Contacts of the helix formed by residues 126 - 137 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14Q GLU* 5.3 1.5 + - - -
109Q GLY* 4.0 6.2 + - - -
110Q PHE* 3.6 25.6 - - - -
123Q ASN 4.5 0.6 + - - -
124Q GLY* 3.1 5.3 - - - -
125Q ILE* 1.3 78.1 - - - +
127Q GLY* 1.3 64.6 + - - +
128Q PRO* 3.4 4.4 - - - +
129Q GLU* 3.2 15.1 + - - +
130Q TYR* 2.8 22.7 + - - +
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Residues in contact with GLY 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q ALA* 3.5 14.3 + - - -
107Q ARG* 3.4 26.3 + - - -
125Q ILE* 3.2 5.9 + - - +
126Q GLY* 1.3 74.3 - - - +
128Q PRO* 1.3 70.9 - - - +
130Q TYR* 3.0 6.8 + - - +
131Q ILE* 2.8 28.8 + - - +
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Residues in contact with PRO 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q PHE* 3.6 21.3 - - + -
13Q PHE* 4.1 24.5 - - + -
14Q GLU* 4.7 2.0 - - - +
104Q ALA* 4.0 12.0 - - + +
126Q GLY* 3.5 2.0 - - - +
127Q GLY* 1.3 88.2 - - - +
129Q GLU* 1.3 70.7 + - - +
131Q ILE* 2.9 15.3 + - + +
132Q TYR* 2.7 34.0 + - - +
212Q SER* 3.7 9.6 + - - -
216Q MET* 4.3 22.4 - - + -
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Residues in contact with GLU 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q VAL* 4.9 3.4 - - + -
7Q GLU 3.4 13.0 - - - +
9Q VAL* 3.7 28.7 - - + +
11Q PHE* 3.8 11.3 - - + -
14Q GLU* 3.4 15.7 - - - +
110Q PHE* 3.1 32.4 - - + -
123Q ASN 4.2 0.2 - - - +
126Q GLY* 3.5 9.1 - - - +
127Q GLY 3.2 0.2 - - - -
128Q PRO* 1.3 108.8 - - - +
130Q TYR* 1.3 66.5 + - - +
132Q TYR* 2.8 11.0 + - - +
133Q SER* 2.6 27.2 + - - -
258Q SR 3.4 16.6 - - - -
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Residues in contact with TYR 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q VAL* 4.2 23.1 - - + +
107Q ARG* 3.5 33.4 - - + -
108Q ALA 4.4 15.9 - - - +
126Q GLY 2.8 13.9 + - - +
127Q GLY* 3.3 10.3 - - - +
129Q GLU* 1.3 75.3 - - - +
131Q ILE* 1.3 72.5 + - + +
133Q SER* 3.0 6.8 + - - -
134Q VAL* 2.8 47.8 + - + +
159Q ALA* 4.0 20.9 - - + -
160Q PHE* 3.4 18.9 - - - -
161Q GLN* 5.3 2.9 - - + -
162Q ASN* 5.0 3.2 + - - -
301Q HEM 2.4 42.9 + - + -
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Residues in contact with ILE 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q MET* 3.5 33.7 - - + +
104Q ALA* 3.6 28.7 - - + +
107Q ARG* 5.6 0.2 - - + -
127Q GLY 2.8 20.3 + - - +
128Q PRO* 3.2 8.3 - - + +
130Q TYR* 1.3 82.3 - - + +
132Q TYR* 1.3 67.7 + - - +
134Q VAL* 3.1 6.3 + - - +
135Q LEU* 3.1 31.6 + - + +
212Q SER* 3.9 12.3 - - - +
215Q LEU* 4.4 25.6 - - + -
301Q HEM 4.0 19.3 - - + -
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Residues in contact with TYR 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q GLU* 3.8 25.1 - - + -
9Q VAL* 3.3 32.0 - - + +
11Q PHE* 4.6 2.9 - + + -
128Q PRO 2.7 15.9 + - - +
129Q GLU* 2.8 13.9 + - - +
131Q ILE* 1.3 72.0 - - - +
133Q SER* 1.3 74.7 + - - +
135Q LEU* 2.9 19.5 + - - +
136Q THR* 2.9 36.7 + - + +
205Q HIS* 3.2 51.7 + + - +
208Q ALA* 3.8 4.3 - - + -
209Q GLU* 3.5 29.6 - - + -
212Q SER* 3.5 10.7 + - - +
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Residues in contact with SER 133 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q VAL* 3.5 10.6 - - - +
7Q GLU* 3.0 36.2 + - - +
129Q GLU 2.6 18.0 + - - -
130Q TYR* 3.2 10.5 - - - -
132Q TYR* 1.3 78.1 - - - +
134Q VAL* 1.3 53.5 + - - +
136Q THR* 3.0 5.9 + - - -
137Q GLY* 2.4 37.9 + - - -
159Q ALA* 3.7 18.8 - - - +
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Residues in contact with VAL 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q TYR* 2.8 65.1 + - + +
131Q ILE* 3.5 7.2 - - - +
133Q SER* 1.3 72.3 - - - +
135Q LEU* 1.3 63.0 + - + +
137Q GLY 3.5 0.7 + - - -
138Q PHE* 3.1 8.7 - - - -
157Q ASN* 2.9 42.6 + - - +
159Q ALA* 4.2 4.5 - - + -
160Q PHE* 4.9 2.2 - - + +
183Q ILE* 4.2 20.9 - - + -
185Q MET* 4.3 14.8 - - + -
301Q HEM 5.0 10.8 - - + -
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Residues in contact with LEU 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q ILE* 3.1 19.2 + - + +
132Q TYR 2.9 6.7 + - - +
134Q VAL* 1.3 77.9 - - + +
136Q THR* 1.3 63.3 + - - +
138Q PHE* 3.6 14.3 + - - +
185Q MET* 4.1 7.6 - - + -
188Q PRO* 3.6 30.4 - - + +
189Q LEU* 4.5 7.6 - - + +
204Q VAL* 4.9 8.9 - - - +
208Q ALA* 3.8 22.4 - - + +
211Q VAL* 3.6 20.9 - - + -
212Q SER* 4.5 1.1 - - - +
301Q HEM 3.6 50.0 - - + -
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Residues in contact with THR 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q GLU* 5.2 8.7 - - + -
132Q TYR* 2.9 44.9 + - + +
133Q SER* 3.4 10.3 - - - -
135Q LEU* 1.3 78.9 - - - +
137Q GLY* 1.3 56.9 + - - +
138Q PHE 2.9 14.8 + - - +
204Q VAL* 5.4 7.9 - - - -
205Q HIS* 5.4 3.9 - - - -
208Q ALA* 4.4 4.0 - - - +
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Residues in contact with GLY 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133Q SER 2.4 21.0 + - - -
134Q VAL 3.5 2.9 + - - -
135Q LEU 3.3 1.2 - - - -
136Q THR* 1.3 69.7 - - - +
138Q PHE* 1.3 57.3 + - - +
139Q PRO* 3.0 8.7 - - - +
157Q ASN* 3.3 13.2 - - - -
158Q ARG* 2.9 42.5 + - - +
159Q ALA* 4.8 1.6 - - - -
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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