Contacts of the helix formed by residues 567 - 579 (chain A) in PDB entry 2O1X
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 567 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A LEU* 4.2 7.2 - - - -
441A SER* 3.6 9.6 - - - -
444A ARG* 2.9 13.1 + - - -
560A GLU* 3.4 13.5 - - - -
562A ASN* 4.0 3.8 - - - -
563A THR 4.4 0.4 + - - -
564A VAL 4.3 3.0 + - - -
565A VAL 3.3 3.0 - - - -
566A GLY* 1.3 76.6 - - - +
568A PHE* 1.3 57.1 + - - -
569A GLY 3.3 2.2 - - - -
570A GLY 3.7 4.4 - - - +
571A ALA* 2.7 31.9 + - - +
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Residues in contact with PHE 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A LEU* 4.7 6.3 - - + +
499A TRP* 3.9 7.2 - + - -
511A LEU* 3.5 31.0 - - + -
512A ALA* 4.6 1.1 - - - -
535A ALA* 3.4 33.0 - - + -
537A PHE 4.5 3.1 - - - -
538A VAL* 3.8 30.5 - - + -
541A LEU* 3.9 23.6 - - + -
558A THR* 3.9 17.0 - - - -
559A VAL 3.9 15.7 - - - -
560A GLU* 2.9 23.2 + - + +
567A GLY* 1.3 71.0 - - - -
569A GLY* 1.3 52.6 + - - +
571A ALA* 3.0 7.8 + - - +
572A VAL* 2.7 49.5 + - + +
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Residues in contact with GLY 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A THR* 3.7 25.1 - - - -
560A GLU* 2.9 15.7 + - - -
568A PHE* 1.3 76.7 - - - +
570A GLY* 1.3 51.7 + - - +
572A VAL* 2.9 5.9 + - - +
573A LEU* 2.8 42.0 + - - +
587A VAL* 4.0 13.9 - - - -
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Residues in contact with GLY 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ARG* 3.8 8.3 - - - -
560A GLU* 4.8 0.4 + - - -
564A VAL 4.9 4.6 + - - -
567A GLY 3.2 12.4 + - - +
569A GLY* 1.3 75.1 - - - +
571A ALA* 1.3 57.1 + - - +
573A LEU* 3.4 4.0 + - - +
574A GLU* 3.0 34.4 + - - +
587A VAL* 5.1 0.6 - - - +
570B GLY* 5.6 0.3 - - - -
574B GLU* 3.8 33.4 - - - +
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Residues in contact with ALA 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ARG* 3.4 32.4 - - - +
538A VAL* 4.7 2.9 - - + +
541A LEU* 3.5 29.2 - - + +
567A GLY 2.7 16.8 + - - +
568A PHE* 3.3 11.2 - - - +
570A GLY* 1.3 71.1 - - - +
572A VAL* 1.3 65.9 + - - +
574A GLU* 3.3 4.9 + - - +
575A ALA* 3.1 17.7 + - - +
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Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 4.9 1.1 - - + -
511A LEU* 4.5 7.4 - - + -
541A LEU* 4.2 9.0 - - + -
546A LEU* 3.9 23.6 - - + -
556A LEU* 5.0 0.9 - - + -
558A THR* 3.8 29.4 - - + -
568A PHE* 2.7 43.8 + - + +
569A GLY 3.4 6.1 - - - +
571A ALA* 1.3 72.5 - - - +
573A LEU* 1.3 64.4 + - + +
575A ALA* 3.0 4.3 + - - +
576A LEU* 3.0 41.0 + - + +
585A VAL* 5.0 5.2 - - + -
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A GLY 2.8 21.9 + - - +
570A GLY* 3.8 5.2 - - - +
572A VAL* 1.3 74.0 - - + +
574A GLU* 1.3 55.5 + - - +
576A LEU* 4.0 7.0 - - + +
577A ASN* 3.0 28.6 + - - +
585A VAL* 4.0 26.7 - - + -
587A VAL* 4.0 14.4 - - + -
573B LEU* 3.9 16.8 - - + +
574B GLU* 3.8 27.6 - - + +
577B ASN* 3.7 45.5 - - + +
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Residues in contact with GLU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ARG* 2.6 35.9 + - - -
570A GLY* 3.0 20.9 + - - +
571A ALA* 3.7 4.9 - - - +
572A VAL 3.2 0.4 - - - -
573A LEU* 1.3 75.5 - - - +
575A ALA* 1.3 57.2 + - - +
577A ASN* 3.4 3.5 - - - +
578A SER* 3.1 30.0 + - - -
564B VAL* 4.1 10.2 - - + +
565B VAL* 3.6 10.7 - - - +
566B GLY* 3.3 21.3 + - - -
570B GLY* 3.8 15.6 - - - +
573B LEU* 3.7 22.0 - - + -
574B GLU* 4.8 0.9 - - - +
587B VAL* 6.4 1.6 - - + -
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Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A LEU* 4.0 9.4 - - + -
543A GLU* 4.0 16.4 - - - +
546A LEU* 3.5 23.6 - - + -
571A ALA 3.1 11.3 + - - +
572A VAL 3.0 10.0 + - - +
574A GLU* 1.3 71.9 - - - +
576A LEU* 1.3 60.4 + - - +
578A SER* 3.1 9.4 + - - -
579A MET* 2.9 38.0 + - + +
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Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A LEU* 4.1 20.0 - - + +
550A GLY* 4.6 4.7 - - - -
556A LEU* 4.8 3.4 - - + -
572A VAL* 3.0 36.3 + - + +
573A LEU* 4.0 9.0 - - + +
575A ALA* 1.3 74.9 - - - +
577A ASN* 1.3 67.8 + - - +
579A MET* 3.2 20.4 + - + +
580A ASN 3.0 4.0 + - - -
581A LEU* 2.9 52.5 + - + +
583A PRO* 4.3 15.0 - - + -
585A VAL* 3.8 26.5 - - + -
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Residues in contact with ASN 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A LEU 3.0 20.0 + - - +
574A GLU 3.4 6.3 - - - +
576A LEU* 1.3 76.9 - - - +
578A SER* 1.3 64.1 + - - +
580A ASN* 2.8 29.3 + - - +
581A LEU 4.4 2.2 + - - -
582A HIS* 5.3 10.7 + - - -
573B LEU* 3.7 23.0 - - + +
583B PRO 5.5 0.2 + - - -
585B VAL* 3.1 47.3 + - - +
587B VAL* 4.1 15.8 + - - +
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Residues in contact with SER 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A GLU* 5.6 1.4 + - - -
574A GLU 3.1 12.3 + - - -
575A ALA* 3.1 14.4 + - - -
577A ASN* 1.3 83.7 - - - +
579A MET* 1.3 60.1 + - - +
580A ASN* 3.3 3.6 + - - +
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Residues in contact with MET 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A GLU* 4.0 28.3 - - - +
546A LEU* 3.9 24.9 - - + -
547A ARG* 3.4 48.8 + - - +
575A ALA* 2.9 31.7 + - + +
576A LEU* 3.6 12.6 - - + +
577A ASN 3.1 0.2 - - - -
578A SER* 1.3 81.4 - - - +
580A ASN* 1.3 65.9 + - - +
581A LEU* 3.4 27.7 + - + +
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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