Contacts of the helix formed by residues 138 - 149 (chain B) in PDB entry 2QPA
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 LEU 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B VAL* 4.1 16.6 - - + -
136B ALA* 5.2 4.0 - - + -
137B GLY* 1.3 71.7 - - - +
139B GLU* 1.3 72.1 + - - +
140B GLY 3.1 4.2 + - - +
141B ALA* 3.9 11.0 - - + +
142B LYS* 3.0 24.4 + - + +
177B THR* 5.0 8.1 - - - +
182B LEU* 3.9 30.5 - - + -
296B ILE* 3.3 36.1 - - + -
297B PRO* 3.7 34.3 - - + +
299B PRO* 6.3 1.9 - - + +
300B ASP* 5.4 0.4 + - - -
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Residues in contact with GLU 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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137B GLY* 2.8 11.6 + - - +
138B LEU* 1.3 83.7 + - - +
140B GLY* 1.3 62.0 + - - +
142B LYS* 3.5 21.7 - - - +
143B GLU* 3.5 7.6 + - - +
300B ASP* 4.2 22.7 - - - +
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Residues in contact with GLY 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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138B LEU* 3.1 0.8 - - - +
139B GLU* 1.3 79.0 + - - +
141B ALA* 1.3 66.9 + - - +
142B LYS 2.9 2.0 - - - -
143B GLU* 2.9 19.6 + - - +
144B ALA* 3.1 11.1 + - - +
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Residues in contact with ALA 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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138B LEU* 3.7 19.0 + - + +
140B GLY* 1.3 73.3 - - - +
142B LYS* 1.3 62.9 + - - +
144B ALA* 3.2 7.9 + - - +
145B LEU* 3.0 26.6 + - - +
182B LEU* 4.3 6.1 - - + -
294B ILE* 3.8 13.6 - - + +
295B TYR 4.3 4.0 + - - +
296B ILE* 3.2 35.9 - - + -
297B PRO* 5.5 0.9 - - + -
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Residues in contact with LYS 142 (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 TRP* 3.4 66.9 + - + +
133B GLU* 5.4 1.0 - - - +
135B VAL* 4.1 13.1 + - + -
136B ALA 4.9 0.6 + - - -
137B GLY 3.1 18.7 + - - -
138B LEU* 3.0 25.7 + - + +
139B GLU* 3.5 13.4 - - - +
141B ALA* 1.3 75.2 - - - +
143B GLU* 1.3 69.7 + - - +
145B LEU* 3.1 12.0 + - - +
146B LYS* 3.1 23.9 + - - +
182B LEU* 4.6 8.5 - - + -
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Residues in contact with GLU 143 (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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139B GLU 3.5 7.3 + - - +
140B GLY* 2.9 13.1 + - - +
142B LYS* 1.3 80.3 - - - +
144B ALA* 1.3 63.8 + - - +
146B LYS* 3.0 21.5 + - - +
147B GLU* 2.8 66.3 + - - +
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Residues in contact with ALA 144 (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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140B GLY 3.1 6.7 + - - +
141B ALA* 3.2 12.3 - - - +
143B GLU* 1.3 79.5 - - - +
145B LEU* 1.3 64.8 + - - +
147B GLU* 3.0 12.8 + - - +
148B ALA* 2.9 24.7 + - - +
292B ARG* 3.9 23.6 + - - +
294B ILE* 3.9 19.5 - - + -
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Residues in contact with LEU 145 (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 TRP* 3.5 16.4 - - + -
141B ALA* 3.0 11.7 + - - +
142B LYS 3.1 2.2 + - - +
144B ALA* 1.3 77.0 - - - +
146B LYS* 1.3 67.7 + - - +
148B ALA* 3.0 3.8 + - - +
149B VAL* 2.9 26.9 + - + +
150B ILE* 4.7 1.6 - - - -
169B ILE* 4.2 22.2 - - + -
171B LEU* 4.1 22.2 - - + -
182B LEU* 3.5 39.5 - - + +
183B ALA* 5.2 0.9 - - - +
186B VAL* 3.3 28.9 - - + -
273B LEU* 4.6 7.4 - - + -
294B ILE* 4.2 7.4 - - + -
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Residues in contact with LYS 146 (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 TRP* 3.6 49.4 - - + +
142B LYS* 3.1 20.1 + - - +
143B GLU* 3.0 22.2 + - - +
145B LEU* 1.3 73.8 - - - +
147B GLU* 1.3 57.4 + - + +
148B ALA 2.9 7.4 + - - -
150B ILE* 2.8 48.7 + - + -
151B LEU* 3.1 8.9 + - - -
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Residues in contact with GLU 147 (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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143B GLU* 2.8 53.6 + - - +
144B ALA* 3.0 12.5 + - - +
146B LYS* 1.3 75.5 - - + +
148B ALA* 1.3 56.6 + - - +
151B LEU* 4.1 30.5 - - + +
152B PRO* 4.3 3.1 - - - +
292B ARG* 6.1 2.7 - - - +
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Residues in contact with ALA 148 (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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144B ALA 2.9 14.7 + - - +
145B LEU* 3.0 4.4 + - + +
147B GLU* 1.3 77.4 - - - +
149B VAL* 1.3 64.6 + - - +
152B PRO* 3.6 16.7 - - - +
166B THR* 3.4 21.8 + - + +
169B ILE* 4.2 18.1 - - + +
271B LEU* 4.3 4.3 - - - +
292B ARG* 4.4 25.4 - - + +
294B ILE* 5.7 0.7 - - + -
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Residues in contact with VAL 149 (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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145B LEU* 2.9 13.0 + - + +
148B ALA* 1.3 78.3 - - - +
150B ILE* 1.3 74.6 + - + +
151B LEU 3.3 1.1 - - - -
152B PRO* 3.2 9.5 - - - +
153B VAL* 3.3 26.1 - - + +
169B ILE* 3.3 31.6 - - + -
186B VAL* 4.2 24.2 - - + -
190B ALA* 4.9 7.6 - - + -
192B SER* 6.0 0.7 - - - +
228B ILE* 5.2 7.0 - - + -
271B LEU* 3.2 31.0 - - + +
273B LEU* 5.3 4.7 - - + -
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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