Contacts of the helix formed by residues 410 - 422 (chain Y) in PDB entry 2Q4G
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 GLY 410 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383Y ASP* 2.9 26.0 + - - -
409Y LEU* 1.3 75.0 - - - +
411Y ASP* 1.3 65.4 + - - -
412Y ALA* 2.8 9.1 + - - -
413Y GLY 2.9 2.4 + - - -
414Y ILE* 2.8 23.9 + - - +
67Z ASN* 4.6 13.5 - - - -
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Residues in contact with ASP 411 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410Y GLY* 1.3 71.0 - - - -
412Y ALA* 1.3 56.7 + - - +
414Y ILE* 3.8 7.6 - - - +
415Y LEU* 3.0 14.6 + - - +
437Y TYR 3.7 5.2 - - - +
438Y TRP* 2.8 28.9 - - - +
439Y SER* 2.8 33.0 + - - +
442Y MET* 2.9 46.9 - - + +
67Z ASN* 3.8 7.4 + - - -
69Z GLN* 4.6 3.6 - - - +
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Residues in contact with ALA 412 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383Y ASP* 4.2 12.1 - - + +
410Y GLY* 2.8 1.6 + - - -
411Y ASP* 1.3 78.1 - - - +
413Y GLY* 1.3 62.6 + - - +
415Y LEU* 3.0 24.8 + - - +
416Y GLN* 3.4 10.4 + - - +
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Residues in contact with GLY 413 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383Y ASP* 2.8 28.7 + - - -
386Y CYS* 2.8 41.8 - - - +
412Y ALA* 1.3 71.3 - - - +
414Y ILE* 1.3 65.2 + - - +
416Y GLN* 2.9 19.6 + - - +
417Y LEU 3.3 2.6 + - - -
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Residues in contact with ILE 414 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386Y CYS* 4.0 0.8 - - - -
409Y LEU* 4.2 20.9 - - + +
410Y GLY 2.8 20.5 + - - +
411Y ASP* 3.9 8.1 - - - +
413Y GLY* 1.3 75.2 - - - +
415Y LEU* 1.3 63.0 + - - +
417Y LEU* 3.2 16.2 + - + +
418Y VAL* 3.0 27.3 + - + +
431Y LEU* 6.4 0.9 - - + -
433Y LEU* 5.0 10.1 - - + -
436Y ILE* 3.8 16.4 - - + -
437Y TYR 5.1 0.2 - - - +
438Y TRP* 3.3 36.3 - - + -
442Y MET* 3.9 22.2 - - + -
446Y LEU* 4.6 9.6 - - + -
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Residues in contact with LEU 415 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411Y ASP 3.0 15.1 + - - +
412Y ALA* 3.0 17.7 + - - +
414Y ILE* 1.3 74.5 - - - +
416Y GLN* 1.3 64.9 + - + +
418Y VAL* 3.2 11.3 + - + +
419Y GLU* 2.9 34.4 + - + +
422Y ARG* 5.6 2.5 - - - +
442Y MET* 4.1 7.2 - - + -
445Y ARG* 3.9 41.5 - - - +
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Residues in contact with GLN 416 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383Y ASP* 3.6 7.1 - - - +
386Y CYS* 3.0 24.1 - - - +
387Y SER* 2.8 46.5 + - - +
390Y ALA* 3.5 14.2 - - + +
412Y ALA 3.8 8.7 - - - +
413Y GLY* 2.9 14.8 + - - +
415Y LEU* 1.3 78.2 - - + +
417Y LEU* 1.3 63.3 + - - +
419Y GLU* 3.1 25.4 + - - +
420Y SER 3.4 7.1 + - - -
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Residues in contact with LEU 417 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386Y CYS* 3.7 23.8 - - - +
389Y LEU* 3.2 41.1 - - + +
390Y ALA* 4.5 3.6 - - - -
393Y LEU* 4.3 11.0 - - + -
402Y LEU* 5.5 0.9 - - + -
404Y LEU* 3.6 28.3 - - + -
409Y LEU* 4.6 5.4 - - + -
413Y GLY 3.8 8.3 - - - +
414Y ILE* 3.2 15.8 + - + +
416Y GLN* 1.3 75.4 - - - +
418Y VAL* 1.3 62.3 + - + +
420Y SER* 3.1 5.5 + - - -
421Y VAL* 3.0 29.1 + - + +
431Y LEU* 5.1 18.6 - - + -
433Y LEU* 5.5 2.9 - - + -
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Residues in contact with VAL 418 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414Y ILE* 3.0 24.2 + - + +
415Y LEU* 3.3 16.8 - - + +
416Y GLN 3.1 0.2 - - - -
417Y LEU* 1.3 74.4 - - + +
419Y GLU* 1.3 68.8 + - - +
421Y VAL* 3.9 7.4 - - + -
422Y ARG* 2.9 40.3 + - + +
431Y LEU* 6.6 0.2 - - + -
442Y MET* 4.7 6.3 - - - -
445Y ARG* 4.3 20.6 - - + +
446Y LEU* 4.1 26.5 - - + -
449Y LEU* 4.6 14.1 - - + -
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Residues in contact with GLU 419 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390Y ALA* 6.0 0.2 - - + -
415Y LEU* 2.9 27.6 + - + +
416Y GLN* 3.1 20.3 + - - +
418Y VAL* 1.3 75.6 - - - +
420Y SER* 1.3 53.5 + - - +
422Y ARG* 3.1 53.6 + - - +
423Y GLN* 2.7 28.4 + - - +
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Residues in contact with SER 420 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390Y ALA* 2.8 41.0 + - - +
393Y LEU* 3.8 13.9 - - - -
394Y LEU* 3.3 21.9 - - - +
416Y GLN 3.4 1.2 + - - -
417Y LEU 3.1 9.2 + - - -
418Y VAL 3.0 0.8 - - - -
419Y GLU* 1.3 78.1 - - - +
421Y VAL* 1.3 62.7 + - - +
422Y ARG 3.3 0.2 - - - -
423Y GLN* 3.3 21.9 + - - +
426Y CYS* 3.1 17.7 - - - +
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Residues in contact with VAL 421 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393Y LEU* 3.7 13.2 - - + -
417Y LEU* 3.0 20.2 + - + +
418Y VAL* 3.7 11.7 - - + +
420Y SER* 1.3 69.9 - - - +
422Y ARG* 1.3 60.7 + - - +
423Y GLN 3.1 2.5 - - - -
426Y CYS* 3.3 22.4 - - - -
428Y LEU* 3.7 25.1 - - + -
431Y LEU* 5.6 8.5 - - + -
449Y LEU* 4.2 16.4 - - + -
453Y LYS* 2.7 36.7 + - - +
456Y LEU* 3.8 20.9 - - + -
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Residues in contact with ARG 422 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415Y LEU* 5.6 3.0 - - - +
418Y VAL* 2.9 20.8 + - + +
419Y GLU* 3.1 64.9 + - - +
421Y VAL* 1.3 78.7 - - - +
423Y GLN* 1.3 77.8 + - + +
424Y PRO* 3.4 7.4 - - - +
445Y ARG* 6.1 1.4 - - - +
449Y LEU* 4.1 20.9 - - + -
453Y LYS* 4.3 8.3 + - - +
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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