Contacts of the helix formed by residues 564 - 579 (chain A) in PDB entry 1OAI
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 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A THR 4.4 0.2 + - - -
563A LEU* 1.4 74.7 - - - +
565A PRO* 1.3 77.4 - - - +
566A GLU* 3.5 7.4 + - - +
567A GLN* 3.0 39.9 + - - +
568A GLN* 2.8 21.4 + - - +
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Residues in contact with PRO 565 (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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563A LEU 4.5 1.1 - - - +
564A SER* 1.3 88.2 - - - +
566A GLU* 1.3 61.6 + - - +
568A GLN* 3.3 7.5 + - + +
569A GLU* 3.1 27.5 + - - +
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Residues in contact with GLU 566 (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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564A SER* 3.2 6.3 + - - +
565A PRO* 1.3 79.5 - - - +
567A GLN* 1.3 63.9 + - + +
569A GLU* 3.3 8.0 + - - +
570A MET* 3.0 38.8 + - + +
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Residues in contact with GLN 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A THR 4.5 1.7 - - - +
563A LEU* 3.6 17.2 - - + +
564A SER* 3.0 35.6 + - - +
566A GLU* 1.3 74.1 - - + +
568A GLN* 1.3 61.6 + - - +
570A MET* 3.2 6.1 + - - +
571A LEU* 2.8 29.8 + - - +
594A TRP* 3.4 65.4 - - + +
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Residues in contact with GLN 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LEU* 4.0 22.6 + - + +
564A SER 2.8 16.7 + - - +
565A PRO* 3.6 9.0 - - + +
567A GLN* 1.3 76.8 - - - +
569A GLU* 1.3 65.2 + - + +
571A LEU* 3.3 17.9 + - - +
572A GLN* 3.1 56.0 + - - +
582A LEU* 5.6 3.2 - - - +
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Residues in contact with GLU 569 (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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565A PRO 3.1 15.3 + - - +
566A GLU* 3.7 8.5 - - + +
567A GLN 3.3 0.2 - - - -
568A GLN* 1.3 76.2 - - - +
570A MET* 1.3 66.4 + - - +
572A GLN* 3.4 19.7 + - - +
573A ALA* 3.1 23.6 + - - +
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Residues in contact with MET 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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566A GLU* 3.0 35.0 + - + +
567A GLN* 3.2 10.7 + - - +
569A GLU* 1.3 77.5 - - - +
571A LEU* 1.3 57.9 + - - +
573A ALA* 3.3 6.4 + - - +
574A PHE* 2.9 31.0 + - - +
589A LEU* 3.8 19.3 - - + -
594A TRP* 3.4 50.3 - - + +
596A TYR* 3.8 22.9 - - + -
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Residues in contact with LEU 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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563A LEU* 3.6 25.6 - - + -
567A GLN 2.8 17.4 + - - +
568A GLN* 3.5 17.7 - - - +
569A GLU 3.3 0.2 - - - -
570A MET* 1.3 75.9 - - - +
572A GLN* 1.3 58.3 + - - +
574A PHE 3.2 0.7 + - - -
575A SER* 2.9 29.3 + - - -
582A LEU* 3.4 35.2 - - + +
585A SER* 3.7 9.0 - - - +
586A GLN* 3.4 43.3 - - + +
589A LEU* 3.8 9.2 - - + +
594A TRP* 4.6 0.7 - - + -
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Residues in contact with GLN 572 (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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568A GLN* 3.1 45.4 + - - +
569A GLU* 4.0 18.5 + - - +
571A LEU* 1.3 76.7 - - - +
573A ALA* 1.3 63.9 + - - +
575A SER* 3.9 1.2 - - - -
576A THR* 3.1 28.1 + - - -
582A LEU* 4.5 15.3 - - + -
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Residues in contact with ALA 573 (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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569A GLU 3.1 17.9 + - - +
570A MET* 3.6 6.1 - - - +
572A GLN* 1.3 79.2 - - - +
574A PHE* 1.3 56.7 + - - +
576A THR* 3.4 4.9 + - - -
577A GLN* 3.0 28.2 + - + +
596A TYR* 3.2 21.3 + - + +
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Residues in contact with PHE 574 (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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570A MET 2.9 18.1 + - - +
571A LEU 3.9 1.1 - - - +
573A ALA* 1.3 74.0 - - - +
575A SER* 1.3 61.8 + - - +
577A GLN* 4.4 2.2 - - + +
578A SER* 2.8 46.0 + - - -
580A MET* 3.8 16.8 - - + -
585A SER* 4.1 18.2 - - - -
588A CYS* 3.8 24.2 - - + -
589A LEU* 3.8 20.2 - - + -
596A TYR* 3.3 30.3 + + + -
599A SER* 3.6 24.7 - - - -
600A ALA* 3.6 27.8 - - + -
603A PHE* 4.0 11.0 - + + -
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Residues in contact with SER 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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571A LEU 2.9 17.0 + - - -
572A GLN 3.9 3.1 - - - -
574A PHE* 1.3 77.0 - - - +
576A THR* 1.3 62.7 + - - +
578A SER* 3.9 0.2 - - - -
579A GLY* 3.0 21.8 + - - -
580A MET 2.7 21.8 + - - +
581A ASN* 3.9 4.3 - - - -
582A LEU* 3.8 24.7 + - - +
585A SER* 3.1 21.0 + - - -
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Residues in contact with THR 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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572A GLN 3.1 18.4 + - - -
573A ALA* 3.7 5.6 - - - -
575A SER* 1.3 80.0 + - - +
577A GLN* 1.3 66.2 + - + +
579A GLY* 3.6 6.4 + - - -
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Residues in contact with GLN 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 ALA* 3.0 20.9 + - + +
574A PHE* 4.0 3.1 - - + +
575A SER 3.3 0.2 - - - -
576A THR* 1.3 81.9 - - + +
578A SER* 1.3 60.7 + - - +
596A TYR* 2.7 35.0 + - + +
600A ALA* 6.0 0.2 - - - +
603A PHE* 5.5 0.2 - - - -
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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
----------------------------------------------------------
574A PHE* 2.8 38.9 + - - -
575A SER 3.6 0.7 + - - -
577A GLN* 1.3 76.7 - - - +
579A GLY* 1.3 58.3 + - - +
580A MET* 3.1 24.7 + - - +
585A SER* 3.7 4.0 + - - -
603A PHE* 3.4 46.2 - - - -
607A LYS* 5.6 0.9 + - - -
617A PHE* 3.7 6.2 - - - -
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Residues in contact with GLY 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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575A SER 3.0 10.8 + - - -
576A THR 3.6 4.9 + - - -
577A GLN 3.4 2.6 - - - -
578A SER* 1.3 77.3 - - - +
580A MET* 1.3 62.1 + - - +
617A PHE* 3.6 27.2 - - - +
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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