Contacts of the helix formed by residues 150 - 155 (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 ILE 150 (chain C).
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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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Residues in contact with LEU 151 (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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351A ILE* 4.7 6.7 - - + +
354A ILE* 4.7 17.9 - - + -
355A GLN* 3.6 38.4 - - + +
388A TRP* 3.2 47.8 - - + -
146C LYS 3.5 1.0 + - - -
147C GLU* 4.4 8.7 - - - +
150C ILE* 1.3 78.5 - - - +
152C PRO* 1.3 71.1 - - + +
154C LYS 4.3 0.4 - - - +
155C PHE* 2.8 51.5 + - + +
158C LEU* 5.9 2.2 - - + -
159C PHE* 3.8 12.8 - - + -
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Residues in contact with PRO 152 (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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147C GLU 4.2 2.5 - - - +
148C ALA* 3.2 26.5 - - - +
149C VAL* 3.6 11.9 - - - +
150C ILE 3.1 5.8 - - - +
151C LEU* 1.3 96.7 - - + +
153C VAL* 1.3 60.9 + - + +
156C PRO* 3.6 20.4 - - - +
159C PHE* 3.3 39.5 - - + +
165C PRO* 3.9 20.6 - - + +
271C LEU* 6.0 2.9 - - + -
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Residues in contact with VAL 153 (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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149C VAL* 3.2 20.0 - - + +
150C ILE* 2.6 34.7 + - + +
152C PRO* 1.3 76.1 - - + +
154C LYS* 1.3 59.8 + - + +
155C PHE 3.3 2.5 - - - -
156C PRO* 3.1 21.3 - - - +
190C ALA* 5.6 8.1 - - + -
226C PRO* 6.2 4.0 - - + -
269C GLY 5.9 2.5 - - - +
271C LEU* 5.9 4.0 - - + -
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Residues in contact with LYS 154 (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* 3.3 8.1 + - + -
389A THR* 3.0 28.7 + - - +
391A ILE 2.8 28.4 + - - +
393A ALA* 4.0 12.0 - - - +
150C ILE* 2.8 32.5 + - + +
153C VAL* 1.3 78.6 - - + +
155C PHE* 1.3 98.2 + - + +
156C PRO* 3.4 4.2 - - - +
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Residues in contact with PHE 155 (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* 4.1 10.8 - + + -
391A ILE* 3.3 16.4 - - + -
392A GLU 3.6 14.1 - - - -
393A ALA* 3.8 12.8 - - - -
396A LEU* 3.3 35.0 - - + -
151C LEU* 2.8 44.6 + - + +
152C PRO 4.3 0.4 - - - -
154C LYS* 1.3 135.7 - - + +
156C PRO* 1.3 55.6 - - - +
157C HIS* 2.8 20.4 + - + -
158C LEU* 3.0 34.0 + - + +
159C PHE* 4.0 2.6 - - - -
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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