Contacts of the helix formed by residues 419 - 428 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.6 39.3 - - + -
146A TYR* 5.0 11.0 - - + -
147A LYS* 4.3 12.1 - - + -
164A TRP* 4.6 13.7 - - + -
226A GLY* 3.7 34.3 - - - +
405A THR* 5.5 4.3 - - + -
416A GLY 3.8 21.3 - - - +
417A GLU* 4.0 2.4 - - - -
418A LEU* 1.3 76.5 - - - +
420A PRO* 1.3 74.8 - - + +
421A ARG 3.3 2.0 - - - -
422A GLU* 3.0 28.4 + - - +
423A ALA 3.0 17.3 + - - -
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Residues in contact with PRO 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER 5.5 2.7 - - - +
226A GLY* 4.8 14.1 - - - +
227A ILE 5.5 0.9 - - - +
228A PRO* 4.9 13.2 - - + -
418A LEU 4.3 3.1 - - - +
419A MET* 1.3 90.7 - - + +
421A ARG* 1.3 61.3 + - + +
423A ALA* 3.3 8.5 - - + +
424A ILE* 2.9 34.8 + - - +
467A LYS* 4.9 14.6 - - - +
485A MET* 5.6 6.7 - - + -
489A VAL* 4.4 20.9 - - + -
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASP* 4.9 18.1 + - - +
223A LEU* 5.9 11.9 - - - +
231A LYS* 5.3 12.3 - - - +
279A PHE* 5.6 3.6 - - - -
316A PHE* 6.3 0.2 - - - -
332A LEU* 3.5 29.4 - - - +
333A PHE* 4.9 13.0 - - + -
419A MET 3.1 1.2 + - - -
420A PRO* 1.3 79.4 - - + +
422A GLU* 1.3 66.3 + - - +
424A ILE* 3.2 16.1 - - - +
425A SER* 3.0 21.2 + - - -
485A MET* 4.9 22.4 - - + +
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.4 8.0 - - - +
147A LYS* 4.1 14.7 - - - +
417A GLU 5.2 0.6 - - - +
418A LEU* 4.8 8.6 - - + -
419A MET* 3.0 46.3 + - - +
421A ARG* 1.3 76.3 + - - +
423A ALA* 1.3 56.9 + - - +
425A SER* 2.7 20.0 + - - +
426A THR* 2.6 31.5 + - - +
445A GLN* 5.7 11.2 - - + -
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Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A LEU* 3.7 33.4 - - + +
419A MET 3.0 16.3 + - - +
420A PRO* 3.3 15.7 - - + +
421A ARG 3.1 0.2 - - - -
422A GLU* 1.3 75.6 - - - +
424A ILE* 1.3 59.6 + - + +
426A THR* 2.9 22.4 + - - -
427A LEU* 3.0 22.7 + - + +
449A TRP* 5.2 0.3 - - - -
463A PHE* 5.3 8.7 - - + -
489A VAL* 5.8 1.8 - - + -
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PHE* 3.6 37.2 - - + -
420A PRO 2.9 19.2 + - - +
421A ARG* 3.2 18.8 - - - +
423A ALA* 1.3 73.1 - - - +
425A SER* 1.3 67.0 + - - +
427A LEU* 3.3 14.4 + - + +
428A PHE* 3.3 32.2 + - + -
485A MET* 6.1 5.2 - - - -
488A PHE* 4.8 19.3 - - + -
489A VAL* 3.7 42.0 - - + +
492A ALA* 4.6 12.6 - - + -
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PHE* 4.9 17.9 - - - -
421A ARG 3.0 13.5 + - - -
422A GLU* 2.7 28.5 + - - +
424A ILE* 1.3 81.1 - - - +
426A THR* 1.3 61.6 + - - +
428A PHE* 3.2 23.2 + - - +
429A ASP* 4.2 0.7 + - - -
445A GLN* 5.4 2.9 + - - -
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Residues in contact with THR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A LEU* 4.8 3.8 - - - +
422A GLU 2.6 20.3 + - - -
423A ALA* 2.9 12.6 + - - -
425A SER* 1.3 76.5 + - - +
427A LEU* 1.3 62.9 + - - +
428A PHE 3.3 0.7 + - - -
429A ASP* 3.3 10.5 - - + +
433A TRP* 3.2 16.0 - - - -
445A GLN* 3.6 23.5 + - + +
446A SER* 3.5 31.4 - - - +
448A VAL* 5.1 1.8 - - + -
449A TRP* 3.4 25.4 - - + +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A ALA* 3.0 38.7 + - + +
424A ILE* 3.8 16.4 - - + +
425A SER 3.3 0.4 - - - -
426A THR* 1.3 76.9 - - - +
428A PHE* 1.3 62.7 + - + +
429A ASP 3.1 1.3 - - - -
433A TRP* 4.3 1.1 - - - -
449A TRP* 4.0 28.0 - - + -
460A ILE* 6.2 1.8 - - + -
463A PHE* 5.0 9.0 - - + -
489A VAL* 5.1 2.0 - - + +
492A ALA* 3.3 42.8 - - + +
493A ALA* 3.7 12.3 - - + +
496A ARG* 2.8 44.0 + - + +
522A GLY* 4.6 0.2 - - - -
525A ALA* 4.1 5.0 - - + +
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Residues in contact with PHE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PHE* 5.0 15.3 - + + -
335A THR* 3.9 39.0 - - + -
337A PHE* 5.0 4.7 - + + -
424A ILE* 3.3 24.1 + - + -
425A SER* 3.2 17.6 + - - +
426A THR 3.2 2.0 - - - -
427A LEU* 1.3 81.4 - - - +
429A ASP* 1.3 60.2 + - - +
430A ASN* 3.5 6.2 + - - +
488A PHE* 5.0 11.7 - + - -
492A ALA* 4.8 9.6 - - + -
522A GLY* 4.1 13.0 - - - -
525A ALA* 3.8 13.2 - - + -
526A VAL* 3.5 49.6 - - + -
529A ALA* 4.9 9.0 - - + -
549A LEU 6.3 0.2 - - - -
550A THR* 4.7 6.1 - - - -
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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