TYR* 1.3 78.1 - - - +
134N VAL* 1.3 54.0 + - - +
136N THR* 3.0 5.2 + - - -
137N GLY* 2.4 38.1 + - - -
159N ALA* 3.7 18.8 - - - -
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Residues in contact with VAL 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N TYR* 2.8 64.4 + - + +
131N ILE* 3.4 7.9 - - - +
133N SER* 1.3 72.6 - - - +
135N LEU* 1.3 62.8 + - + +
137N GLY 3.4 1.0 + - - -
138N PHE* 3.0 14.6 - - + -
157N ASN* 2.9 42.6 + - - +
159N ALA* 3.9 5.6 - - + +
160N PHE* 4.9 1.6 - - + +
183N ILE* 4.2 20.2 - - + -
185N MET* 4.3 10.8 - - + -
301N HEM 4.9 10.8 - - + -
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Residues in contact with LEU 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131N ILE* 3.0 20.3 + - + +
132N TYR 2.9 7.2 + - - +
134N VAL* 1.3 77.3 - - + +
136N THR* 1.3 62.3 + - - +
138N PHE* 3.5 15.5 + - - +
185N MET* 4.1 7.6 - - + -
188N PRO* 3.8 22.8 - - + +
189N LEU* 3.9 14.9 - - + +
204N VAL* 4.9 7.3 - - - +
208N ALA* 3.8 23.1 - - + +
211N VAL* 3.6 21.3 - - + -
212N SER* 4.5 0.9 - - - +
301N HEM 3.5 50.7 - - + -
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Residues in contact with THR 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N GLU* 5.1 8.5 - - + -
132N TYR* 2.8 44.9 + - + +
133N SER* 3.4 9.9 - - - -
135N LEU* 1.3 78.1 - - - +
137N GLY* 1.3 58.3 + - - +
138N PHE 2.9 15.3 + - - +
158N ARG* 5.7 1.2 + - - -
204N VAL* 5.4 7.8 - - - +
205N HIS* 5.5 3.9 - - - -
208N ALA* 4.4 3.9 - - - +
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Residues in contact with GLY 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N SER 2.4 21.7 + - - -
134N VAL 3.9 2.5 - - - -
135N LEU 3.3 0.8 - - - -
136N THR* 1.3 69.7 - - - +
138N PHE* 1.3 58.5 + - - +
139N PRO* 2.9 9.5 - - - +
157N ASN* 3.3 11.5 - - - -
158N ARG* 2.9 45.7 + - - +
159N ALA* 4.8 0.9 - - - -
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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