Contacts of the helix formed by residues 378 - 388 (chain B) in PDB entry 2ADM
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 GLU 378 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ARG* 2.7 47.1 + - - -
62A GLY* 6.2 3.8 - - - -
63A THR* 5.5 2.3 + - - -
377B SER* 1.3 74.9 - - - +
379B ALA* 1.3 57.6 + - - +
381B GLN* 3.1 9.1 + - - +
382B LYS* 2.8 32.9 + - - +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B LEU* 4.6 9.9 - - + +
374B TRP* 4.6 16.6 - - + -
377B SER* 3.3 7.9 + - - +
378B GLU* 1.3 79.9 - - - +
380B MET* 1.3 61.1 + - - +
382B LYS* 4.1 7.4 - - - +
383B HIS* 3.1 25.5 + - - +
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B LEU* 5.2 1.6 - - + -
341B VAL* 3.8 15.3 - - + -
374B TRP* 3.6 35.6 - - + +
375B LEU* 3.2 42.8 - - + +
377B SER* 3.1 8.8 + - - +
379B ALA* 1.3 79.1 - - - +
381B GLN* 1.3 64.8 + - - +
383B HIS* 3.4 12.5 + - - +
384B VAL* 3.1 26.2 + - - +
403B LEU* 4.2 24.0 - - + -
404B PRO* 3.6 30.5 - - + +
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Residues in contact with GLN 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B THR 5.6 0.7 - - - +
340B ARG* 3.1 19.6 - - + +
341B VAL 2.8 45.9 + - - -
375B LEU 3.6 11.1 + - - -
376B ASN* 3.5 19.0 + - - +
377B SER 3.1 13.6 + - - +
378B GLU* 3.1 8.3 + - - +
380B MET* 1.3 78.1 - - - +
382B LYS* 1.3 57.2 + - - +
384B VAL* 3.4 3.4 + - - +
385B ARG* 2.9 32.4 + - - +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLU* 3.8 25.1 - - - +
378B GLU 2.8 17.9 + - - +
379B ALA* 4.1 6.5 - - - +
381B GLN* 1.3 76.8 - - - +
383B HIS* 1.3 53.6 + - - +
385B ARG* 3.8 5.8 - - - +
386B THR* 2.5 44.1 + - - +
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Residues in contact with HIS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLU* 4.9 6.3 + - - +
250B THR* 3.6 50.4 - - - +
253B LEU* 3.7 22.3 - - + +
254B GLU* 3.8 13.5 + - + +
379B ALA 3.1 20.5 + - - +
380B MET* 3.6 7.9 - - - +
382B LYS* 1.3 78.7 - - - +
384B VAL* 1.3 71.3 + - + +
386B THR* 3.6 5.7 - - - -
387B LEU* 3.3 42.6 + - + +
402B ARG 5.3 0.2 + - - -
403B LEU* 5.0 3.1 - - + +
404B PRO* 3.8 26.8 - - + +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B THR* 3.7 32.3 - - + +
340B ARG* 4.6 3.4 - - - +
341B VAL* 3.8 13.9 - - + -
380B MET* 3.1 17.2 + - - +
381B GLN* 3.9 3.8 - - - +
383B HIS* 1.3 78.4 - - + +
385B ARG* 1.3 64.6 + - - +
386B THR 3.4 0.2 + - - -
387B LEU* 3.4 1.1 + - - -
388B TYR* 3.1 42.2 + - + +
389B ARG 4.0 0.2 + - - -
395B LEU* 4.3 15.0 - - + -
403B LEU* 3.7 30.7 - - + -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B TYR* 4.9 2.8 + - - -
339B THR* 5.1 8.5 + - - +
381B GLN 2.9 19.6 + - - +
382B LYS* 3.8 5.8 - - - +
384B VAL* 1.3 78.3 - - - +
386B THR* 1.3 63.6 + - - +
389B ARG* 3.0 76.6 + - - +
390B ASP* 3.5 16.4 + - - +
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Residues in contact with THR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TRP* 5.2 4.0 - - + -
245B PHE* 3.3 31.2 - - - +
247B THR* 3.8 24.7 - - + +
249B GLU* 3.9 13.2 + - - +
250B THR* 3.8 13.9 - - + -
382B LYS* 2.5 33.6 + - - +
383B HIS* 3.6 5.8 - - - -
384B VAL 3.2 0.2 - - - -
385B ARG* 1.3 80.3 - - - +
387B LEU* 1.3 62.1 + - - +
389B ARG* 3.9 9.0 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ARG* 3.3 55.4 - - + +
245B PHE* 3.0 35.9 + - - +
246B GLU* 4.1 6.1 - - + -
250B THR* 4.0 21.8 - - + +
254B GLU* 4.5 0.2 - - - +
383B HIS* 3.3 43.8 + - + +
384B VAL* 4.9 0.4 - - + -
386B THR* 1.3 81.3 - - - +
388B TYR* 1.3 85.5 + - + +
389B ARG* 5.0 0.2 - - - -
391B PHE* 3.8 5.0 - - - -
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Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.8 25.4 - - + -
242B ILE* 4.4 8.3 - - + +
244B ARG* 3.7 41.1 + - + -
339B THR* 4.4 6.6 + - + +
384B VAL* 3.1 30.4 + - + +
387B LEU* 1.3 95.9 - - + +
389B ARG* 1.3 70.5 - - - +
391B PHE* 3.0 32.8 + + + +
392B VAL* 4.8 0.6 + - + +
399B MET* 3.8 62.9 + - + -
402B ARG* 4.5 12.0 - - - +
403B LEU* 5.9 1.1 - - + -
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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