Contacts of the helix formed by residues 126 - 137 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E GLU* 5.6 0.7 - - - -
109E GLY* 4.0 6.5 + - - -
110E PHE* 3.6 24.2 - - - -
123E ASN 4.6 0.6 + - - -
124E GLY* 3.3 2.8 - - - -
125E ILE* 1.3 80.4 - - - +
127E GLY* 1.3 65.3 + - - +
128E PRO* 3.4 5.5 - - - +
129E GLU* 3.2 12.4 + - - +
130E TYR* 2.8 23.2 + - - +
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Residues in contact with GLY 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ALA* 3.5 15.6 + - - -
107E ARG* 3.3 27.0 + - - -
125E ILE* 3.5 4.6 - - - +
126E GLY* 1.3 75.5 - - - +
128E PRO* 1.4 70.6 - - - +
130E TYR* 3.1 5.2 + - - +
131E ILE* 2.8 29.8 + - - +
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Residues in contact with PRO 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PHE* 3.6 22.2 - - + -
13E PHE* 4.1 25.1 - - + -
14E GLU* 5.1 0.9 - - - +
104E ALA* 3.8 12.3 - - + +
126E GLY* 3.5 2.5 - - - +
127E GLY* 1.4 88.3 - - - +
129E GLU* 1.3 68.0 + - - +
131E ILE* 3.1 14.2 + - + +
132E TYR* 2.7 34.7 + - - +
212E SER* 3.6 10.7 + - - +
216E MET* 4.4 21.8 - - + -
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Residues in contact with GLU 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 4.8 4.5 - - + -
7E GLU 3.5 23.6 - - - +
9E VAL* 3.6 18.8 - - + +
11E PHE* 3.8 8.2 - - + -
14E GLU* 2.8 25.9 - - - +
110E PHE* 3.5 24.6 - - + -
126E GLY* 3.2 13.6 + - - +
128E PRO* 1.3 94.5 - - - +
130E TYR* 1.3 54.3 + - - +
132E TYR* 2.8 11.7 + - - +
133E SER* 2.6 37.7 + - - -
257E SR 2.9 17.5 - - - -
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Residues in contact with TYR 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 4.1 24.1 - - + +
107E ARG* 3.6 34.8 - - + -
108E ALA 4.5 7.9 - - - +
109E GLY* 4.5 5.6 - - - -
126E GLY 2.8 13.1 + - - +
127E GLY* 3.3 11.2 - - - +
129E GLU* 1.3 76.5 - - - +
131E ILE* 1.3 71.4 + - + +
133E SER* 3.1 6.6 + - - -
134E VAL* 2.8 47.1 + - + +
159E ALA* 4.0 20.6 - - + -
160E PHE* 3.4 17.8 - - - -
161E GLN* 5.0 3.5 + - + -
162E ASN* 5.2 1.8 + - - -
301E HEM 2.6 42.4 + - + +
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E MET* 3.7 22.4 - - + +
104E ALA* 3.6 37.9 - - + +
127E GLY 2.8 21.4 + - - +
128E PRO* 3.3 8.7 - - + +
130E TYR* 1.3 82.6 - - + +
132E TYR* 1.3 67.1 + - - +
134E VAL* 3.0 13.0 + - - +
135E LEU* 3.0 24.4 + - + +
212E SER* 3.8 13.5 - - - +
215E LEU* 4.4 26.2 - - + -
301E HEM 4.1 18.2 - - + -
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Residues in contact with TYR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLU* 3.9 23.3 - - + -
9E VAL* 3.3 31.0 - - + -
11E PHE* 4.6 3.1 - + + -
128E PRO 2.7 16.3 + - - +
129E GLU* 2.8 13.9 + - - +
131E ILE* 1.3 71.9 - - - +
133E SER* 1.3 75.3 + - - +
135E LEU* 2.9 11.0 + - - +
136E THR* 2.9 44.9 + - + +
205E HIS* 3.1 51.3 + + - +
208E ALA* 3.8 4.3 - - + -
209E GLU* 3.5 30.7 - - + -
212E SER* 3.5 10.9 + - - +
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Residues in contact with SER 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 3.6 7.7 - - - -
7E GLU* 3.1 36.0 + - - +
129E GLU 2.6 18.3 + - - -
130E TYR* 3.3 9.6 - - - -
132E TYR* 1.3 76.9 - - - +
134E VAL* 1.3 54.6 + - - +
136E THR* 3.0 5.2 + - - -
137E GLY* 2.5 37.4 + - - -
159E ALA* 3.8 20.2 - - - -
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E TYR* 2.8 63.3 + - + +
131E ILE* 3.4 7.6 - - - +
133E SER* 1.3 71.6 - - - +
135E LEU* 1.3 60.8 + - + +
137E GLY 3.4 0.3 + - - -
138E PHE* 2.8 26.9 - - - -
157E ASN* 2.9 26.0 + - - +
159E ALA* 4.0 5.6 - - + +
160E PHE* 4.9 1.1 - - + +
183E ILE* 4.0 20.4 - - + -
185E MET* 4.3 16.4 - - + -
301E HEM 4.8 11.0 - - + -
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E ILE* 3.0 19.9 + - + +
132E TYR 2.9 7.2 + - - +
134E VAL* 1.3 77.8 - - + +
136E THR* 1.3 62.4 + - - +
138E PHE* 3.6 14.4 + - - +
185E MET* 4.2 4.7 - - + -
188E PRO* 3.6 26.7 - - + +
189E LEU* 4.7 8.6 - - + +
204E VAL* 4.9 9.5 - - - +
208E ALA* 3.9 22.2 - - + +
211E VAL* 3.6 20.9 - - + -
212E SER* 4.5 1.1 - - - +
301E HEM 3.4 54.5 - - + -
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Residues in contact with THR 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLU* 5.0 11.7 - - + -
132E TYR* 2.9 44.6 + - + +
133E SER* 3.5 10.8 - - - -
135E LEU* 1.3 79.1 - - - +
137E GLY* 1.3 56.6 + - - +
138E PHE* 2.9 15.2 + - - +
158E ARG* 5.6 1.4 + - - -
204E VAL* 5.4 8.0 - - - +
205E HIS* 5.4 3.9 - - - -
208E ALA* 4.4 4.6 - - - +
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Residues in contact with GLY 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E SER 2.5 22.2 + - - -
134E VAL 3.9 2.5 - - - -
135E LEU 3.3 1.4 - - - -
136E THR* 1.3 69.3 - - - +
138E PHE* 1.3 63.2 + - - +
139E PRO* 3.0 8.9 - - - +
157E ASN* 3.2 7.8 - - - -
158E ARG* 2.8 43.9 + - - +
159E ALA* 4.8 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