Contacts of the helix formed by residues 253 - 260 (chain A) in PDB entry 1OQY
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 ALA 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASN* 3.0 26.3 + - - +
252A PRO* 1.3 82.5 - - + +
254A LEU* 1.3 58.2 + - - +
256A PRO* 3.0 22.6 - - - +
257A ALA* 3.4 10.8 + - - +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A VAL* 3.4 52.9 - - + +
248A ILE* 4.1 2.0 - - - -
250A GLN* 5.5 4.5 - - + +
251A ASN* 3.2 29.3 + - + +
252A PRO 3.1 0.4 - - - -
253A ALA* 1.3 79.6 - - - +
255A LEU* 1.3 56.0 + - - +
257A ALA* 3.8 11.7 - - + -
258A LEU* 2.6 45.3 + - + +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A MET* 4.8 5.2 - - + +
248A ILE* 3.1 39.5 - - + +
252A PRO* 3.4 16.4 + - + +
254A LEU* 1.3 78.1 - - - +
256A PRO* 1.3 66.2 - - + +
258A LEU* 3.6 1.7 - - - +
259A LEU* 2.8 43.0 + - + +
281A ILE* 4.8 28.9 - - + -
284A LEU* 5.0 9.6 - - + -
285A ASN* 3.8 19.1 - - - +
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Residues in contact with PRO 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PRO 3.0 16.8 - - - +
253A ALA* 3.0 21.1 - - - +
255A LEU* 1.3 93.6 - - + +
257A ALA* 1.3 63.6 + - - +
259A LEU* 4.3 3.8 - - + -
260A GLN* 2.7 51.5 + - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ALA 3.4 15.3 - - - +
254A LEU* 3.0 17.0 + - + +
256A PRO* 1.3 82.4 - - - +
258A LEU* 1.3 60.2 + - + +
260A GLN* 4.3 2.9 - - - +
261A GLN* 2.9 28.4 + - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLN 4.3 6.7 - - - +
243A ASN* 3.7 36.1 - - + +
244A MET* 3.5 33.0 - - + -
247A VAL* 4.1 9.6 - - + -
254A LEU* 2.6 27.5 + - + +
255A LEU 3.6 0.9 - - - +
257A ALA* 1.3 75.4 - - + +
259A LEU* 1.3 62.5 + - - +
260A GLN 3.0 1.8 - - - -
261A GLN* 2.7 14.0 + - + +
262A LEU* 2.7 55.0 + - + +
263A GLY 2.9 2.8 + - - -
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A MET* 3.4 25.0 - - + +
255A LEU* 2.8 30.7 + - + +
256A PRO* 4.0 4.7 - - + +
258A LEU* 1.3 74.8 - - - +
260A GLN* 1.3 65.6 + - + +
263A GLY* 3.0 9.4 - - - +
264A GLN* 2.6 33.9 + - - +
270A LEU* 5.5 2.0 - - + +
273A ILE* 4.0 17.5 - - + -
277A GLN* 5.2 14.1 - - + +
280A PHE* 4.0 19.1 - - + -
281A ILE* 5.8 6.3 - - + -
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Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PRO* 2.7 48.6 + - - +
257A ALA* 4.5 3.3 - - - +
258A LEU 3.0 0.6 - - - -
259A LEU* 1.3 88.6 - - + +
261A GLN* 1.3 61.9 + - - +
264A GLN* 3.4 35.3 - - - +
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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