Contacts of the helix formed by residues 575 - 593 (chain A) in PDB entry 1OFD
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 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A TYR* 4.0 8.4 - - - -
573A VAL 4.8 1.8 - - - -
574A ASN* 1.3 74.8 - - - +
576A LEU* 1.3 64.6 + - - +
577A GLU* 3.3 11.0 + - - +
578A ASP* 3.0 38.4 + - - +
579A ALA* 3.0 12.3 + - - +
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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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568A TYR* 3.5 25.4 + - + +
575A SER* 1.3 72.6 - - - +
577A GLU* 1.3 56.4 + - - +
579A ALA* 3.3 2.1 + - - +
580A LEU* 2.8 42.8 + - + +
615A PHE 4.4 1.3 - - - +
616A ILE* 3.7 41.3 - - + -
617A PRO* 4.3 4.5 - - + -
620A LEU* 3.9 9.4 - - + -
758A ILE* 3.6 19.5 - - + +
759A ALA* 6.0 0.2 - - - -
761A VAL* 3.4 33.7 - - + -
762A ALA* 3.8 23.6 - - + +
765A VAL* 5.7 0.4 - - + -
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Residues in contact with GLU 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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575A SER* 3.1 10.0 + - - +
576A LEU* 1.3 79.8 - - - +
578A ASP* 1.3 58.4 + - - +
580A LEU* 3.4 6.5 + - + +
581A THR* 3.0 31.2 + - - +
744A TYR* 4.7 4.9 + - + -
758A ILE* 3.8 39.5 - - + +
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Residues in contact with ASP 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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573A VAL* 3.8 11.3 - - - +
574A ASN* 3.5 14.7 - - - +
575A SER* 3.0 39.7 + - - +
577A GLU* 1.3 76.8 - - - +
579A ALA* 1.3 64.5 + - - +
581A THR* 3.4 10.9 - - + -
582A ASN* 2.9 37.1 + - - +
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Residues in contact with ALA 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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567A LEU 5.6 0.2 - - - +
568A TYR* 3.4 42.0 - - + -
574A ASN* 5.7 1.1 - - + -
575A SER 3.0 19.4 + - - +
576A LEU* 3.6 4.3 - - - +
578A ASP* 1.3 79.4 + - - +
580A LEU* 1.3 55.6 + - - +
582A ASN* 3.5 6.5 + - - +
583A LEU* 2.9 28.4 + - - +
616A ILE* 3.7 11.3 - - + +
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Residues in contact with LEU 580 (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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576A LEU* 2.8 33.6 + - + +
577A GLU* 3.4 7.0 - - + +
579A ALA* 1.3 73.7 - - - +
581A THR* 1.3 63.7 + - - +
583A LEU* 3.3 13.0 + - + +
584A VAL* 3.0 23.7 + - - +
616A ILE* 3.8 23.2 - - + +
620A LEU* 3.5 35.0 - - + +
624A ALA* 3.8 25.6 - - + -
744A TYR* 3.4 27.6 + - + +
758A ILE* 4.3 14.6 - - + -
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Residues in contact with THR 581 (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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577A GLU* 3.0 19.4 + - - +
578A ASP* 3.4 14.8 - - + -
580A LEU* 1.3 76.6 - - - +
582A ASN* 1.3 65.3 + - - +
584A VAL* 3.5 3.1 + - - +
585A LYS* 3.1 62.0 + - + +
744A TYR* 3.5 14.4 + - - -
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Residues in contact with ASN 582 (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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578A ASP* 2.9 25.3 + - - +
579A ALA* 3.6 7.2 - - - +
581A THR* 1.3 76.8 - - - +
583A LEU* 1.3 57.5 + - - +
585A LYS* 3.9 8.4 - - - +
586A THR* 2.7 44.4 + - - +
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Residues in contact with LEU 583 (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 VAL* 3.4 28.5 - - + -
565A SER 4.1 11.9 - - - +
566A THR* 4.7 3.6 - - + -
579A ALA 2.9 18.5 + - - +
580A LEU* 3.4 13.5 - - + +
582A ASN* 1.3 75.0 - - - +
584A VAL* 1.3 57.9 + - + +
586A THR* 3.2 5.5 + - - -
587A ALA* 2.9 28.0 + - + +
600A LEU* 4.4 6.5 - - + -
616A ILE* 4.0 17.7 - - + -
621A ALA* 3.8 29.6 - - + +
624A ALA* 5.1 1.6 - - + -
625A VAL* 3.7 29.8 - - + -
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Residues in contact with VAL 584 (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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580A LEU 3.0 15.7 + - - +
581A THR* 3.9 4.3 - - - +
583A LEU* 1.3 81.6 - - + +
585A LYS* 1.3 62.2 + - + +
587A ALA* 3.3 6.8 + - - +
588A ILE* 3.0 40.4 + - + +
624A ALA* 3.8 22.0 - - + +
625A VAL* 4.3 6.1 - - + +
628A HIS* 3.5 57.7 - - + +
744A TYR* 4.2 6.1 - - - +
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Residues in contact with LYS 585 (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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581A THR* 3.1 45.5 + - + +
582A ASN* 3.9 8.3 - - - +
584A VAL* 1.3 81.8 - - + +
586A THR* 1.3 58.9 + - - +
588A ILE* 3.7 8.4 - - + +
589A ALA* 3.0 30.4 + - - +
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Residues in contact with THR 586 (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 VAL* 4.2 19.5 - - + -
582A ASN* 2.7 31.2 + - - +
583A LEU* 3.5 6.1 - - - -
585A LYS* 1.3 75.8 - - - +
587A ALA* 1.3 55.3 + - - +
589A ALA* 3.3 5.3 + - - +
590A THR* 2.8 49.4 + - - +
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Residues in contact with ALA 587 (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 VAL* 4.9 5.3 - - + +
583A LEU* 2.9 19.7 + - + +
584A VAL* 3.6 4.9 - - - +
586A THR* 1.3 76.6 - - - +
588A ILE* 1.3 56.9 + - - +
590A THR* 3.3 4.0 + - - -
591A VAL* 2.8 36.5 + - - +
598A LEU* 3.7 24.6 - - + +
600A LEU* 5.5 0.2 - - + -
625A VAL* 4.0 25.8 - - + -
629A LEU* 4.3 4.7 - - + -
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Residues in contact with ILE 588 (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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584A VAL* 3.0 37.7 + - + +
585A LYS* 3.7 9.0 - - + +
587A ALA* 1.3 75.1 - - - +
589A ALA* 1.3 52.8 + - - +
591A VAL* 3.2 3.6 + - - +
592A GLN* 2.8 54.7 + - - +
628A HIS* 4.2 8.7 - - + +
629A LEU* 3.9 21.1 - - + -
632A ALA* 4.1 22.0 - - + -
634A LEU* 3.8 16.9 - - + +
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Residues in contact with ALA 589 (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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585A LYS 3.0 18.1 + - - +
586A THR* 3.7 6.3 - - - +
588A ILE* 1.3 76.5 - - - +
590A THR* 1.3 57.4 + - - +
592A GLN* 3.1 16.2 + - - +
593A ALA* 2.9 30.0 + - - +
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Residues in contact with THR 590 (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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562A ALA* 3.4 33.0 - - + -
563A GLU 5.8 0.2 - - - +
564A VAL* 4.5 7.3 - - + +
586A THR* 2.8 38.1 + - - +
587A ALA* 3.5 6.5 - - - -
589A ALA* 1.3 73.6 - - - +
591A VAL* 1.3 60.8 + - - +
593A ALA* 3.3 14.4 + - + +
594A GLY 3.4 0.5 + - - -
595A ALA* 3.3 25.4 + - + +
598A LEU* 3.7 10.3 - - + -
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Residues in contact with VAL 591 (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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587A ALA 2.8 22.0 + - - +
588A ILE 3.6 4.0 - - - +
590A THR* 1.3 74.6 - - - +
592A GLN* 1.3 62.8 + - - +
594A GLY* 3.1 14.9 + - - -
595A ALA 4.0 10.8 + - - +
598A LEU* 3.7 27.1 - - + -
629A LEU* 4.4 11.9 - - + -
634A LEU* 4.0 24.2 - - + +
637A LYS* 3.7 32.5 - - + +
638A ALA* 4.0 14.1 - - + -
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Residues in contact with GLN 592 (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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588A ILE* 2.8 38.6 + - - +
589A ALA* 3.1 17.0 + - - +
591A VAL* 1.3 71.9 - - - +
593A ALA* 1.3 59.4 + - - +
594A GLY* 3.3 1.5 + - - -
634A LEU* 3.8 23.7 - - + +
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Residues in contact with ALA 593 (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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560A GLN* 4.2 8.2 + - - +
589A ALA 2.9 14.3 + - - +
590A THR* 3.7 9.4 - - - +
591A VAL 3.2 0.6 - - - -
592A GLN* 1.3 75.8 - - - +
594A GLY* 1.3 56.2 + - - +
595A ALA 3.7 1.6 - - - -
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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