Contacts of the helix formed by residues 131 - 141 (chain B) in PDB entry 2QF9
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 THR 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B MSE 4.9 3.8 - - - +
130B ALA* 1.3 78.0 - - - +
132B ASP* 1.3 65.2 + - - +
133B ALA* 3.5 8.9 + - - +
134B GLU* 2.9 35.0 + - - +
135B MSE 3.0 22.4 + - - +
211B HIS* 4.4 17.7 - - + -
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Residues in contact with ASP 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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56B GLN* 5.7 2.3 + - - -
130B ALA 5.5 0.2 - - - +
131B THR* 1.3 73.7 - - - +
133B ALA* 1.3 58.2 + - - +
135B MSE 3.2 9.8 + - - +
136B LYS* 2.9 45.9 + - - +
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Residues in contact with ALA 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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131B THR* 3.2 8.6 - - - +
132B ASP* 1.3 80.2 - - - +
134B GLU* 1.3 57.8 + - + +
136B LYS* 3.3 15.1 + - - +
137B LYS* 2.8 29.0 + - - +
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Residues in contact with GLU 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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129B MSE 4.4 0.9 - - - +
130B ALA* 3.3 11.8 - - + +
131B THR* 2.9 40.5 + - - +
133B ALA* 1.3 72.8 - - + +
135B MSE 1.3 67.2 + - - +
137B LYS* 3.3 6.0 + - + +
138B LEU* 3.0 21.0 + - - +
149B TYR* 3.3 30.2 + - - +
153B LEU* 4.0 19.0 - - + +
210B HIS* 4.9 8.1 - - - +
211B HIS* 2.7 35.4 + - - -
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Residues in contact with MSE 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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56B GLN* 3.9 30.1 - - + +
59B GLU* 3.8 17.5 - - + -
60B MSE 3.8 52.3 - - - +
63B ILE* 3.8 32.9 - - + +
130B ALA* 4.1 3.6 - - + -
131B THR 3.0 20.2 + - - +
132B ASP* 3.2 10.7 + - - +
134B GLU* 1.3 76.2 - - - +
136B LYS* 1.3 61.6 + - + +
138B LEU* 3.4 6.9 + - - +
139B GLY* 3.2 17.0 + - - -
153B LEU* 5.1 0.9 - - - -
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Residues in contact with LYS 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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132B ASP* 2.9 35.9 + - - +
133B ALA* 3.6 13.9 - - - +
134B GLU 3.2 0.2 - - - -
135B MSE 1.3 73.3 - - + +
137B LYS* 1.3 66.9 + - - +
139B GLY* 3.1 12.9 + - - -
140B THR* 3.3 18.3 + - + +
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Residues in contact with LYS 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 ALA 2.8 20.7 + - - +
134B GLU* 3.5 6.3 - - + +
136B LYS* 1.3 72.2 - - - +
138B LEU* 1.3 63.7 + - - +
140B THR* 2.7 30.5 + - - +
141B LEU* 3.5 20.5 - - + +
149B TYR* 3.5 48.1 + - + +
210B HIS* 6.0 1.8 + - - -
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Residues in contact with LEU 138 (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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60B MSE 3.4 41.5 - - + +
63B ILE* 3.7 23.6 - - + -
64B VAL* 4.5 5.4 - - + +
67B ARG* 3.9 5.2 - - + +
134B GLU 3.0 13.4 + - - +
135B MSE 3.6 9.9 - - - +
137B LYS* 1.3 76.1 - - - +
139B GLY* 1.3 58.5 + - - +
140B THR 3.1 4.9 + - - -
141B LEU* 3.1 18.2 + - + +
146B ALA* 3.7 30.3 - - + +
149B TYR* 3.9 18.6 - - + -
150B TYR* 3.8 22.0 - - + +
153B LEU* 4.5 4.9 - - + -
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Residues in contact with GLY 139 (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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63B ILE* 3.7 18.3 - - - +
67B ARG* 3.2 28.6 + - - -
135B MSE 3.2 7.0 + - - -
136B LYS* 3.1 10.7 + - - -
138B LEU* 1.3 77.2 - - - +
140B THR* 1.3 58.4 + - - +
141B LEU 3.5 0.4 - - - -
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Residues in contact with THR 140 (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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67B ARG* 3.6 11.0 + - - +
136B LYS* 3.3 18.2 - - + +
137B LYS* 2.7 22.1 + - - +
139B GLY* 1.3 79.8 - - - +
141B LEU* 1.3 71.3 + - - +
142B ASP* 4.1 5.4 + - - +
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Residues in contact with LEU 141 (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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67B ARG* 2.7 34.1 + - - +
137B LYS* 3.5 26.5 - - + +
138B LEU* 3.1 7.2 + - - +
140B THR* 1.3 89.6 - - - +
142B ASP* 1.3 57.2 + - - +
145B GLN* 3.8 29.6 - - + +
146B ALA* 3.7 17.5 - - - +
149B TYR* 3.4 44.6 - - + -
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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