Contacts of the helix formed by residues 402 - 416 (chain A) in PDB entry 3A4Y
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 GLU 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG 4.0 6.7 - - - +
11A GLU* 5.0 1.8 - - - +
12A VAL* 4.3 9.5 - - + +
188A THR 5.2 0.6 + - - -
344A GLN* 3.7 21.9 + - - +
401A GLY* 1.3 73.8 - - - +
403A GLU* 1.3 66.2 + - - +
404A GLU* 3.3 17.6 - - - +
405A LYS* 2.7 50.5 + - + +
406A LEU* 2.9 20.7 + - - +
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Residues in contact with GLU 403 (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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10A ARG* 4.0 36.2 + - + +
401A GLY 3.6 2.4 + - - -
402A GLU* 1.3 70.1 - - - +
404A GLU* 1.3 68.0 + - - +
406A LEU* 3.2 7.5 + - - +
407A LEU* 2.8 57.8 + - + +
422A LEU* 4.3 11.9 - - + -
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASP* 5.6 0.7 - - - -
402A GLU* 3.9 17.7 - - - +
403A GLU* 1.3 95.5 + - + +
405A LYS* 1.3 65.3 + - + +
407A LEU* 3.2 10.2 + - - +
408A ALA* 2.9 30.5 + - - +
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLY 3.9 15.9 - - - +
188A THR 3.9 15.1 + - - +
189A TYR* 6.0 1.6 - - - -
190A GLY* 3.5 18.5 - - - +
191A ASP* 2.8 44.6 - - + +
192A ARG* 4.7 8.8 - - - +
344A GLN* 5.7 0.6 + - - -
402A GLU* 2.7 47.9 + - + +
404A GLU* 1.3 81.2 - - + +
406A LEU* 1.3 62.3 + - - +
408A ALA 3.4 1.0 + - - -
409A LEU* 3.3 15.9 + - - +
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Residues in contact with LEU 406 (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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10A ARG* 4.4 13.2 - - - +
187A GLY* 3.3 28.7 - - - +
398A LEU* 3.2 53.4 - - + +
399A VAL* 3.7 17.0 - - - +
401A GLY* 3.5 31.9 - - - +
402A GLU 2.9 11.2 + - - +
403A GLU 3.5 4.5 - - - +
405A LYS* 1.3 77.4 - - - +
407A LEU* 1.3 58.3 + - - +
409A LEU* 3.3 3.9 + - - +
410A GLY* 3.0 21.3 + - - -
422A LEU* 4.0 21.6 - - + +
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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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403A GLU* 2.8 44.7 + - + +
404A GLU* 3.4 8.1 - - - +
406A LEU* 1.3 69.8 - - - +
408A ALA* 1.3 66.8 + - - +
409A LEU 3.0 1.8 - - - -
410A GLY* 2.9 3.5 + - - +
411A LYS* 2.8 25.7 + - - +
422A LEU* 3.3 34.3 - - + -
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Residues in contact with ALA 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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190A GLY 3.9 11.0 - - - +
191A ASP* 3.9 17.0 - - + -
383A GLN* 4.8 1.8 - - - +
404A GLU 2.9 16.4 + - - +
405A LYS 3.4 6.7 + - - +
407A LEU* 1.3 76.3 - - - +
409A LEU* 1.3 59.7 + - - +
411A LYS* 3.8 8.2 - - - +
412A LEU* 3.5 26.0 + - - +
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Residues in contact with LEU 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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186A GLU 4.2 5.2 - - - +
187A GLY* 4.0 25.8 - - - -
190A GLY* 3.7 18.1 + - - +
383A GLN* 5.4 2.7 - - + -
386A LEU* 4.4 17.5 - - + -
387A LEU* 4.6 11.9 - - + -
390A LEU* 4.7 8.7 - - + -
398A LEU* 3.9 20.4 - - + -
405A LYS 3.3 8.8 + - - +
406A LEU 3.3 8.5 + - - +
407A LEU 3.0 0.6 - - - -
408A ALA* 1.3 78.2 - - - +
410A GLY* 1.3 65.6 + - - +
412A LEU* 3.2 7.6 + - + +
413A LEU* 2.9 47.0 + - + +
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Residues in contact with GLY 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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398A LEU* 3.9 1.5 - - - +
406A LEU 3.0 11.5 + - - -
407A LEU* 2.9 7.7 + - - -
409A LEU* 1.3 74.7 - - - +
411A LYS* 1.3 54.9 + - - +
413A LEU* 4.4 1.3 - - - -
414A ALA* 2.7 38.1 + - - +
420A VAL* 3.5 32.3 - - - +
422A LEU* 5.6 2.5 - - - -
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Residues in contact with LYS 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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407A LEU 2.8 14.6 + - - +
408A ALA* 3.8 9.9 - - - +
409A LEU 3.2 0.2 - - - -
410A GLY* 1.3 74.3 - - - +
412A LEU* 1.3 64.3 + - + +
414A ALA* 3.0 8.7 + - - +
415A LEU* 2.9 56.2 + - + +
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Residues in contact with LEU 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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383A GLN* 3.5 42.0 - - + +
387A LEU* 4.4 21.8 - - + -
408A ALA 3.5 14.8 - - - +
409A LEU* 3.2 8.6 + - + +
411A LYS* 1.3 86.2 - - + +
413A LEU* 1.3 63.2 + - - +
415A LEU* 3.5 17.4 + - + +
416A ARG* 3.2 28.7 + - - +
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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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387A LEU* 3.9 20.6 - - + -
390A LEU* 4.2 19.3 - - + -
396A VAL* 4.2 27.8 - - + -
398A LEU* 4.3 9.0 - - + -
409A LEU* 2.9 39.3 + - + +
410A GLY* 3.7 4.3 - - - +
412A LEU* 1.3 76.5 - - - +
414A ALA* 1.3 61.4 + - - +
416A ARG* 3.1 14.7 + - - +
418A GLN* 3.0 55.3 + - + +
420A VAL* 4.4 13.7 - - + -
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Residues in contact with ALA 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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410A GLY 2.7 21.3 + - - +
411A LYS* 3.3 7.6 - - - +
413A LEU* 1.3 69.4 - - - +
415A LEU* 1.3 59.1 + - + +
416A ARG 3.0 4.5 - - - -
417A GLY* 3.0 19.8 + - - -
418A GLN 3.6 12.2 + - - +
420A VAL* 4.2 10.7 - - + +
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Residues in contact with LEU 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 LYS* 2.9 48.3 + - + +
412A LEU* 3.9 15.5 - - + +
414A ALA* 1.3 77.2 - - + +
416A ARG* 1.3 59.8 + - - +
417A GLY 3.2 0.7 + - - -
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Residues in contact with ARG 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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387A LEU* 3.0 59.7 + - - +
388A ASP* 5.3 2.0 + - - +
390A LEU 3.8 1.2 - - - -
391A GLN* 3.3 36.9 - - - +
392A GLY 4.8 0.2 - - - +
412A LEU* 3.2 16.7 + - - +
413A LEU* 3.1 15.0 + - - +
414A ALA 3.0 1.2 - - - -
415A LEU* 1.3 80.8 - - - +
417A GLY* 1.3 57.8 + - - +
418A GLN* 3.4 25.5 + - + +
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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