Contacts of the helix formed by residues 475 - 482 (chain D) in PDB entry 4QG0
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 475 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471D GLU 5.2 0.9 + - - -
472D ASP* 2.9 24.6 + - - +
474D GLU* 1.3 80.0 - - - +
476D LEU* 1.3 63.5 + - - +
477D PRO* 3.6 1.1 - - - -
478D LYS* 3.2 21.3 + - - +
479D GLU* 3.1 32.2 + - - +
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Residues in contact with LEU 476 (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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468D ILE* 4.2 19.3 - - + -
472D ASP* 3.3 18.8 - - + +
473D TYR* 3.2 19.5 + - + +
475D SER* 1.3 75.7 - - - +
477D PRO* 1.4 70.8 - - + +
479D GLU* 3.0 32.8 + - - +
480D VAL* 3.1 16.5 + - - +
500D VAL* 3.9 24.5 - - + +
502D VAL* 3.8 28.7 - - + -
550D ILE* 5.4 1.6 - - + -
572D TRP* 4.3 12.8 + - + -
576D ARG* 4.2 13.9 - - - +
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Residues in contact with PRO 477 (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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473D TYR 3.8 5.4 - - - +
474D GLU 3.7 14.1 - - - +
476D LEU* 1.4 93.9 - - + +
478D LYS* 1.3 58.3 + - + +
480D VAL* 3.4 3.6 + - + +
481D ALA* 3.0 29.3 + - - +
495D ALA* 3.5 28.6 - - + +
498D PHE* 3.7 24.4 - - + +
499D ILE* 5.7 0.2 - - - -
500D VAL* 3.6 20.2 - - + +
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Residues in contact with LYS 478 (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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474D GLU* 5.0 4.5 - - - +
475D SER* 3.2 22.8 + - - +
476D LEU 3.1 0.6 - - - -
477D PRO* 1.3 77.2 - - + +
479D GLU* 1.3 66.0 + - + +
481D ALA* 3.4 2.0 + - - +
482D SER* 3.0 26.2 + - - -
495D ALA* 3.7 23.3 - - + +
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Residues in contact with GLU 479 (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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475D SER* 3.1 21.0 + - - +
476D LEU* 3.0 18.9 + - - +
478D LYS* 1.3 75.4 - - + +
480D VAL* 1.3 62.8 + - - +
482D SER* 2.9 22.4 + - - -
483D ALA* 3.4 6.9 + - - +
572D TRP* 3.1 27.5 + - + +
576D ARG* 2.5 39.2 + - - -
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Residues in contact with VAL 480 (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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476D LEU 3.1 14.5 + - - +
477D PRO* 3.6 7.9 - - + +
479D GLU* 1.3 77.0 - - - +
481D ALA* 1.3 60.9 + - - +
483D ALA* 3.2 18.9 + - - +
498D PHE* 3.7 33.2 - - + -
500D VAL* 4.3 17.0 - - + -
552D VAL* 4.9 6.3 - - + -
568D TYR* 3.4 24.7 - - + +
569D PHE* 4.4 6.7 - - - +
572D TRP* 3.6 37.0 - - + -
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Residues in contact with ALA 481 (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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477D PRO 3.0 15.2 + - - +
478D LYS* 4.0 3.4 - - - +
480D VAL* 1.3 75.8 - - - +
482D SER* 1.3 57.6 + - - +
483D ALA 3.2 3.7 + - - +
484D LYS* 5.7 0.7 + - - +
493D LEU 4.2 8.4 - - - +
494D LYS* 3.8 6.7 - - - -
495D ALA* 3.4 32.1 - - + +
498D PHE* 3.9 13.0 - - + -
568D TYR* 3.6 17.6 - - - -
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Residues in contact with SER 482 (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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478D LYS 3.0 13.9 + - - -
479D GLU* 2.9 18.4 + - - -
481D ALA* 1.3 75.5 - - - +
483D ALA* 1.3 62.9 + - - +
484D LYS* 3.9 11.3 + - - +
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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