Contacts of the helix formed by residues 564 - 576 (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 GLY 564 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437D LEU 3.9 2.7 - - - -
438D SER* 3.4 10.1 - - - -
441D ARG* 3.2 14.0 + - - -
557D GLU* 3.6 11.2 - - - -
559D ASN* 3.7 3.6 - - - -
560D ALA 3.7 8.1 - - - -
561D ILE 3.4 6.4 + - - -
562D MSE 3.1 6.1 + - - -
563D GLY* 1.3 78.3 - - - +
565D ALA* 1.3 65.7 + - - -
566D GLY 3.4 2.5 - - - -
567D SER* 3.1 15.4 + - - -
568D GLY 3.3 1.2 + - - -
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Residues in contact with ALA 565 (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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437D LEU* 4.3 4.9 + - + +
441D ARG* 4.2 1.5 - - - +
511D PHE* 3.7 36.6 - - + -
535D VAL* 3.8 30.3 - - + -
538D LEU* 4.5 3.1 - - - +
557D GLU* 2.8 22.7 + - + +
564D GLY* 1.3 69.9 - - - -
566D GLY* 1.3 62.9 + - - +
568D GLY* 3.0 12.1 + - - -
569D VAL* 3.3 13.3 + - - +
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Residues in contact with GLY 566 (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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511D PHE* 4.9 0.2 - - - -
555D THR* 3.5 34.7 - - - -
557D GLU* 2.9 16.8 + - - -
565D ALA* 1.3 73.8 - - - +
567D SER* 1.3 61.0 + - - +
569D VAL* 3.0 14.5 + - - +
570D ASN* 3.0 16.6 + - - -
584D ASN* 3.5 10.8 - - - +
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Residues in contact with SER 567 (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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567C SER* 2.6 29.8 + - - -
570C ASN* 5.2 0.2 + - - -
571C GLU* 2.7 24.0 + - - +
441D ARG* 3.8 1.7 + - - -
557D GLU* 4.6 1.0 + - - -
561D ILE 4.1 4.1 + - - -
563D GLY* 3.6 5.0 - - - -
564D GLY 3.1 27.3 + - - -
565D ALA 3.1 0.2 - - - -
566D GLY* 1.3 75.9 - - - +
568D GLY* 1.3 59.8 + - - +
570D ASN* 3.2 17.0 + - - +
571D GLU* 3.1 24.6 + - - +
584D ASN* 4.3 2.7 + - - +
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Residues in contact with GLY 568 (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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562C MSE 5.9 1.1 - - - -
441D ARG* 3.2 26.9 - - - +
538D LEU* 3.4 13.4 - - - +
564D GLY 3.3 3.6 + - - -
565D ALA 3.0 8.8 + - - -
567D SER* 1.3 77.0 - - - +
569D VAL* 1.3 64.9 + - - +
571D GLU* 3.2 7.2 + - - +
572D VAL* 3.0 26.9 + - - +
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Residues in contact with VAL 569 (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* 4.2 11.4 - - + -
511D PHE* 3.8 27.4 - - + -
538D LEU* 4.0 6.1 - - + -
543D ILE* 4.0 33.9 - - + -
553D LEU* 4.7 4.7 - - + -
555D THR* 4.0 18.6 - - + -
565D ALA 3.3 12.9 + - - +
566D GLY 3.0 9.5 + - - +
568D GLY* 1.3 74.7 - - - +
570D ASN* 1.3 65.1 + - - +
572D VAL* 3.2 4.2 + - - +
573D LEU* 3.2 30.5 + - + +
582D VAL* 4.9 4.9 - - + -
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Residues in contact with ASN 570 (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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570C ASN* 4.0 18.4 - - + -
571C GLU* 4.2 12.1 - - - +
574C MSE 3.6 22.7 - - + +
566D GLY 3.0 13.2 + - - +
567D SER* 3.2 13.4 + - - +
569D VAL* 1.3 75.6 - - - +
571D GLU* 1.3 58.2 + - - +
573D LEU* 3.3 3.8 + - - +
574D MSE 2.9 35.0 + - - +
582D VAL* 2.9 29.7 - - - +
584D ASN* 2.9 31.9 - - - +
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Residues in contact with GLU 571 (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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561C ILE* 4.3 8.4 - - + +
562C MSE 3.5 22.3 - - - +
563C GLY 2.9 11.4 + - - -
567C SER* 2.8 24.0 + - - +
570C ASN* 4.0 21.1 - - - +
584C ASN* 4.6 7.7 + - - +
441D ARG* 2.5 35.4 + - - -
567D SER 3.1 10.7 + - - +
568D GLY* 3.3 7.4 - - - +
569D VAL 3.2 0.2 - - - -
570D ASN* 1.3 76.1 - - - +
572D VAL* 1.3 58.1 + - + +
574D MSE 3.3 2.3 + - - +
575D ALA* 2.8 33.6 + - - +
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Residues in contact with VAL 572 (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* 3.8 19.1 - - + -
540D GLU* 3.8 54.3 - - + +
543D ILE* 4.0 20.2 - - + -
544D LEU* 4.7 4.2 - - + +
568D GLY 3.0 16.3 + - - +
569D VAL 3.2 5.6 + - - +
571D GLU* 1.3 76.1 - - + +
573D LEU* 1.3 62.0 + - - +
575D ALA* 3.4 4.1 + - - +
576D HIS* 2.7 39.4 + - + +
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Residues in contact with LEU 573 (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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574C MSE 4.5 6.5 - - + -
543D ILE* 3.9 16.6 - - + -
544D LEU* 4.0 15.5 - - + -
547D ALA* 3.6 24.2 - - + -
553D LEU* 3.8 24.9 - - + -
569D VAL* 3.2 14.1 + - + +
570D ASN 3.7 6.3 - - - +
572D VAL* 1.3 75.6 - - - +
574D MSE 1.3 64.4 + - - +
576D HIS 3.4 1.2 + - - -
577D ARG 3.1 2.9 + - - -
578D LYS* 2.8 49.8 + - + +
579D PRO* 5.2 0.2 - - + -
580D VAL* 3.9 22.2 - - + +
582D VAL* 4.4 11.2 - - + -
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Residues in contact with MSE 574 (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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570C ASN* 3.7 42.2 - - + +
573C LEU* 4.4 7.4 - - + -
574C MSE 4.2 24.2 - - + -
579C PRO* 5.3 1.1 - - + -
580C VAL 3.4 23.1 - - - +
581C PRO* 4.3 4.5 - - - -
582C VAL* 3.2 47.5 - - + +
584C ASN* 4.3 3.6 - - - +
618C TRP* 3.0 14.7 + - - -
570D ASN 2.9 21.2 + - - +
571D GLU 3.8 3.6 - - - +
573D LEU* 1.3 74.1 - - - +
575D ALA* 1.3 67.0 + - - +
577D ARG* 2.9 13.4 + - - +
579D PRO* 4.6 9.9 - - - -
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Residues in contact with ALA 575 (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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583C LEU* 5.7 4.7 - - - +
584C ASN* 5.7 1.7 - - - +
618C TRP* 3.4 21.3 - - - +
621C LEU* 3.8 6.6 - - - +
540D GLU* 6.0 0.7 - - - +
571D GLU 2.8 18.8 + - - +
572D VAL* 3.6 8.3 - - - +
573D LEU 3.3 0.2 - - - -
574D MSE 1.3 79.3 - - - +
576D HIS* 1.3 64.1 + - + +
577D ARG 3.2 0.2 - - - -
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Residues in contact with HIS 576 (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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621C LEU* 4.3 17.0 - - + +
540D GLU* 3.9 24.8 + - - +
544D LEU* 3.6 37.8 - - + +
572D VAL* 2.7 37.9 + - + +
573D LEU 3.4 1.3 + - - +
574D MSE 3.1 0.4 - - - -
575D ALA* 1.3 83.3 - - + +
577D ARG* 1.3 70.8 + - - +
578D LYS* 3.2 19.9 + - + +
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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