Contacts of the helix formed by residues 354 - 361 (chain D) in PDB entry 5M8Q
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 SER 354 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D VAL* 3.6 2.0 - - - -
341D LEU 4.0 4.3 - - - -
342D PHE 3.3 3.6 + - - -
343D ASP* 2.4 36.9 + - - -
344D THR* 3.8 16.6 - - - -
351D SER* 4.0 6.9 + - - -
352D THR* 3.0 1.2 - - - +
353D ASN* 1.3 75.9 - - - +
355D PHE* 1.3 54.5 + - - +
357D ASN* 3.1 24.6 + - - +
358D THR* 2.7 37.0 + - - -
363D SER* 4.7 0.4 + - - -
367D GLY* 4.9 0.2 - - - -
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Residues in contact with PHE 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 3.9 20.0 - - + -
336D CYS* 3.3 24.9 - - - -
337D LEU* 4.4 2.7 - - + -
339D VAL* 3.2 26.1 - - - +
341D LEU 3.1 18.1 + - - +
342D PHE* 3.7 15.5 - + - +
354D SER* 1.3 71.6 - - - +
356D ARG* 1.3 67.4 + - - +
358D THR* 2.9 13.0 + - - -
359D VAL* 2.9 40.4 + - + +
410D VAL* 4.1 5.6 - - + -
411D PHE* 4.0 20.4 - + - -
414D TRP* 3.2 53.4 - + + +
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Residues in contact with ARG 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D GLU* 3.9 3.2 - - - +
217D GLY 3.1 31.3 + - - +
218D PRO* 3.8 19.3 - - + +
220D PHE* 4.2 7.3 - - + -
221D LEU* 4.3 13.4 - - + +
342D PHE* 2.9 33.1 + - + +
343D ASP* 2.9 28.7 + - - +
347D PHE 4.0 0.4 - - - -
348D TYR 2.6 35.8 + - - +
351D SER* 4.0 0.6 - - - -
354D SER* 3.8 1.1 - - - +
355D PHE* 1.3 82.6 - - - +
357D ASN* 1.3 86.0 + - - +
359D VAL* 4.1 0.9 - - - +
360D GLU* 2.9 56.0 + - - +
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Residues in contact with ASN 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D TYR 3.6 6.7 - - - -
349D SER* 3.0 22.8 + - - -
350D ASN 3.9 0.2 - - - -
351D SER 2.8 29.9 + - - +
354D SER* 3.1 17.9 + - - +
356D ARG* 1.3 100.4 + - - +
358D THR* 1.3 58.2 + - - +
360D GLU* 4.4 0.9 - - - -
361D GLY 3.1 18.1 + - - -
362D PHE* 3.0 38.6 + - - +
363D SER* 3.3 13.7 + - - +
369D TYR* 4.6 0.8 - - - -
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Residues in contact with THR 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D CYS* 3.5 28.3 - - + -
339D VAL* 4.1 5.3 - - + +
354D SER 2.7 23.4 + - - -
355D PHE* 2.9 7.4 + - - -
357D ASN* 1.3 76.7 - - - +
359D VAL* 1.3 64.0 + - - +
361D GLY* 3.2 14.2 + - - -
363D SER* 3.9 11.2 + - - +
364D ASP 3.3 21.3 - - - +
365D PRO* 3.6 13.2 - - + +
367D GLY* 3.6 20.3 - - - +
376D LEU* 3.1 14.6 - - - +
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Residues in contact with VAL 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D PHE* 4.7 0.2 - - - -
221D LEU* 4.7 8.7 - - + -
336D CYS* 3.4 19.3 - - - -
355D PHE* 2.9 48.6 + - + +
356D ARG 4.3 1.6 - - - +
358D THR* 1.3 71.4 - - - +
360D GLU* 1.3 66.9 + - - +
376D LEU* 3.4 10.9 - - + +
377D HIS* 3.0 27.9 + - + +
407D THR* 3.7 27.4 - - + +
410D VAL* 4.1 17.7 - - + -
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Residues in contact with GLU 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D HIS* 3.5 10.6 - - - +
216D GLU 2.7 26.3 + - - -
220D PHE* 3.2 52.1 - - + +
356D ARG* 2.9 38.0 + - - +
357D ASN* 4.3 4.0 - - - +
359D VAL* 1.3 75.0 - - - +
361D GLY* 1.3 58.5 + - - +
362D PHE* 2.9 26.8 - - + -
377D HIS* 2.9 7.6 + - + +
378D ASN* 2.8 36.6 + - - +
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Residues in contact with GLY 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ASN 3.1 6.5 + - - -
358D THR 3.3 15.0 - - - -
359D VAL 3.2 0.4 - - - -
360D GLU* 1.3 78.8 - - - +
362D PHE* 1.3 62.1 + - - +
363D SER 3.4 3.9 - - - +
374D SER* 3.4 9.0 - - - -
375D SER 3.0 40.5 + - - +
378D ASN* 3.6 8.8 + - - -
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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