Contacts of the helix formed by residues 439 - 453 (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 SER 439 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411Y ASP* 2.8 15.5 + - - +
437Y TYR* 4.9 3.1 - - - -
438Y TRP* 1.3 76.8 - - - +
440Y GLU* 1.3 60.7 + - - +
441Y GLU* 3.2 11.9 + - - +
442Y MET* 3.2 17.5 + - - +
443Y GLU* 2.9 25.6 + - - +
4Z ARG* 3.4 4.3 - - - +
69Z GLN* 4.0 16.5 + - - +
111Z GLU* 4.6 4.9 - - - -
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Residues in contact with GLU 440 (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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439Y SER* 1.3 73.2 - - - +
441Y GLU* 1.3 61.1 + - + +
443Y GLU* 3.2 11.0 - - + +
444Y ASP* 2.7 44.4 + - - +
4Z ARG* 3.5 10.0 - - - +
111Z GLU* 3.8 24.7 + - - +
112Z GLY* 6.1 1.4 - - - -
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Residues in contact with GLU 441 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439Y SER* 3.2 8.7 + - - +
440Y GLU* 1.3 87.3 - - + +
442Y MET* 1.3 58.1 + - - +
444Y ASP* 3.0 15.8 + - + +
445Y ARG* 2.9 47.8 + - - +
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Residues in contact with MET 442 (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* 2.9 63.5 - - + +
414Y ILE* 3.9 18.6 - - + -
415Y LEU* 4.1 16.6 - - + +
418Y VAL* 4.7 3.4 - - - -
438Y TRP* 4.0 10.8 - - + -
439Y SER* 3.2 4.1 + - - +
441Y GLU* 1.3 76.3 - - - +
443Y GLU* 1.3 56.4 - - - +
445Y ARG* 3.0 31.9 + - - +
446Y LEU* 2.8 51.4 + - + +
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Residues in contact with GLU 443 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438Y TRP* 3.0 31.7 + - + +
439Y SER 2.9 19.5 + - - +
440Y GLU* 3.2 11.7 - - - +
442Y MET* 1.3 77.5 - - - +
444Y ASP* 1.3 60.0 + - - +
446Y LEU* 3.2 3.6 + - - +
447Y GLN* 2.8 64.7 + - + +
2Z GLU 5.5 1.0 - - - +
4Z ARG* 4.2 31.6 + - + +
7Z LYS* 5.8 2.6 + - - +
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Residues in contact with ASP 444 (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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440Y GLU* 2.7 36.2 + - - +
441Y GLU* 3.0 14.0 + - + +
443Y GLU* 1.3 76.7 - - - +
445Y ARG* 1.3 62.0 + - - +
447Y GLN* 3.3 6.0 + - - +
448Y ALA* 3.0 26.1 + - - +
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Residues in contact with ARG 445 (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* 3.9 31.7 - - - +
418Y VAL* 4.3 19.0 - - + +
422Y ARG* 6.1 1.4 - - - +
441Y GLU* 2.9 33.9 + - - +
442Y MET* 3.0 32.9 + - - +
444Y ASP* 1.3 77.6 - - - +
446Y LEU* 1.3 56.1 + - - +
448Y ALA* 3.8 5.0 - - - +
449Y LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 446 (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* 4.6 9.0 - - + -
418Y VAL* 4.1 19.1 - - + -
431Y LEU* 5.9 2.5 - - + -
433Y LEU* 4.8 5.2 - - + -
438Y TRP* 3.2 54.5 - - + +
442Y MET* 2.8 29.2 + - + +
443Y GLU* 3.8 5.4 - - - +
445Y ARG* 1.3 71.8 - - - +
447Y GLN* 1.3 60.4 + - - +
448Y ALA 3.1 2.0 - - - -
449Y LEU* 3.6 24.2 - - + +
450Y GLU* 2.9 45.7 + - - +
458Y VAL* 5.0 10.3 - - + -
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Residues in contact with GLN 447 (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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443Y GLU* 2.8 53.1 + - + +
444Y ASP* 3.9 6.1 - - - +
446Y LEU* 1.3 73.8 - - + +
448Y ALA* 1.3 59.1 + - - +
450Y GLU* 3.6 15.9 + - - +
451Y LYS* 3.1 34.4 + - + +
2Z GLU 4.8 12.1 + - - +
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Residues in contact with ALA 448 (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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444Y ASP 3.0 17.3 + - - +
445Y ARG* 3.8 6.1 - - - +
447Y GLN* 1.3 75.8 - - - +
449Y LEU* 1.3 54.6 + - - +
451Y LYS* 2.9 6.7 + - - +
452Y ASP* 2.7 52.9 + - - +
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Residues in contact with LEU 449 (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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418Y VAL* 4.6 13.7 - - + -
421Y VAL* 4.2 22.4 - - + +
422Y ARG* 4.1 29.8 - - + -
431Y LEU* 6.0 2.5 - - + -
445Y ARG* 2.9 19.1 + - + +
446Y LEU* 3.6 25.1 - - + +
448Y ALA* 1.3 75.4 - - - +
450Y GLU* 1.3 58.8 + - - +
452Y ASP* 4.4 6.3 - - + -
453Y LYS* 2.9 45.9 + - + +
456Y LEU* 4.9 4.7 - - + -
458Y VAL* 4.4 18.4 - - + -
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Residues in contact with GLU 450 (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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438Y TRP* 5.9 1.0 - - - -
446Y LEU* 2.9 30.1 + - - +
447Y GLN* 3.7 16.0 - - - +
448Y ALA 3.2 0.2 - - - -
449Y LEU* 1.3 76.5 - - - +
451Y LYS* 1.3 60.8 + - + +
453Y LYS 4.2 1.1 - - - +
454Y PRO* 4.0 18.5 - - - +
456Y LEU 4.7 9.5 - - - +
458Y VAL* 3.3 56.8 + - + +
460Y SER* 5.6 0.7 + - - -
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Residues in contact with LYS 451 (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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112W PRO* 5.5 4.2 - - - +
447Y GLN* 3.1 25.1 + - - +
448Y ALA* 2.9 11.1 + - - +
450Y GLU* 1.3 80.2 - - - +
452Y ASP* 1.3 65.3 + - - +
453Y LYS 3.2 2.0 - - - -
454Y PRO* 3.2 18.9 - - - +
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Residues in contact with ASP 452 (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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112W PRO* 5.5 0.4 - - - +
142W ARG* 2.7 36.4 + - - +
448Y ALA* 2.7 38.4 + - - +
449Y LEU* 4.1 6.3 + - + +
451Y LYS* 1.3 78.0 - - - +
453Y LYS* 1.3 54.1 + - + +
454Y PRO* 3.5 2.2 - - - -
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Residues in contact with LYS 453 (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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142W ARG* 3.9 8.1 - - - +
170W ASP* 4.8 6.1 - - - -
421Y VAL 2.7 30.2 + - - +
422Y ARG* 4.4 9.4 - - - +
423Y GLN 3.0 22.0 + - - -
424Y PRO* 4.1 11.7 + - - +
426Y CYS* 3.2 19.1 + - - -
428Y LEU 5.3 3.1 + - - -
449Y LEU* 2.9 25.9 + - + +
450Y GLU 4.2 1.7 - - - +
452Y ASP* 1.3 81.1 - - + +
454Y PRO* 1.3 57.6 - - - +
455Y SER* 3.1 26.0 - - - +
456Y LEU* 3.0 43.0 + - + +
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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