Contacts of the helix formed by residues 381 - 391 (chain B) in PDB entry 2N97
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 CYS 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ALA* 4.3 14.1 - - - -
348B GLU* 3.6 24.0 - - - +
352B ASN* 5.3 5.4 - - - -
379B GLU* 3.2 8.7 - - + +
380B ALA* 1.3 86.2 - - - +
382B PRO* 1.4 65.0 - - - +
383B VAL* 3.1 8.1 - - + -
384B ARG* 2.9 40.0 + - - +
385B ALA 3.8 0.5 + - - -
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Residues in contact with PRO 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 5.8 0.2 - - - -
356B GLY 5.1 2.0 - - - +
359B TRP* 3.3 51.6 - - + +
376B PHE* 3.4 32.1 - - + +
377B THR* 4.2 2.0 - - + +
379B GLU 3.6 5.6 - - - +
380B ALA 3.2 14.1 - - - +
381B CYS* 1.4 84.1 - - - +
383B VAL* 1.3 57.3 + - + +
385B ALA* 3.3 6.9 + - + +
386B LEU* 2.9 30.6 + - - +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL* 4.3 15.5 - - + +
348B GLU* 4.0 23.8 - - + +
351B LEU* 4.0 40.6 - - + -
352B ASN 5.9 0.2 - - - +
359B TRP* 4.8 7.0 - - + -
381B CYS* 4.2 9.6 - - + +
382B PRO* 1.3 81.6 - - + +
384B ARG* 1.3 56.6 + - - +
386B LEU* 4.2 7.4 - - + -
387B LEU* 2.9 57.8 + - + +
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Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLU* 3.7 29.9 + - - +
379B GLU* 4.7 20.3 + - + +
381B CYS* 2.9 36.5 + - - +
383B VAL* 1.3 75.2 - - - +
385B ALA* 1.3 64.0 + - + +
387B LEU* 4.1 6.6 - - - +
388B ALA* 3.1 30.8 + - - +
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Residues in contact with ALA 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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375B SER 5.2 2.2 - - - +
376B PHE* 3.6 24.4 - - + +
379B GLU* 5.4 6.7 - - + -
381B CYS 4.7 1.1 - - - +
382B PRO* 3.3 11.1 + - + +
384B ARG* 1.3 82.8 - - + +
386B LEU* 1.3 58.2 + - - +
388B ALA* 3.6 4.4 + - - +
389B SER* 2.9 33.4 + - - -
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Residues in contact with LEU 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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359B TRP* 4.0 44.9 - - + +
362B LEU* 5.1 7.0 - - + -
363B ALA* 4.8 8.1 - - + +
366B LEU* 4.7 8.3 - - + -
368B TYR* 4.2 18.8 - - + -
376B PHE* 3.6 27.3 - - + -
382B PRO 2.9 18.1 + - - +
383B VAL* 3.7 6.7 - - + +
385B ALA* 1.3 74.9 - - - +
387B LEU* 1.3 57.0 + - + +
389B SER* 3.2 2.1 + - - -
390B TRP* 2.8 47.9 + - + +
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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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336B TYR* 3.6 51.3 - - + +
344B ARG* 5.2 3.4 - - + +
347B VAL* 3.9 17.3 - - + -
348B GLU* 5.3 4.5 - - + -
383B VAL* 2.9 44.7 + - + +
384B ARG* 4.1 6.1 - - - +
386B LEU* 1.3 75.8 - - + +
388B ALA* 1.3 56.3 + - - +
390B TRP* 3.5 11.5 + - + +
391B ALA* 3.0 31.4 + - - +
401B LEU* 5.0 11.2 - - + -
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Residues in contact with ALA 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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384B ARG 3.1 20.0 + - - +
385B ALA* 3.9 4.7 - - - +
387B LEU* 1.3 77.0 - - - +
389B SER* 1.3 61.3 + - - +
391B ALA* 3.6 15.1 + - - +
392B THR* 3.7 11.6 - - - +
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Residues in contact with SER 389 (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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368B TYR* 4.0 12.2 + - - -
372B HIS* 5.1 5.4 - - - -
376B PHE* 3.7 23.4 - - - -
385B ALA 2.9 19.7 + - - -
386B LEU 3.7 0.9 - - - -
388B ALA* 1.3 72.8 - - - +
390B TRP* 1.3 60.1 + - - +
392B THR* 3.0 30.4 + - - +
393B GLN* 5.0 1.2 - - - +
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Residues in contact with TRP 390 (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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336B TYR* 4.4 10.8 - + + -
366B LEU* 3.5 37.8 - - + +
368B TYR* 3.7 16.3 + + - +
386B LEU* 2.8 27.4 + - + +
387B LEU* 3.9 11.7 - - + +
389B SER* 1.3 72.7 - - - +
391B ALA* 1.3 58.0 + - - +
392B THR 3.1 5.4 + - - -
393B GLN* 3.2 47.9 + - - +
395B SER* 3.4 19.4 + - - -
396B ALA* 3.5 37.6 - - + +
397B THR 3.5 21.5 - - - -
400B ALA* 4.4 8.1 - - + -
401B LEU* 3.7 40.2 - - + -
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 5.1 8.1 - - + -
337B SER* 4.3 27.8 + - - -
387B LEU 3.0 18.9 + - - +
388B ALA* 3.7 9.6 - - - +
389B SER 3.4 0.6 - - - -
390B TRP* 1.3 74.3 - - - +
392B THR* 1.3 57.8 + - - +
393B GLN 3.2 7.0 + - - +
396B ALA* 4.0 13.7 - - + +
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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