Contacts of the helix formed by residues 390 - 395 (chain E) in PDB entry 6O81
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 ALA 390 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D THR* 4.6 2.2 - - - +
309D HIS 5.0 1.3 - - - +
311D PRO* 3.8 27.4 - - + -
386E LEU* 3.7 26.7 - - + +
387E LEU* 3.5 13.8 + - + +
388E ILE 3.2 1.0 - - - -
389E PRO* 1.3 76.0 - - - +
391E ALA* 1.3 59.5 + - - +
392E SER 3.3 2.2 - - - -
393E TYR* 3.0 11.0 + - - +
394E VAL* 3.0 27.7 + - - +
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Residues in contact with ALA 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D THR* 5.9 0.4 - - - +
334E LEU* 5.2 0.7 - - + -
361E VAL* 4.2 11.4 - - + -
387E LEU 3.2 11.0 + - - +
388E ILE* 3.2 16.1 + - + +
390E ALA* 1.3 77.9 - - - +
392E SER* 1.3 57.0 + - - +
394E VAL* 3.5 10.2 - - + +
395E LEU* 3.1 37.4 + - + +
423E LEU* 3.8 29.4 - - + -
426E VAL* 5.6 1.8 - - + -
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Residues in contact with SER 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D HIS* 3.6 26.2 - - - -
253D THR* 3.8 17.8 + - - -
314D ASP* 2.6 31.0 + - - +
388E ILE 4.4 1.2 + - - -
389E PRO 3.4 7.6 + - - -
391E ALA* 1.3 78.4 - - - +
393E TYR* 1.3 61.3 + - - +
396E PRO* 3.5 7.4 - - - +
426E VAL* 3.9 15.1 - - - +
430E HIS* 3.3 19.0 + - - -
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Residues in contact with TYR 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A SER 5.3 0.3 - - - -
339A ARG* 2.7 85.0 + - + +
340A HIS 6.2 0.4 - - - -
286D HIS* 3.6 42.8 - + + -
288D PHE* 3.2 34.1 - + - -
309D HIS* 5.4 6.7 - + + -
311D PRO* 3.7 19.5 - - + -
313D PHE 6.0 0.2 - - - +
314D ASP* 5.2 5.2 - - - +
386E LEU* 4.8 7.9 - - + -
389E PRO 5.2 0.4 - - - +
390E ALA* 3.0 16.4 + - - +
392E SER* 1.3 82.6 + - - +
394E VAL* 1.3 61.6 + - + +
395E LEU 3.5 0.2 - - - -
396E PRO* 3.6 8.7 - - - +
397E GLU* 5.3 0.9 - - - -
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Residues in contact with VAL 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 4.2 0.7 - - - +
334E LEU* 4.0 17.5 - - + -
357E ARG* 5.9 1.1 - - - +
359E VAL* 3.8 31.2 - - + -
361E VAL* 4.9 1.6 - - + -
384E SER* 5.7 0.9 - - - +
386E LEU* 3.7 21.3 - - + -
390E ALA 3.0 13.2 + - - +
391E ALA* 3.5 14.1 - - - +
393E TYR* 1.3 79.9 - - + +
395E LEU* 1.3 62.2 + - - +
397E GLU* 2.8 41.8 + - + +
398E VAL* 3.4 14.3 + - + -
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Residues in contact with LEU 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E LEU* 3.9 9.0 - - + -
391E ALA 3.1 25.1 + - - +
394E VAL* 1.3 71.8 - - - +
396E PRO* 1.3 70.5 - - + +
397E GLU 3.2 0.4 + - - -
398E VAL* 3.4 24.7 + - + +
401E VAL* 3.8 21.1 - - + -
423E LEU* 4.4 13.9 - - + +
426E VAL* 3.7 16.2 - - + -
427E ALA* 3.7 27.4 - - + +
430E HIS* 3.8 15.3 - - + +
432E VAL* 3.4 42.7 - - + +
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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
------------------------------------------------------------
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