Contacts of the helix formed by residues 126 - 137 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B GLU* 5.3 1.9 + - - -
109B GLY* 4.1 6.2 + - - -
110B PHE* 3.6 19.3 - - - -
123B ASN 4.6 0.4 + - - -
124B GLY* 3.3 3.0 - - - -
125B ILE* 1.3 79.3 - - - +
127B GLY* 1.3 65.5 + - - +
128B PRO* 4.2 1.6 - - - +
129B GLU* 3.1 23.8 + - - +
130B TYR* 2.8 23.2 + - - +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 3.3 18.4 + - - -
107B ARG* 3.2 27.6 + - - -
125B ILE* 3.4 1.2 - - - +
126B GLY* 1.3 76.1 - - - +
128B PRO* 1.3 69.7 - - - +
130B TYR* 3.2 4.9 + - - +
131B ILE* 2.9 29.9 + - - +
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Residues in contact with PRO 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 3.6 22.9 - - + -
13B PHE* 4.1 25.6 - - + -
14B GLU* 5.2 2.5 - - - +
104B ALA* 3.9 16.7 - - + +
126B GLY* 3.5 2.5 - - - +
127B GLY* 1.3 88.9 - - - +
129B GLU* 1.3 67.8 + - - +
131B ILE* 3.1 11.3 + - + +
132B TYR* 2.7 34.1 + - - +
212B SER* 3.6 10.4 + - - -
216B MET* 4.4 20.9 - - + -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.9 4.7 - - + -
7B GLU 3.5 22.2 - - - +
9B VAL* 3.7 17.9 - - + +
11B PHE* 4.0 7.2 - - + -
14B GLU* 3.2 15.7 - - - +
110B PHE* 3.5 17.3 - - + -
126B GLY* 3.1 21.6 - - - +
128B PRO* 1.3 87.5 - - - +
130B TYR* 1.3 56.6 + - - +
132B TYR* 2.8 10.8 + - - +
133B SER* 2.6 38.5 + - - -
257B SR 2.9 26.7 - - - -
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.1 23.8 - - + +
107B ARG* 3.6 33.4 - - + -
108B ALA 4.6 6.3 - - - +
109B GLY* 4.6 5.4 - - - -
126B GLY 2.8 13.5 + - - +
127B GLY* 3.3 9.6 - - - +
129B GLU* 1.3 75.3 - - - +
131B ILE* 1.3 71.4 + - + +
133B SER* 3.1 6.6 + - - -
134B VAL* 2.8 48.3 + - + +
159B ALA* 4.0 20.2 - - + -
160B PHE* 3.5 17.4 - - - -
161B GLN* 5.0 3.3 + - + -
162B ASN* 5.2 2.0 + - - -
301B HEM 2.4 44.3 + - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B MET* 3.6 32.5 - - + -
104B ALA* 3.7 26.0 - - + +
107B ARG* 5.6 0.2 - - + -
127B GLY 2.9 18.3 + - - +
128B PRO* 3.3 8.7 - - + +
130B TYR* 1.3 80.6 - - + +
132B TYR* 1.3 68.5 + - - +
134B VAL* 3.1 8.5 + - - +
135B LEU* 3.0 31.7 + - + +
212B SER* 3.8 13.0 - - - +
215B LEU* 4.4 28.0 - - + -
301B HEM 4.2 18.2 - - + -
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 4.0 21.3 - - + -
9B VAL* 3.3 32.7 - - + +
11B PHE* 4.6 2.9 - + + -
128B PRO 2.7 16.7 + - - +
129B GLU* 2.8 15.7 + - - +
131B ILE* 1.3 69.0 - - - +
133B SER* 1.3 76.1 + - - +
135B LEU* 2.8 18.9 + - - +
136B THR* 2.9 38.1 + - + +
205B HIS* 3.1 52.5 + + - +
208B ALA* 3.8 3.8 - - + -
209B GLU* 3.5 29.2 - - + -
212B SER* 3.5 11.4 + - - +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.6 8.3 - - - -
7B GLU* 3.1 35.2 + - - +
129B GLU 2.6 18.5 + - - -
130B TYR* 3.3 10.1 - - - -
132B TYR* 1.3 79.0 - - - +
134B VAL* 1.3 53.7 + - - +
136B THR* 3.0 5.0 + - - -
137B GLY* 2.4 37.9 + - - -
159B ALA* 3.8 19.7 - - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 2.8 65.5 + - + +
131B ILE* 3.5 7.0 - - - +
133B SER* 1.3 73.2 - - - +
135B LEU* 1.3 63.4 + - + +
137B GLY 3.4 2.1 + - - -
138B PHE* 3.4 6.5 - - - -
157B ASN* 3.0 43.4 + - - +
159B ALA* 4.2 5.2 - - + -
160B PHE* 4.9 1.8 - - + +
183B ILE* 4.2 20.4 - - + -
185B MET* 4.3 14.1 - - + -
301B HEM 4.8 10.8 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 3.0 20.1 + - + +
132B TYR 2.8 7.2 + - - +
134B VAL* 1.3 77.3 - - + +
136B THR* 1.3 63.0 + - - +
138B PHE* 3.5 16.7 + - - +
185B MET* 4.2 7.6 - - + -
188B PRO* 3.9 15.4 - - + +
189B LEU* 3.8 26.0 - - + +
204B VAL* 4.8 3.8 - - - +
208B ALA* 3.8 16.2 - - + +
211B VAL* 3.6 31.4 - - + -
212B SER* 4.4 0.9 - - - +
301B HEM 3.7 47.1 - - + -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 5.3 7.9 - - + -
132B TYR* 2.9 44.6 + - + +
133B SER* 3.5 10.8 - - - -
135B LEU* 1.3 79.9 - - - +
137B GLY* 1.3 56.7 + - - +
138B PHE 2.9 14.7 + - - +
158B ARG* 5.4 1.9 + - - -
204B VAL* 5.4 7.6 - - - +
205B HIS* 5.4 3.7 - - - -
208B ALA* 4.4 3.9 - - - +
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B SER 2.4 20.2 + - - -
134B VAL 3.9 2.7 - - - -
135B LEU 3.4 1.2 - - - -
136B THR* 1.3 70.7 - - - +
138B PHE* 1.3 56.5 + - - +
139B PRO* 3.1 8.1 - - - +
157B ASN* 3.2 12.1 - - - -
158B ARG* 2.8 47.6 + - - +
159B 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