Contacts of the helix formed by residues 575 - 593 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568B TYR* 3.9 8.7 - - - -
573B VAL 4.7 1.8 - - - -
574B ASN* 1.3 75.5 - - - +
576B LEU* 1.3 64.5 + - - +
577B GLU* 3.5 10.1 + - - +
578B ASP* 2.7 45.0 + - - +
579B ALA* 3.1 12.3 + - - +
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Residues in contact with LEU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B TYR* 3.6 25.0 + - + +
575B SER* 1.3 73.6 - - - +
577B GLU* 1.3 56.9 + - - +
579B ALA* 3.3 0.9 + - - +
580B LEU* 2.9 32.9 + - + +
615B PHE 4.4 1.8 - - - +
616B ILE* 3.7 45.3 - - + -
617B PRO* 4.4 4.0 - - + -
620B LEU* 4.0 5.2 - - + -
758B ILE* 3.6 27.1 - - + +
761B VAL* 3.6 31.0 - - + -
762B ALA* 3.7 24.1 - - + +
765B VAL* 5.5 0.9 - - + -
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Residues in contact with GLU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B SER* 3.2 9.2 + - - +
576B LEU* 1.3 79.8 - - - +
578B ASP* 1.3 58.2 + - + +
580B LEU* 3.3 7.4 - - - +
581B THR* 3.0 31.3 + - - +
744B TYR* 4.6 5.9 + - + -
758B ILE* 3.8 41.9 - - + +
759B ALA 5.8 0.2 + - - -
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Residues in contact with ASP 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B VAL* 4.0 7.3 - - - +
574B ASN* 3.4 16.0 - - - +
575B SER* 2.7 45.6 + - - +
577B GLU* 1.3 75.7 - - + +
579B ALA* 1.3 64.0 + - - +
580B LEU 3.1 0.9 - - - -
581B THR* 3.6 10.7 - - - +
582B ASN* 2.9 42.4 + - - +
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Residues in contact with ALA 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B LEU 5.6 0.4 - - - +
568B TYR* 3.6 40.8 - - + -
574B ASN* 5.8 1.3 - - + -
575B SER 3.1 17.3 + - - +
576B LEU 3.6 4.7 - - - +
578B ASP* 1.3 79.1 + - - +
580B LEU* 1.3 57.5 + - - +
582B ASN* 3.4 8.6 + - - +
583B LEU* 2.8 29.5 + - - +
616B ILE* 3.8 11.5 - - + +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B LEU* 2.9 25.3 + - + +
577B GLU* 3.3 11.2 - - + +
578B ASP 3.1 0.2 - - - -
579B ALA* 1.3 74.5 - - - +
581B THR* 1.3 58.4 + - - +
583B LEU* 3.2 14.8 + - + +
584B VAL* 2.9 33.8 + - - +
616B ILE* 3.7 23.1 - - + +
620B LEU* 3.6 34.3 - - + +
624B ALA* 3.9 25.1 - - + -
744B TYR* 3.4 24.0 + - + +
758B ILE* 4.2 16.2 - - + -
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Residues in contact with THR 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B GLU* 3.0 20.2 + - - +
578B ASP* 3.6 14.6 - - - +
580B LEU* 1.3 74.3 - - - +
582B ASN* 1.3 60.4 + - - +
584B VAL* 3.9 4.1 - - + +
585B LYS* 3.1 59.2 + - + +
744B TYR* 3.4 14.2 + - - +
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Residues in contact with ASN 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B ASN* 5.6 4.2 + - - -
578B ASP* 2.9 30.4 + - - +
579B ALA* 3.7 7.4 - - - +
581B THR* 1.3 77.3 - - - +
583B LEU* 1.3 57.6 + - - +
585B LYS* 3.4 11.4 + - - +
586B THR* 2.8 40.2 + - - +
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Residues in contact with LEU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B VAL* 3.7 25.1 - - + -
565B SER 4.4 11.2 - - - +
566B THR* 4.8 3.1 - - + -
579B ALA 2.8 18.7 + - - +
580B LEU* 3.3 15.3 - - + +
582B ASN* 1.3 75.5 - - - +
584B VAL* 1.3 57.7 + - - +
586B THR* 3.2 6.0 + - - -
587B ALA* 2.8 27.5 + - + +
600B LEU* 4.4 7.9 - - + -
616B ILE* 3.8 23.8 - - + -
621B ALA* 3.8 28.9 - - + +
624B ALA* 5.1 1.3 - - + -
625B VAL* 3.8 26.0 - - + -
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Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B LEU 2.9 17.1 + - - +
581B THR* 3.9 5.2 - - + +
583B LEU* 1.3 77.9 - - + +
585B LYS* 1.3 67.1 + - + +
587B ALA* 3.4 6.6 + - - +
588B ILE* 3.1 33.4 + - + +
624B ALA* 3.7 23.3 - - + +
625B VAL* 4.3 7.0 - - + +
628B HIS* 3.6 54.1 - - + +
744B TYR* 4.2 7.6 - - - +
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Residues in contact with LYS 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B THR* 3.1 42.8 + - + +
582B ASN* 3.9 11.7 - - - +
584B VAL* 1.3 81.0 - - + +
586B THR* 1.3 61.8 + - - +
588B ILE* 3.5 8.8 + - + +
589B ALA* 3.0 25.5 + - - +
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Residues in contact with THR 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B VAL* 4.0 21.1 - - + -
582B ASN* 2.8 25.4 + - - +
583B LEU* 3.5 6.7 - - - -
585B LYS* 1.3 75.3 - - - +
587B ALA* 1.3 60.2 + - - +
589B ALA* 3.3 5.3 + - - +
590B THR* 2.9 42.7 + - - +
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Residues in contact with ALA 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B VAL* 5.0 4.7 - - + -
583B LEU* 2.8 20.1 + - + +
584B VAL 3.8 4.5 - - - +
586B THR* 1.3 76.8 - - - +
588B ILE* 1.3 57.9 + - + +
590B THR* 3.4 4.6 + - - -
591B VAL* 3.0 35.3 + - - +
598B LEU* 3.7 24.9 - - + +
600B LEU* 5.3 0.2 - - + -
625B VAL* 4.1 24.7 - - + -
629B LEU* 4.6 5.4 - - + -
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B VAL* 3.1 36.5 + - + +
585B LYS* 3.8 7.9 - - + +
587B ALA* 1.3 77.0 - - + +
589B ALA* 1.3 62.2 + - - +
591B VAL* 3.4 2.9 + - - +
592B GLN* 3.0 42.5 + - - +
628B HIS* 4.0 20.4 - - + +
629B LEU* 3.9 24.0 - - + -
632B ALA* 4.2 16.4 - - + -
634B LEU* 3.8 12.4 - - + +
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Residues in contact with ALA 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B LYS 3.0 17.0 + - - +
586B THR* 3.9 5.2 - - - +
588B ILE* 1.3 75.9 - - - +
590B THR* 1.3 58.3 + - - +
592B GLN* 3.2 16.9 + - - +
593B ALA* 2.9 29.7 + - - +
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Residues in contact with THR 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B ALA* 3.3 33.9 - - + -
564B VAL* 4.6 6.2 - - + +
586B THR* 2.9 30.8 + - - +
587B ALA* 3.6 6.7 - - - -
589B ALA* 1.3 77.0 - - - +
591B VAL* 1.3 60.8 + - - +
593B ALA* 3.2 17.0 + - - +
594B GLY 3.4 0.7 + - - -
595B ALA* 3.2 25.0 + - + +
598B LEU* 3.8 8.7 - - + -
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Residues in contact with VAL 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B ALA 3.0 21.1 + - - +
588B ILE 3.8 4.0 - - - +
589B ALA 3.3 0.2 - - - -
590B THR* 1.3 75.3 - - - +
592B GLN* 1.3 62.3 + - - +
594B GLY* 3.1 14.9 + - - -
595B ALA* 3.8 12.3 + - - +
598B LEU* 4.0 25.4 - - + -
629B LEU* 4.0 14.6 - - + -
634B LEU* 4.0 24.6 - - + +
637B LYS* 3.7 31.8 - - + +
638B ALA* 4.2 12.8 - - + -
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Residues in contact with GLN 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B ILE* 3.0 29.5 + - - +
589B ALA* 3.2 21.7 + - - +
591B VAL* 1.3 76.2 - - - +
593B ALA* 1.3 58.5 + - - +
594B GLY* 3.1 4.4 + - - -
634B LEU* 3.8 22.8 - - + +
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Residues in contact with ALA 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B GLN* 4.1 9.2 + - - +
589B ALA 2.9 16.0 + - - +
590B THR* 3.2 9.1 + - - +
592B GLN* 1.3 75.5 - - - +
594B GLY* 1.3 56.6 + - - +
595B ALA 3.8 1.1 - - - -
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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