Contacts of the helix formed by residues 406 - 419 (chain R) in PDB entry 6XOX
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 ASN 406 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A GLN 5.0 5.2 + - - +
392A GLU* 3.2 21.1 - - + +
166R LEU* 6.2 0.2 - - - +
172R LEU* 5.8 0.8 - - - +
176R ARG* 4.3 23.0 - - - +
177R ASN* 5.1 4.6 + - - +
401R LEU 4.7 1.6 + - - +
402R TYR* 4.2 18.4 + - - +
403R CYS 3.3 17.2 + - - +
405R VAL* 1.3 80.4 - - - +
407R ASN* 1.3 85.5 + - - +
408R GLU* 3.4 14.3 + - - +
409R VAL* 3.4 16.2 + - + +
410R GLN* 3.3 21.5 + - - +
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Residues in contact with ASN 407 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 4.5 19.6 + - - +
392A GLU* 2.9 26.5 + - - +
405R VAL 3.4 4.4 + - - +
406R ASN* 1.3 76.8 + - - +
408R GLU* 1.3 80.0 + - - +
410R GLN* 3.4 10.5 + - - +
411R LEU* 2.8 40.5 + - + +
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Residues in contact with GLU 408 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 5.3 9.3 - - - +
171R HIS* 5.8 9.3 - - + -
172R LEU* 4.2 18.6 - - + +
176R ARG* 3.6 23.9 + - - -
177R ASN* 5.1 1.0 + - - -
406R ASN* 3.2 11.2 + - - +
407R ASN* 1.3 91.8 + - - +
409R VAL* 1.3 61.0 + - - +
411R LEU* 3.4 8.4 + - + +
412R GLU* 2.9 31.4 + - - +
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Residues in contact with VAL 409 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R ILE* 4.0 24.5 - - + -
166R LEU* 4.4 9.2 - - + -
169R PHE* 4.5 1.1 - - + -
172R LEU* 3.8 25.4 - - + -
402R TYR 4.9 0.2 - - - +
403R CYS* 3.3 34.5 - - - +
404R PHE* 5.6 0.4 - - + -
406R ASN* 3.4 18.1 + - + +
407R ASN 3.4 0.6 - - - -
408R GLU* 1.3 75.9 - - - +
410R GLN* 1.3 59.3 + - + +
412R GLU* 3.1 8.9 + - - +
413R PHE* 2.9 48.9 + - + -
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Residues in contact with GLN 410 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403R CYS 5.3 0.4 - - - +
404R PHE 3.1 27.6 + - - +
405R VAL* 3.9 13.4 + - - +
406R ASN 3.3 13.7 + - - +
407R ASN* 3.8 11.3 - - - +
409R VAL* 1.3 75.8 - - - +
411R LEU* 1.3 61.3 + - + +
413R PHE* 3.2 16.6 + - + +
414R ARG* 2.9 52.0 + - - +
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Residues in contact with LEU 411 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407R ASN* 2.8 32.6 + - + +
408R GLU* 3.5 9.6 - - - +
410R GLN* 1.3 77.9 - - + +
412R GLU* 1.3 58.2 + - + +
414R ARG* 3.4 26.9 + - + +
415R LYS* 2.9 39.9 + - + +
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Residues in contact with GLU 412 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASP* 5.3 0.2 - - - +
169R PHE* 3.5 33.1 - - + +
171R HIS* 2.8 45.2 + - + +
172R LEU* 4.1 21.1 - - + -
408R GLU 2.9 18.1 + - - +
409R VAL* 3.1 9.6 + - - +
411R LEU* 1.3 75.4 - - + +
413R PHE* 1.3 58.1 + - - +
415R LYS* 3.5 27.9 + - - +
416R SER* 2.9 33.8 + - - -
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Residues in contact with PHE 413 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165R ILE* 3.5 34.1 - - + -
169R PHE* 4.2 9.9 - + - -
403R CYS 5.7 0.2 - - - -
404R PHE* 5.6 12.1 - + - -
409R VAL* 2.9 41.5 + - + -
410R GLN* 3.2 20.6 + - + +
412R GLU* 1.3 76.4 - - - +
414R ARG* 1.3 58.3 + - + +
416R SER* 3.3 2.5 + - - -
417R TRP* 2.9 32.0 + - - +
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Residues in contact with ARG 414 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410R GLN* 2.9 39.1 + - - +
411R LEU* 3.9 25.6 - - + +
413R PHE* 1.3 75.7 - - + +
415R LYS* 1.3 58.4 + - - +
417R TRP* 3.2 7.0 + - - +
418R GLU* 2.9 37.0 + - + +
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Residues in contact with LYS 415 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B PHE* 5.2 6.7 - - + -
310B GLY 3.7 2.0 + - - -
311B HIS 4.4 0.7 - - - -
312B ASP* 2.8 44.4 + - + +
411R LEU* 2.9 26.4 + - + +
412R GLU* 3.5 35.1 + - - +
414R ARG* 1.3 76.7 - - - +
416R SER* 1.3 57.2 + - - +
418R GLU* 4.0 5.3 - - - +
419R ARG* 2.6 75.3 + - - +
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Residues in contact with SER 416 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169R PHE* 4.7 17.6 - - - -
412R GLU* 2.9 23.2 + - - -
413R PHE* 4.1 3.4 - - - -
415R LYS* 1.3 77.0 - - - +
417R TRP* 1.3 59.6 + - - +
419R ARG* 4.0 13.5 - - - +
420R TRP* 3.2 23.2 + - - +
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Residues in contact with TRP 417 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413R PHE 2.9 18.1 + - - +
414R ARG* 3.2 6.7 + - - +
416R SER* 1.3 77.2 - - - +
418R GLU* 1.3 73.3 + - - +
419R ARG 3.3 0.2 - - - -
420R TRP* 3.3 47.4 + + + +
421R ARG* 3.2 51.4 + - + +
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Residues in contact with GLU 418 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414R ARG* 2.9 23.0 + - + +
415R LYS* 3.9 6.0 + - - +
416R SER 3.5 0.2 - - - -
417R TRP* 1.3 85.8 - - - +
419R ARG* 1.3 58.7 + - - +
420R TRP 3.2 2.5 + - - -
421R ARG* 3.4 48.7 + - - +
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Residues in contact with ARG 419 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 5.2 6.1 + - - +
293B ASN* 3.7 18.6 + - - +
309B ALA* 3.7 18.9 - - + +
310B GLY* 3.0 39.4 + - - +
311B HIS 4.3 5.5 + - - -
415R LYS* 2.6 68.0 + - - +
416R SER* 4.0 12.6 - - - +
418R GLU* 1.3 78.2 - - - +
420R TRP* 1.3 58.7 + - - +
421R ARG 3.6 0.2 - - - -
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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