Contacts of the helix formed by residues 270 - 277 (chain A) in PDB entry 1OH7
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 ASP 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 5.8 5.8 - - + +
168A ALA* 4.1 10.3 - - + -
268A ILE 3.9 0.2 + - - -
269A MET* 1.3 78.3 - - - +
271A ALA* 1.3 62.4 + - - +
272A ALA* 4.3 2.6 - - - +
273A THR* 2.5 40.4 + - - -
274A ARG* 3.3 19.6 + - - +
652A ARG* 4.4 16.1 - - - +
653A ILE 3.1 7.1 + - - +
654A PHE* 3.4 19.3 - - + +
655A THR 3.2 26.9 + - - +
679A ASN* 5.1 7.8 + - - +
680A ILE* 4.8 2.6 - - - +
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Residues in contact with ALA 271 (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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164A GLU 5.5 0.8 + - - +
167A ALA* 4.9 9.0 - - + -
168A ALA* 4.1 20.9 - - - +
171A GLN* 2.9 36.1 - - + +
270A ASP* 1.3 72.6 - - - +
272A ALA* 1.3 67.3 + - - +
273A THR 3.3 0.2 + - - -
274A ARG* 3.4 3.5 + - - +
275A ARG* 3.3 25.0 + - - +
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Residues in contact with ALA 272 (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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270A ASP* 3.9 3.1 + - - +
271A ALA* 1.3 78.5 - - - +
273A THR* 1.3 56.1 + - - +
275A ARG* 3.3 23.8 + - - +
276A ASN* 2.8 32.4 + - - +
655A THR* 3.5 33.4 - - + +
656A ARG* 5.1 1.3 - - - +
657A VAL* 5.5 2.9 - - + +
676A GLU* 4.2 12.3 - - - +
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Residues in contact with THR 273 (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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269A MET* 3.7 22.4 - - + -
270A ASP* 2.5 34.3 + - - -
271A ALA 3.2 0.4 - - - -
272A ALA* 1.3 77.2 - - - +
274A ARG* 1.3 62.9 + - - +
276A ASN* 3.3 0.8 + - - -
277A LEU* 3.2 46.2 + - + +
628A ALA* 5.5 0.4 - - + -
653A ILE* 3.6 21.7 + - + -
654A PHE 3.3 4.0 - - - -
655A THR* 2.8 30.4 + - - +
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Residues in contact with ARG 274 (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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168A ALA* 3.1 26.9 + - - +
169A GLU* 5.9 0.2 + - - -
171A GLN* 4.1 18.8 - - + +
172A ARG* 3.3 31.5 - - - +
267A ILE 5.0 2.8 + - - -
268A ILE* 5.3 3.6 - - - +
269A MET* 3.0 47.3 + - - +
270A ASP 3.3 8.5 + - - +
271A ALA* 3.7 8.5 - - - +
273A THR* 1.3 80.2 - - - +
275A ARG* 1.3 60.0 + - - +
278A GLU* 3.6 13.0 + - - -
279A ILE* 3.8 26.5 + - + +
281A GLN 5.1 1.0 - - - +
312A HIS* 3.1 57.5 + - + +
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Residues in contact with ARG 275 (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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171A GLN* 3.6 22.5 + - - +
271A ALA* 3.3 16.4 + - - +
272A ALA* 3.6 32.5 - - - +
273A THR 3.2 0.6 - - - -
274A ARG* 1.3 76.5 - - - +
276A ASN* 1.3 64.7 + - - +
277A LEU 3.1 2.5 - - - -
278A GLU* 3.2 16.7 + - - +
281A GLN 4.7 4.0 - - - +
282A ASN 5.4 0.2 - - - -
283A LEU* 3.4 29.2 - - + +
676A GLU* 5.0 9.3 + - - -
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Residues in contact with ASN 276 (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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272A ALA 2.8 18.0 + - - +
273A THR* 3.3 4.2 + - - +
275A ARG* 1.3 76.4 - - - +
277A LEU* 1.3 62.4 + - - +
278A GLU* 4.3 7.3 - - - +
283A LEU* 4.6 10.3 - - - +
624A MET* 6.1 2.6 - - - +
625A ARG* 3.1 66.9 + - - +
655A THR* 3.8 27.2 + - + +
657A VAL* 3.8 17.8 - - + +
691A LEU* 5.1 5.1 - - - +
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Residues in contact with LEU 277 (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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269A MET* 4.9 1.6 - - - -
273A THR* 3.2 32.5 + - + +
275A ARG 3.1 0.4 - - - -
276A ASN* 1.3 81.0 - - - +
278A GLU* 1.3 75.1 + - - +
279A ILE* 3.1 14.9 + - + -
291A LEU 4.7 2.4 + - - -
585A HIS* 5.7 2.3 - - - -
587A VAL* 5.5 2.6 - - - +
625A ARG* 3.7 44.2 - - + +
628A ALA* 3.7 27.6 - - + +
629A LEU* 3.8 34.9 - - + +
632A LEU* 4.4 12.8 - - + -
653A ILE* 5.7 0.7 - - + -
655A THR* 5.8 0.2 - - - +
691A LEU* 5.2 2.0 - - + -
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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