Contacts of the helix formed by residues 539 - 549 (chain D) in PDB entry 2O1S
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 ASP 539 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495D GLY 3.4 19.5 + - - +
496D LYS* 3.2 18.9 - - - +
497D GLY* 2.7 32.6 + - - +
532D MSE 4.4 15.4 + - + +
534D PHE* 4.9 1.8 + - - +
537D PRO 3.9 1.0 + - - -
538D LEU* 1.3 71.5 - - - +
540D GLU* 1.3 61.9 + - - +
541D ALA* 3.8 7.1 + - - +
542D LEU* 3.0 34.9 + - + +
543D ILE* 3.0 23.7 + - - +
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Residues in contact with GLU 540 (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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538D LEU* 2.8 20.4 + - + +
539D ASP* 1.3 70.3 + - - +
541D ALA* 1.3 64.4 + - - +
543D ILE* 2.9 6.7 + - - +
544D LEU* 2.9 28.1 + - + +
572D VAL* 3.8 43.1 - - + +
575D ALA* 6.0 0.7 - - - +
576D HIS* 3.9 20.6 + - + +
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Residues in contact with ALA 541 (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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496D LYS* 6.0 3.8 - - - -
539D ASP* 3.4 7.0 + - - +
540D GLU* 1.3 77.7 - - - +
542D LEU* 1.3 62.5 + - - +
544D LEU* 3.3 11.0 + - - +
545D GLU* 3.0 35.8 + - + +
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Residues in contact with LEU 542 (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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497D GLY* 3.9 25.6 - - - +
498D ILE* 4.2 2.0 - - - +
499D VAL* 4.4 14.6 - - + -
530D VAL* 4.0 21.8 - - + -
532D MSE 4.6 6.3 - - - -
539D ASP* 3.0 36.1 + - + +
541D ALA* 1.3 73.9 - - - +
543D ILE* 1.3 66.3 + - + +
545D GLU* 3.3 21.8 + - - +
546D MSE 3.1 49.1 + - + +
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Residues in contact with ILE 543 (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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509D LEU* 4.4 10.5 - - + -
532D MSE 3.5 28.9 - - + -
538D LEU* 3.8 21.5 - - + -
539D ASP 3.0 18.7 + - - +
540D GLU* 2.9 7.7 + - - +
542D LEU* 1.3 77.6 - - - +
544D LEU* 1.3 64.2 + - - +
546D MSE 3.3 5.4 + - - +
547D ALA* 3.0 20.8 + - - +
553D LEU* 4.4 5.1 - - + +
569D VAL* 4.0 21.5 - - + -
572D VAL* 4.0 24.0 - - + -
573D LEU* 3.9 28.7 - - + -
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Residues in contact with LEU 544 (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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540D GLU* 2.9 22.1 + - + +
541D ALA* 3.7 10.3 - - - +
543D ILE* 1.3 76.0 - - - +
545D GLU* 1.3 61.8 + - + +
547D ALA* 3.1 6.7 + - - +
548D ALA* 3.0 23.9 + - - +
572D VAL* 4.7 6.3 - - + +
573D LEU* 4.0 20.2 - - + -
576D HIS* 3.6 52.5 - - + +
578D LYS* 4.5 13.9 - - + +
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Residues in contact with GLU 545 (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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541D ALA* 3.0 32.4 + - + +
542D LEU* 3.5 26.7 + - - +
544D LEU* 1.3 76.3 - - + +
546D MSE 1.3 76.8 + - + +
548D ALA* 3.1 16.3 + - - +
549D SER* 3.1 15.6 + - - -
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Residues in contact with MSE 546 (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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499D VAL* 4.7 12.3 - - + -
502D ARG* 6.3 0.4 - - - +
507D ALA* 4.3 2.7 - - + -
509D LEU* 4.5 16.6 - - + -
528D THR* 3.9 28.7 - - - -
530D VAL* 4.7 3.6 - - + -
542D LEU* 3.1 32.8 + - + +
543D ILE* 3.7 7.2 - - - +
545D GLU* 1.3 95.1 - - + +
547D ALA* 1.3 62.9 + - - +
549D SER* 3.7 10.3 - - - +
550D HIS* 2.9 40.1 + - + +
553D LEU* 3.7 16.7 - - + +
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Residues in contact with ALA 547 (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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543D ILE 3.0 14.7 + - - +
544D LEU* 3.1 9.2 + - - +
546D MSE 1.3 76.9 - - - +
548D ALA* 1.3 58.9 + - - +
550D HIS 3.3 17.9 - - - +
553D LEU* 4.0 13.2 - - + +
573D LEU* 3.6 26.5 - - + -
578D LYS* 5.4 3.8 - - + -
580D VAL* 3.5 31.2 - - + +
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Residues in contact with ALA 548 (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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544D LEU 3.0 16.0 + - - +
545D GLU* 3.1 7.6 + - - +
547D ALA* 1.3 78.7 - - - +
549D SER* 1.3 56.6 + - - +
550D HIS 3.6 1.5 + - - -
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Residues in contact with SER 549 (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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504D GLU* 5.6 0.7 - - - -
505D LYS 4.9 2.8 + - - -
545D GLU 3.1 14.3 + - - -
546D MSE 3.3 7.5 + - - +
548D ALA* 1.3 77.8 - - - +
550D HIS* 1.3 95.2 + - - +
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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