Contacts of the helix formed by residues 419 - 428 (chain B) in PDB entry 6QVC
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 MET 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.6 38.4 - - + -
146B TYR* 5.0 11.2 - - + -
147B LYS* 4.3 11.2 - - + -
164B TRP* 4.6 14.6 - - + -
226B GLY* 3.7 34.3 - - - +
405B THR* 5.5 3.6 - - + -
416B GLY 3.8 21.1 - - - +
417B GLU* 4.0 2.4 - - - -
418B LEU* 1.3 76.6 - - - +
420B PRO* 1.3 75.3 - - + +
421B ARG 3.3 2.0 - - - -
422B GLU* 3.0 27.8 + - - +
423B ALA 3.0 16.5 + - - -
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Residues in contact with PRO 420 (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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225B SER 5.5 2.9 - - - +
226B GLY* 4.8 14.1 - - - +
227B ILE 5.5 0.7 - - - +
228B PRO* 4.9 13.2 - - + -
418B LEU 4.3 3.1 - - - +
419B MET* 1.3 89.4 - - + +
421B ARG* 1.3 61.2 + - + +
423B ALA* 3.3 8.9 - - + +
424B ILE* 2.9 34.3 + - - +
467B LYS* 4.9 14.4 - - - +
485B MET* 5.6 7.9 - - + -
489B VAL* 4.4 20.9 - - + -
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Residues in contact with ARG 421 (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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136B ASP* 4.9 17.1 + - - +
223B LEU* 5.9 12.3 - - - +
231B LYS* 5.3 12.1 - - - +
279B PHE* 5.6 3.8 - - - -
316B PHE* 6.3 0.2 - - - -
332B LEU* 3.5 30.1 - - - +
333B PHE* 4.9 13.5 - - + -
419B MET 3.1 0.8 + - - -
420B PRO* 1.3 79.3 - - + +
422B GLU* 1.3 67.4 + - - +
424B ILE* 3.2 16.1 - - - +
425B SER* 3.0 20.7 + - - -
485B MET* 4.9 21.8 - - + +
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Residues in contact with GLU 422 (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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143B LEU* 4.4 6.9 - - - +
147B LYS* 4.1 14.9 - - - +
417B GLU 5.2 0.8 - - - +
418B LEU* 4.8 9.0 - - + -
419B MET* 3.0 46.9 + - - +
421B ARG* 1.3 76.1 + - - +
423B ALA* 1.3 57.4 + - - +
425B SER* 2.7 18.9 + - - +
426B THR* 2.6 31.9 + - - +
445B GLN* 5.7 10.8 - - + -
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Residues in contact with ALA 423 (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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418B LEU* 3.7 34.3 - - + +
419B MET 3.0 14.9 + - - +
420B PRO* 3.3 15.0 - - + +
421B ARG 3.1 0.4 - - - -
422B GLU* 1.3 77.5 - - - +
424B ILE* 1.3 61.0 + - + +
426B THR* 2.9 21.5 + - - -
427B LEU* 3.0 22.6 + - + +
449B TRP* 5.2 0.5 - - - -
463B PHE* 5.3 9.0 - - + -
489B VAL* 5.8 1.8 - - + -
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Residues in contact with ILE 424 (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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333B PHE* 3.6 37.0 - - + -
420B PRO 2.9 18.4 + - - +
421B ARG* 3.2 19.7 - - + +
423B ALA* 1.3 73.3 - - + +
425B SER* 1.3 65.7 + - - +
427B LEU* 3.3 14.9 + - + +
428B PHE* 3.3 32.9 + - + -
485B MET* 6.1 5.2 - - - -
488B PHE* 4.8 19.7 - - + -
489B VAL* 3.7 41.5 - - + -
492B ALA* 4.6 11.9 - - + -
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Residues in contact with SER 425 (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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333B PHE* 4.9 17.0 - - - -
421B ARG 3.0 13.6 + - - -
422B GLU* 2.7 28.6 + - - +
424B ILE* 1.3 81.0 - - - +
426B THR* 1.3 61.4 + - - +
428B PHE* 3.2 24.1 + - - +
429B ASP* 4.2 0.5 + - - -
445B GLN* 5.4 3.1 + - - -
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Residues in contact with THR 426 (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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418B LEU* 4.8 4.3 - - + +
422B GLU* 2.6 20.8 + - - +
423B ALA* 2.9 12.0 + - - -
425B SER* 1.3 77.4 + - - +
427B LEU* 1.3 62.3 + - - +
428B PHE 3.3 0.7 + - - -
429B ASP* 3.3 10.0 - - - +
433B TRP* 3.2 16.3 - - - -
445B GLN* 3.6 23.4 + - + +
446B SER* 3.5 32.3 - - - +
448B VAL* 5.1 1.3 - - + -
449B TRP* 3.4 25.4 - - + +
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Residues in contact with LEU 427 (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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423B ALA* 3.0 39.5 + - + +
424B ILE* 3.3 15.7 + - + +
425B SER 3.3 0.8 - - - -
426B THR* 1.3 76.9 - - - +
428B PHE* 1.3 61.6 + - + +
429B ASP 3.1 1.3 - - - -
433B TRP* 4.3 1.1 - - - -
449B TRP* 4.0 28.3 - - + -
460B ILE* 6.2 2.0 - - + -
463B PHE* 5.0 9.2 - - + -
489B VAL* 5.1 1.6 - - + +
492B ALA* 3.3 43.1 - - + +
493B ALA* 3.7 12.6 - - + -
496B ARG* 2.8 43.8 + - + +
522B GLY* 4.6 0.3 - - - -
525B ALA* 4.1 5.5 - - + +
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Residues in contact with PHE 428 (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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333B PHE* 5.0 14.4 - + + -
335B THR* 3.9 38.7 - - + -
336B ASN 5.6 0.2 + - - -
337B PHE* 5.0 5.2 - + + -
424B ILE* 3.3 25.2 + - + -
425B SER* 3.2 15.7 + - - +
426B THR 3.2 1.8 - - - -
427B LEU* 1.3 82.1 - - - +
429B ASP* 1.3 60.4 + - - +
430B ASN* 3.5 5.5 + - - +
488B PHE* 5.0 11.7 - + - -
492B ALA* 4.8 9.0 - - + -
496B ARG* 4.4 0.2 - - - -
522B GLY* 4.1 12.6 - - - -
525B ALA* 3.8 14.4 - - + -
526B VAL* 3.5 48.9 - - + -
529B ALA* 4.9 8.7 - - + -
550B THR* 4.7 6.5 - - - -
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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