Contacts of the helix formed by residues 402 - 416 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ARG 4.0 3.6 - - - -
11D GLU* 4.7 1.6 - - - +
12D VAL* 3.8 11.2 - - + +
188D THR 5.3 1.4 + - - +
341D TYR* 4.3 10.9 + - - -
344D GLN* 4.2 18.3 + - - +
401D GLY* 1.3 70.5 - - - -
403D GLU* 1.3 57.0 + - - +
404D GLU* 3.8 18.6 - - - +
405D LYS* 2.6 74.2 + - + +
406D LEU* 2.9 9.8 + - - +
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Residues in contact with GLU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 3.3 56.7 + - + +
401D GLY 3.4 0.6 + - - -
402D GLU* 1.3 68.5 - - - +
404D GLU* 1.3 62.9 + - + +
406D LEU* 3.0 8.5 + - - +
407D LEU* 2.7 62.2 + - + +
422D LEU* 4.1 2.9 - - + +
424D ARG* 5.3 0.9 + - - -
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Residues in contact with GLU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D GLU* 3.8 21.1 - - - +
403D GLU* 1.3 87.5 + - - +
405D LYS* 1.3 70.2 + - + +
407D LEU* 3.2 11.3 + - - +
408D ALA* 2.9 25.1 + - - +
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Residues in contact with LYS 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLY 3.8 17.5 - - - +
188D THR 4.1 12.1 + - - +
190D GLY* 3.5 12.9 - - - +
191D ASP* 2.9 43.2 + - + +
192D ARG* 4.4 7.3 - - - +
341D TYR* 4.9 10.5 + - - -
402D GLU* 2.6 58.0 + - + +
404D GLU* 1.3 79.5 - - + +
406D LEU* 1.3 58.7 - - - +
408D ALA* 3.3 4.4 - - - +
409D LEU* 3.1 18.4 + - - +
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Residues in contact with LEU 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 4.2 13.0 - - - +
187D GLY* 4.0 13.7 - - - +
398D LEU* 3.3 28.5 - - + +
399D VAL* 4.2 27.1 - - - +
401D GLY* 3.3 35.2 - - - +
402D GLU 2.9 16.8 + - - +
403D GLU* 3.3 7.6 - - - +
405D LYS* 1.3 73.3 - - - +
407D LEU* 1.3 55.8 + - - +
409D LEU* 3.0 2.7 + - - -
410D GLY* 2.5 34.5 + - - -
422D LEU* 3.9 29.6 - - + -
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D GLU* 2.7 49.7 + - + +
404D GLU* 3.6 8.7 - - - +
406D LEU* 1.3 71.7 - - - +
408D ALA* 1.3 57.3 + - - +
410D GLY* 3.8 2.0 - - - +
411D LYS* 2.9 30.0 + - - +
422D LEU* 3.3 33.9 - - + -
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Residues in contact with ALA 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D GLY 3.7 9.4 - - - +
191D ASP* 4.3 12.1 - - + +
383D GLN* 5.3 0.7 - - - +
404D GLU 2.9 12.6 + - - +
405D LYS* 3.3 11.2 - - - +
407D LEU* 1.3 81.0 - - - +
409D LEU* 1.3 62.7 + - - +
411D LYS* 3.2 8.7 + - - +
412D LEU* 3.0 24.7 + - + +
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Residues in contact with LEU 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D GLU 5.3 1.6 - - - +
187D GLY* 5.2 1.3 - - - -
190D GLY* 3.2 31.8 + - - +
383D GLN* 4.3 12.3 - - + +
386D LEU* 4.2 21.5 - - + -
387D LEU* 3.8 30.5 - - + +
390D LEU* 5.7 2.7 - - + -
398D LEU* 3.5 22.4 - - + -
405D LYS 3.1 3.4 + - - +
406D LEU* 3.0 6.6 + - - +
408D ALA* 1.3 79.1 - - - +
410D GLY* 1.3 62.4 - - - +
411D LYS 3.2 0.5 + - - -
412D LEU* 3.2 7.0 + - + +
413D LEU* 3.1 51.0 + - + +
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Residues in contact with GLY 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D LEU* 4.1 11.2 - - - -
406D LEU 2.5 21.9 + - - -
407D LEU* 3.8 2.5 - - - -
409D LEU* 1.3 74.4 - - - +
411D LYS* 1.3 61.9 + - - +
413D LEU* 3.2 2.6 + - - +
414D ALA* 3.0 16.2 + - - +
420D VAL* 3.1 30.6 - - - +
422D LEU* 5.6 3.1 - - - -
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Residues in contact with LYS 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D LEU 2.9 14.4 + - - +
408D ALA* 3.5 10.8 - - - +
409D LEU 3.2 0.2 - - - -
410D GLY* 1.3 71.5 - - - +
412D LEU* 1.3 62.0 + - + +
414D ALA* 2.5 38.4 + - + +
415D LEU* 2.9 32.0 + - + -
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D GLN* 4.1 21.5 - - + +
387D LEU* 3.7 38.6 - - + -
408D ALA* 3.0 28.7 - - + +
409D LEU* 3.2 7.5 + - + +
411D LYS* 1.3 83.1 - - + +
413D LEU* 1.3 62.8 + - - +
415D LEU* 3.1 24.9 + - + +
416D ARG* 3.1 14.6 + - - +
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Residues in contact with LEU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D LEU* 3.9 14.8 - - + -
390D LEU* 4.2 15.0 - - + -
396D VAL* 4.0 14.8 - - + -
398D LEU* 3.9 17.7 - - + -
409D LEU* 3.1 36.3 + - + +
410D GLY 3.3 7.6 - - - +
411D LYS 3.0 0.6 - - - -
412D LEU* 1.3 77.3 - - - +
414D ALA* 1.3 58.2 + - - +
416D ARG* 3.6 21.5 + - - +
418D GLN* 2.9 55.6 + - + +
420D VAL* 3.9 16.2 - - + -
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Residues in contact with ALA 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D GLY 3.0 10.3 + - - +
411D LYS* 2.5 26.6 + - + +
413D LEU* 1.3 68.7 - - - +
415D LEU* 1.3 57.6 + - + +
416D ARG 3.0 3.8 - - - -
417D GLY* 2.8 22.7 + - - -
418D GLN 3.8 10.4 + - - +
420D VAL* 4.4 7.0 - - + -
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D LYS* 2.9 39.0 + - + +
412D LEU* 3.1 15.7 + - + +
414D ALA* 1.3 77.7 - - + +
416D ARG* 1.3 56.0 + - - +
417D GLY 3.1 3.8 + - - -
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Residues in contact with ARG 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D LEU* 2.7 47.6 + - - +
388D ASP* 5.0 3.0 + - - -
390D LEU 4.2 0.2 - - - -
391D GLN* 3.7 35.4 - - - +
392D GLY 5.6 0.4 - - - +
412D LEU 3.1 13.5 + - - +
413D LEU* 3.7 19.5 - - - +
414D ALA 3.0 1.4 - - - -
415D LEU* 1.3 76.2 - - - +
417D GLY* 1.3 62.8 + - - +
418D GLN* 3.3 29.9 + - + +
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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