Contacts of the helix formed by residues 138 - 150 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C VAL* 3.7 21.1 - - + -
136C ALA* 6.1 0.4 - - + -
137C GLY* 1.3 74.5 - - - +
139C GLU* 1.3 63.5 + - - +
140C GLY 3.5 0.9 - - - -
141C ALA* 4.3 11.0 - - + +
142C LYS* 2.9 32.9 + - + +
177C THR* 4.7 10.5 - - - +
182C LEU* 3.7 18.4 - - + -
296C ILE* 3.3 38.6 - - + -
297C PRO* 3.4 37.2 - - + +
298C LEU 6.1 0.2 - - - -
299C PRO* 6.1 2.5 - - + +
300C ASP* 5.8 0.2 + - - -
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Residues in contact with GLU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLY* 3.9 20.4 - - - +
138C LEU* 1.3 73.1 + - - +
140C GLY* 1.3 71.2 + - - +
142C LYS* 3.1 23.8 - - - +
143C GLU* 3.1 7.4 + - - +
300C ASP* 4.5 9.5 - - - +
303C ALA* 5.5 0.3 - - - +
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Residues in contact with GLY 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLU* 1.3 77.8 - - - +
141C ALA* 1.3 66.6 + - - +
143C GLU* 2.7 21.3 + - - +
144C ALA* 2.9 12.1 + - - -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 4.2 19.2 - - + +
140C GLY* 1.3 71.4 - - - +
142C LYS* 1.3 64.9 + - - +
144C ALA* 3.1 6.3 + - - +
145C LEU* 2.9 28.1 + - + +
182C LEU* 4.9 1.1 - - + -
294C ILE* 4.1 15.6 - - + +
295C TYR 4.3 6.3 - - - +
296C ILE* 3.4 33.0 - - + -
297C PRO* 5.3 1.1 - - + -
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TRP* 2.7 63.5 + - + +
135C VAL* 3.4 37.2 + - - +
136C ALA 3.7 2.4 + - - -
137C GLY 3.4 21.4 + - - +
138C LEU* 2.9 19.9 + - + +
139C GLU* 3.1 12.8 + - + +
140C GLY 2.7 3.4 + - - -
141C ALA* 1.3 78.2 - - + +
143C GLU* 1.3 64.3 + - - +
145C LEU* 3.1 19.9 + - + +
146C LYS* 3.1 21.1 + - - +
182C LEU* 5.5 6.3 - - + -
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLN 3.8 4.2 - - - +
388A TRP* 3.6 19.3 + - - -
139C GLU 3.1 6.1 + - - +
140C GLY* 2.7 14.5 + - - +
142C LYS* 1.3 75.7 - - - +
144C ALA* 1.3 52.1 + - - +
146C LYS* 2.7 51.1 + - - +
147C GLU* 2.7 77.8 + - - +
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLY 2.9 10.0 + - - +
141C ALA* 3.1 16.6 - - - +
143C GLU* 1.3 76.5 - - - +
145C LEU* 1.3 64.3 + - - +
147C GLU* 3.2 13.2 + - - +
148C ALA* 3.0 25.2 + - - +
292C ARG* 4.3 20.3 + - - +
294C ILE* 4.4 15.9 - - + -
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TRP* 4.6 4.7 - - + -
141C ALA* 2.9 36.6 + - + +
142C LYS* 3.1 11.0 + - - +
144C ALA* 1.3 74.1 - - - +
146C LYS* 1.3 53.5 + - - +
148C ALA* 3.0 4.0 + - - -
149C VAL* 2.7 44.5 + - + +
150C ILE* 4.1 2.2 - - - -
169C ILE* 5.6 1.3 - - + -
171C LEU* 4.4 17.5 - - + -
182C LEU* 3.4 34.1 - - + -
186C VAL* 3.4 34.3 - - + -
273C LEU* 4.6 11.4 - - + -
294C ILE* 3.9 19.5 - - + +
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A TRP* 4.5 12.3 - - + -
389A THR* 6.5 0.9 - - - -
132C TRP* 3.5 48.6 - - + +
142C LYS* 3.1 7.9 + - - +
143C GLU* 2.7 52.0 + - - +
145C LEU* 1.3 74.7 - - - +
147C GLU* 1.3 55.7 + - - +
148C ALA 2.7 10.7 + - - -
150C ILE* 2.6 55.0 + - + +
151C LEU 3.5 1.4 + - - -
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLN* 3.0 68.1 + - + +
388A TRP* 4.5 4.9 - - + -
143C GLU* 2.7 59.9 + - - +
144C ALA* 3.7 10.5 - - - +
146C LYS* 1.3 69.7 - - - +
148C ALA* 1.3 57.5 + - - +
151C LEU* 4.4 11.2 - - - +
152C PRO* 4.2 10.5 - - - +
159C PHE* 5.3 2.8 - - - -
292C ARG* 5.6 4.3 + - - +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ALA 3.0 15.6 + - - +
145C LEU* 3.0 4.4 + - - +
146C LYS 2.7 6.5 + - - -
147C GLU* 1.3 77.8 - - - +
149C VAL* 1.3 60.2 + - - +
152C PRO* 3.2 18.7 - - - +
165C PRO* 5.4 1.6 - - - +
166C THR* 4.8 14.8 + - - +
169C ILE* 4.3 17.7 - - + +
271C LEU* 4.8 4.9 - - - +
292C ARG* 4.8 21.8 - - + +
294C ILE* 5.5 2.0 - - + -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU* 2.7 24.7 + - + +
148C ALA* 1.3 74.6 - - - +
150C ILE* 1.3 67.0 - - + +
152C PRO* 3.6 5.6 - - - +
153C VAL* 3.2 27.2 - - + +
169C ILE* 3.4 32.1 - - + -
186C VAL* 4.3 20.4 - - + -
190C ALA* 5.3 6.1 - - + -
228C ILE* 5.2 7.6 - - + -
271C LEU* 3.7 30.6 - - + +
273C LEU* 5.6 2.7 - - + -
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A TRP* 3.8 24.5 - - + -
132C TRP* 4.9 4.3 - - + -
145C LEU 3.7 5.2 - - - +
146C LYS* 2.6 52.3 + - + +
149C VAL* 1.3 78.6 - - + +
151C LEU* 1.3 71.8 + - - +
152C PRO 3.0 1.3 - - - -
153C VAL* 2.6 29.4 + - + +
154C LYS* 2.8 20.0 + - + -
186C VAL* 4.3 14.1 - - + -
189C GLU* 4.8 13.5 - - + +
190C ALA* 4.8 8.5 - - + -
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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