Contacts of the helix formed by residues 249 - 256 (chain A) in PDB entry 1OBC
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 ARG 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A THR* 2.9 7.1 + - - +
248A THR* 1.3 95.5 - - - +
250A PRO* 1.3 58.7 - - - +
251A ASP* 2.9 44.0 + - - +
252A THR* 2.8 36.3 + - - +
338A MET* 3.5 7.3 - - - +
343A HIS* 4.3 15.2 + - - +
362A ILE* 4.0 12.3 - - - +
377A TYR 5.6 0.2 + - - -
378A GLU* 3.5 26.0 + - - +
379A GLU 4.5 12.0 + - - -
380A PRO* 5.1 0.8 - - - +
394A SER* 4.6 3.6 + - - -
395A GLU* 5.5 2.2 + - - -
398A LYS* 4.0 13.4 - - - +
1815A NVA 3.5 33.6 - - + +
1816A 2AD 4.9 0.4 - - - +
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Residues in contact with PRO 250 (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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228A GLU 4.2 3.8 - - - +
229A GLY* 4.5 0.2 - - - -
230A ALA* 4.1 19.5 - - + -
232A ILE* 4.4 9.4 - - + -
247A THR* 4.0 15.2 - - + +
248A THR* 3.2 11.0 - - - +
249A ARG* 1.3 89.2 - - - +
251A ASP* 1.3 62.1 + - - +
252A THR 3.1 2.3 + - - -
253A LEU* 3.3 12.7 + - - +
338A MET* 4.7 0.2 - - + -
398A LYS* 3.8 29.6 - - + +
401A VAL* 3.4 31.8 - - + +
402A ILE* 4.1 13.0 - - + -
405A LEU* 5.1 0.4 - - + -
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Residues in contact with ASP 251 (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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249A ARG* 2.9 56.0 + - - -
250A PRO* 1.3 75.5 - - - +
252A THR* 1.3 56.6 + - - +
253A LEU 3.5 0.6 + - - -
254A PHE* 5.3 0.9 + - - -
361A VAL* 4.6 2.6 - - - +
362A ILE* 3.6 20.5 - - + +
383A MET* 3.3 30.1 - - - +
386A SER* 4.8 1.7 + - - -
394A SER* 3.7 28.4 - - - +
397A GLY 4.2 2.2 - - - -
398A LYS* 3.6 22.1 - - + +
401A VAL* 4.3 4.7 - - - -
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Residues in contact with THR 252 (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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249A ARG* 2.8 49.2 + - - +
250A PRO 3.1 0.2 - - - -
251A ASP* 1.3 84.0 - - - +
253A LEU* 1.3 52.8 + - - +
254A PHE 3.3 2.9 - - - -
255A GLY* 2.8 29.8 + - - -
256A ALA 3.7 2.8 + - - -
338A MET* 3.7 1.4 - - - +
340A VAL* 3.5 20.9 - - - +
343A HIS* 4.2 7.0 - - + -
361A VAL* 3.8 8.7 - - - -
362A ILE* 3.8 12.8 - - + -
1815A NVA 3.3 21.4 - - + +
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Residues in contact with LEU 253 (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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232A ILE* 3.9 18.4 - - + -
234A PHE* 3.7 29.4 - - + -
250A PRO 3.3 15.8 + - - +
251A ASP 3.5 1.0 + - - -
252A THR* 1.3 77.7 + - - +
254A PHE* 1.3 65.2 + - + +
255A GLY 3.0 1.6 + - - -
256A ALA* 3.0 7.7 + - - +
313A ASN* 2.9 28.1 + - - +
314A PRO* 4.5 4.9 - - + -
315A ALA* 3.7 26.7 - - + -
338A MET* 3.8 19.4 - - + +
401A VAL* 4.4 7.0 - - + -
404A TRP* 4.0 6.1 - - + -
405A LEU* 3.9 27.8 - - + -
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Residues in contact with PHE 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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251A ASP 5.7 0.2 - - - -
252A THR 3.2 1.4 + - - -
253A LEU* 1.3 82.9 - - + +
255A GLY* 1.3 56.8 + - - +
256A ALA 3.4 0.8 + - - -
313A ASN* 4.4 0.2 - - - -
315A ALA* 3.7 35.9 - - + -
316A THR* 3.7 27.8 - - + +
318A GLU* 4.4 3.6 - - - +
359A LYS* 3.1 24.2 + - - +
361A VAL* 3.7 4.0 - - + -
383A MET* 5.1 4.7 - - + -
385A ASN 3.5 17.3 - - - +
386A SER* 3.5 45.8 - - - +
387A GLY* 3.8 7.0 - - - -
388A PRO* 4.6 4.7 - - + -
389A PHE* 3.6 32.1 - + - -
401A VAL* 5.4 3.4 - - + -
404A TRP* 4.9 7.6 - + - -
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Residues in contact with GLY 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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252A THR 2.8 14.0 + - - -
254A PHE* 1.3 78.8 - - - +
256A ALA* 1.3 60.7 + - - +
257A THR* 3.2 14.8 + - - +
340A VAL* 3.6 19.6 - - - +
341A PRO* 4.1 2.3 - - - +
359A LYS* 3.9 18.3 - - - +
361A VAL* 3.6 18.3 - - - +
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Residues in contact with ALA 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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234A PHE* 4.4 8.3 - - + -
252A THR 3.7 1.2 + - - -
253A LEU 3.0 16.0 + - - +
254A PHE 3.4 0.4 - - - -
255A GLY* 1.3 76.2 - - - +
257A THR* 1.3 60.0 + - - +
258A PHE 3.5 1.8 - - - +
313A ASN* 3.2 19.8 + - - +
318A GLU* 3.9 5.0 - - - +
320A ILE* 3.8 11.1 - - + +
338A MET* 4.0 33.0 - - + -
339A ALA 3.2 13.0 - - - +
340A VAL* 3.9 3.8 - - + -
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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