Contacts of the helix formed by residues 564 - 576 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU 3.9 6.5 - - - -
438A SER* 3.1 14.1 + - - -
441A ARG* 2.8 23.3 + - - -
557A GLU* 3.7 5.4 - - - -
559A ASN* 3.9 1.3 - - - -
560A ALA 3.6 13.2 + - - -
561A ILE 3.5 4.6 + - - -
562A MSE 3.2 3.0 - - - -
563A GLY* 1.3 76.6 - - - +
565A ALA* 1.3 65.6 + - - -
566A GLY 3.4 2.2 - - - -
567A SER* 3.2 2.2 - - - -
568A GLY 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 4.4 4.5 + - + +
441A ARG* 4.5 1.1 - - - +
511A PHE* 3.6 37.6 - - + -
535A VAL* 3.8 30.1 - - + -
538A LEU* 4.6 2.7 - - - +
557A GLU* 2.9 17.4 + - + +
564A GLY* 1.3 69.1 - - - -
566A GLY* 1.3 66.8 + - - +
568A GLY* 2.9 12.5 + - - +
569A VAL* 3.0 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A PHE* 4.5 1.4 - - - -
555A THR* 3.3 35.4 - - - -
557A GLU* 3.0 14.1 + - - -
565A ALA* 1.3 75.8 - - - +
567A SER* 1.3 63.2 + - - +
569A VAL* 2.9 5.1 + - - +
570A ASN* 2.9 25.6 + - - +
584A ASN* 3.3 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.7 2.3 + - - -
561A ILE 3.9 6.2 + - - -
563A GLY 3.7 3.8 + - - -
564A GLY 3.2 22.6 + - - -
566A GLY* 1.3 75.7 - - - +
568A GLY* 1.3 57.3 + - - +
570A ASN* 3.3 15.0 + - - +
571A GLU* 3.0 31.5 + - - +
584A ASN* 4.0 2.4 + - - +
567B SER* 2.8 23.2 + - - -
571B GLU* 2.6 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.5 26.2 - - - +
538A LEU* 3.4 14.2 - - - +
564A GLY 3.1 6.9 + - - -
565A ALA 2.9 9.7 + - - -
567A SER* 1.3 74.5 - - - +
569A VAL* 1.3 63.2 + - - +
571A GLU* 3.2 7.7 + - - +
572A VAL* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LEU* 4.3 11.4 - - + -
511A PHE* 3.8 23.3 - - + -
538A LEU* 4.1 6.1 - - + -
543A ILE* 3.9 35.2 - - + -
553A LEU* 4.5 4.3 - - + -
555A THR* 3.9 23.3 - - + -
565A ALA 3.0 15.1 + - - +
566A GLY 2.9 8.4 + - - +
568A GLY* 1.3 73.6 - - - +
570A ASN* 1.3 65.5 + - - +
572A VAL* 3.1 12.5 + - - +
573A LEU* 3.2 23.5 + - + +
582A VAL* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLY 2.9 17.5 + - - +
567A SER* 3.4 13.8 - - - +
568A GLY 3.3 0.2 - - - -
569A VAL* 1.3 76.8 - - - +
571A GLU* 1.3 61.0 + - - +
573A LEU* 3.3 9.0 + - - +
574A MSE 3.0 30.3 + - + +
582A VAL* 3.5 21.2 - - - +
584A ASN* 2.8 36.6 + - - +
570B ASN* 4.2 15.9 - - + -
571B GLU* 4.1 13.3 - - - +
574B MSE 3.9 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG* 3.0 36.2 + - - -
567A SER 3.0 17.5 + - - +
568A GLY* 3.4 7.3 - - - +
569A VAL 3.2 0.2 - - - -
570A ASN* 1.3 77.2 - - - +
572A VAL* 1.3 62.4 + - + +
574A MSE 3.5 2.0 + - - +
575A ALA* 3.0 25.1 + - - +
561B ILE* 4.3 8.5 - - + +
562B MSE 3.6 19.3 - - - +
563B GLY 3.0 10.0 + - - -
567B SER* 2.5 30.3 + - - +
570B ASN* 3.8 18.2 - - - +
584B ASN* 4.3 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LEU* 3.8 18.8 - - + -
540A GLU* 3.4 45.8 - - + +
543A ILE* 4.2 11.4 - - + -
544A LEU* 4.2 9.2 - - + -
568A GLY 3.1 15.0 + - - +
569A VAL 3.1 6.8 + - - +
571A GLU* 1.3 74.4 - - + +
573A LEU* 1.3 65.7 + - - +
575A ALA* 3.3 5.8 + - - +
576A HIS* 3.0 43.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ILE* 4.0 9.2 - - + -
544A LEU* 3.9 21.3 - - + -
547A ALA* 3.7 23.1 - - + -
553A LEU* 4.0 15.3 - - + -
569A VAL* 3.2 15.7 + - + +
570A ASN* 3.3 6.7 + - - +
572A VAL* 1.3 76.1 - - - +
574A MSE 1.3 69.7 + - + +
576A HIS 3.3 2.4 + - - -
577A ARG 3.0 3.8 + - - -
578A LYS* 2.9 49.1 + - + +
580A VAL* 4.1 9.2 - - + +
582A VAL* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ASN* 3.0 20.6 + - + +
571A GLU 3.8 5.2 - - - +
573A LEU* 1.3 85.7 - - + +
575A ALA* 1.3 63.2 + - - +
577A ARG* 3.1 10.8 + - - +
579A PRO* 3.5 33.2 - - + -
580A VAL 4.6 0.2 - - - +
570B ASN* 3.7 30.5 - - + +
573B LEU* 5.8 1.3 - - - -
574B MSE 4.5 21.1 - - - +
579B PRO* 5.2 1.1 - - + -
580B VAL 3.7 12.1 - - - +
581B PRO* 4.1 1.3 - - - -
582B VAL* 3.2 46.0 - - - +
584B ASN* 4.5 3.1 - - - +
618B TRP* 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLU 3.0 19.2 + - - +
572A VAL* 3.6 7.0 - - - +
573A LEU 3.2 0.2 - - - -
574A MSE 1.3 77.9 - - - +
576A HIS* 1.3 64.2 + - + +
577A ARG 3.1 0.2 - - - -
582B VAL 5.0 0.7 - - - -
583B LEU* 5.7 5.2 - - - -
584B ASN 6.2 0.9 - - - +
618B TRP* 3.2 23.6 + - - +
621B LEU* 3.5 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A GLU* 3.1 25.2 + - - -
544A LEU* 3.5 32.6 - - + +
572A VAL* 3.0 33.3 + - + +
573A LEU 3.3 1.5 + - - +
575A ALA* 1.3 79.7 + - + +
577A ARG* 1.3 70.5 + - - +
578A LYS* 3.0 37.3 + - + +
621B LEU* 4.0 14.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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