Contacts of the helix formed by residues 406 - 420 (chain A) in PDB entry 2V9V
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 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A LEU* 1.3 74.0 - - - +
407A LEU* 1.3 64.0 + - - +
408A GLU* 3.5 14.0 + - - +
409A GLU* 3.0 30.1 + - - +
410A THR* 2.9 27.6 + - - -
1512A CL 3.9 14.1 - - - -
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Residues in contact with LEU 407 (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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396A TRP* 3.4 35.8 - - + -
397A GLN* 3.8 48.7 - - + +
400A ALA* 3.9 21.3 - - + -
405A LEU 3.8 0.2 + - - -
406A SER* 1.3 73.0 - - - +
408A GLU* 1.3 64.4 + - - +
410A THR* 3.3 1.2 + - - -
411A ARG* 2.8 22.4 + - - +
1512A CL 3.3 21.3 - - + +
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Residues in contact with GLU 408 (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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406A SER* 3.3 11.3 + - - +
407A LEU* 1.3 78.8 - - - +
409A GLU* 1.3 63.4 - - - +
411A ARG* 3.4 15.8 + - - +
412A LYS* 3.1 60.0 + - + +
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Residues in contact with GLU 409 (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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379A PRO* 4.2 11.8 - - - +
380A GLU 5.6 0.2 + - - -
405A LEU* 3.4 28.5 - - + +
406A SER* 3.0 23.1 + - - +
408A GLU* 1.3 76.0 - - + +
410A THR* 1.3 68.3 + - - +
412A LYS* 3.3 7.7 + - + +
413A LEU* 3.0 40.5 + - + +
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Residues in contact with THR 410 (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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383A LEU* 4.2 22.9 - - + -
396A TRP* 4.0 24.7 - - + +
399A ALA* 5.0 0.9 - - + -
400A ALA* 3.3 23.3 - - + +
405A LEU* 3.4 15.0 - - - +
406A SER 2.9 18.5 + - - -
407A LEU* 3.7 4.5 - - - -
409A GLU* 1.3 77.3 - - - +
411A ARG* 1.3 57.3 + - - +
413A LEU* 3.3 1.9 + - - +
414A LEU* 2.8 51.9 + - + +
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Residues in contact with ARG 411 (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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396A TRP* 4.0 18.3 - - + -
407A LEU 2.8 16.8 + - - +
408A GLU* 3.6 14.6 + - - +
410A THR* 1.3 77.8 - - - +
412A LYS* 1.3 88.8 + - - +
414A LEU* 3.2 8.3 + - - +
415A GLN* 2.8 65.4 + - + +
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Residues in contact with LYS 412 (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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408A GLU* 3.1 42.2 + - + +
409A GLU* 3.9 7.4 - - + +
411A ARG* 1.3 107.3 - - - +
413A LEU* 1.3 63.3 + - + +
415A GLN* 3.4 13.2 + - - +
416A SER* 3.2 20.8 + - - -
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Residues in contact with LEU 413 (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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380A GLU* 3.7 50.3 - - + +
383A LEU* 3.8 24.9 - - + -
405A LEU* 4.0 16.8 - - + -
409A GLU* 3.0 35.2 + - + +
410A THR 3.8 3.4 - - - +
412A LYS* 1.3 78.4 - - + +
414A LEU* 1.3 57.7 + - - +
416A SER* 2.9 11.3 + - - +
417A MET* 2.9 37.3 + - + +
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Residues in contact with LEU 414 (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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383A LEU* 4.9 2.5 - - + -
387A ILE* 3.5 32.3 - - + -
396A TRP* 3.9 26.7 - - + -
399A ALA* 6.2 0.7 - - + -
410A THR* 2.8 40.2 + - + +
411A ARG* 3.6 6.1 - - - +
413A LEU* 1.3 76.1 - - - +
415A GLN* 1.3 57.9 + - + +
417A MET* 3.7 8.0 - - - +
418A ALA* 2.8 32.1 + - - +
423A VAL* 4.0 14.2 - - + +
425A LEU* 4.3 21.9 - - + +
432A LEU* 6.0 1.8 - - + -
434A ALA* 3.9 12.8 - - + -
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Residues in contact with GLN 415 (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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411A ARG* 2.8 60.6 + - + +
412A LYS* 3.7 11.3 + - - +
413A LEU 3.2 0.2 - - - -
414A LEU* 1.3 76.6 - - + +
416A SER* 1.3 57.6 + - - +
418A ALA* 3.7 6.2 + - - +
419A ALA* 3.1 26.3 + - - +
425A LEU* 5.5 5.6 - - + -
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Residues in contact with SER 416 (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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380A GLU* 4.8 6.1 + - - -
412A LYS 3.2 12.0 + - - -
413A LEU* 2.9 26.4 + - - +
415A GLN* 1.3 74.4 - - - +
417A MET* 1.3 62.0 + - - +
419A ALA* 3.3 7.5 + - - +
420A ALA* 3.0 28.8 + - - +
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Residues in contact with MET 417 (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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380A GLU* 4.0 25.6 - - + +
383A LEU* 4.1 14.1 - - + -
384A ALA* 3.9 36.6 - - + +
387A ILE* 4.3 14.6 - - - -
388A GLN* 5.9 0.4 - - - -
413A LEU* 2.9 26.4 + - + +
414A LEU* 3.7 7.0 - - - +
416A SER* 1.3 79.1 + - - +
418A ALA* 1.3 58.1 + - - +
420A ALA* 3.3 5.6 + - - -
421A GLY 3.2 3.5 + - - -
422A GLN* 2.9 36.1 + - + +
423A VAL* 3.6 31.2 - - + -
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Residues in contact with ALA 418 (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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414A LEU 2.8 19.9 + - - +
415A GLN* 3.9 6.3 - - - +
417A MET* 1.3 71.8 - - - +
419A ALA* 1.3 65.0 + - - +
421A GLY* 3.0 13.9 + - - -
423A VAL* 3.5 22.0 + - + +
425A LEU* 4.2 19.1 - - + -
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Residues in contact with ALA 419 (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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415A GLN 3.1 18.1 + - - +
416A SER* 3.3 8.7 + - - +
418A ALA* 1.3 77.6 - - - +
420A ALA* 1.3 58.9 + - - +
421A GLY 3.2 0.7 + - - -
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Residues in contact with ALA 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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416A SER 3.0 16.4 + - - +
417A MET* 3.7 7.0 - - - +
418A ALA 3.2 0.4 - - - -
419A ALA* 1.3 74.7 - - - +
421A GLY* 1.3 57.4 + - - +
422A GLN* 3.0 29.1 + - + +
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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