Contacts of the helix formed by residues 573 - 584 (chain B) in PDB entry 1O94
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 GLU 573 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B PRO* 3.6 27.4 - - + +
272B ARG* 2.9 36.1 + - - +
273B PHE* 3.6 15.4 - - + -
348B CYS* 4.2 8.1 - - - +
440B TRP* 4.7 12.3 + - - -
539B TYR* 4.2 8.1 + - - -
540B PHE* 5.7 0.2 - - - +
568B MET* 3.1 23.8 + - + +
571B THR* 2.7 34.9 + - - +
572B LEU* 1.3 78.4 - - - +
574B TYR* 1.3 65.3 + - - +
575B PRO* 3.6 1.1 - - - -
576B ASN 3.4 3.4 + - - -
577B MET* 2.9 22.4 + - - +
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Residues in contact with TYR 574 (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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591A ASP* 4.6 8.0 + - - -
608A TRP* 3.9 25.5 + + - -
563B HIS* 4.0 13.4 + - - -
564B LEU 3.5 21.4 + - - -
565B ALA* 3.4 24.2 - - + -
568B MET* 2.9 24.7 + - - +
569B HIS* 3.4 39.4 - + - +
573B GLU* 1.3 78.4 - - - +
575B PRO* 1.3 68.3 - - + +
577B MET* 3.6 2.8 - - - +
578B MET* 2.8 64.3 + - + +
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Residues in contact with PRO 575 (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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608A TRP* 3.6 32.9 - - + -
262B ALA 5.1 4.5 - - - +
263B GLU* 3.3 39.3 - - + +
266B GLU* 5.9 0.2 - - - +
569B HIS* 5.8 1.1 - - - +
572B LEU* 3.8 14.6 - - - +
573B GLU 3.6 2.7 - - - -
574B TYR* 1.3 96.7 - - + +
576B ASN* 1.3 61.6 + - - +
578B MET 3.4 0.3 + - - -
579B ARG* 3.1 32.9 + - - +
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Residues in contact with ASN 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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612A SER* 3.7 13.9 + - - +
624A ARG* 2.9 31.8 + - - -
265B GLY 5.5 0.8 + - - -
266B GLU* 2.9 22.8 + - - -
270B PRO* 5.8 0.8 - - - +
273B PHE* 3.5 33.1 - - + -
274B TYR* 3.5 22.8 + - - -
572B LEU 5.4 2.4 + - - +
573B GLU 3.4 2.6 + - - -
574B TYR 3.3 0.2 - - - -
575B PRO* 1.3 78.4 - - - +
577B MET* 1.3 60.8 + - - +
579B ARG* 3.1 11.8 + - - +
580B ARG* 2.9 29.8 + - - +
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Residues in contact with MET 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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272B ARG* 3.6 28.3 - - - +
273B PHE* 3.4 6.6 - - + -
543B PRO* 3.5 42.0 - - + +
547B GLU* 3.5 23.8 - - + +
568B MET* 3.7 26.7 - - + -
573B GLU 2.9 18.9 + - - +
574B TYR* 3.6 6.1 - - - +
576B ASN* 1.3 77.2 - - - +
578B MET* 1.3 71.1 + - + +
580B ARG* 3.2 11.0 + - + +
581B LEU* 3.0 35.1 + - + +
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Residues in contact with MET 578 (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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591A ASP* 5.7 1.6 - - - +
608A TRP* 3.6 30.9 - - + +
564B LEU* 4.6 9.0 - - + -
565B ALA* 4.1 17.3 - - + -
574B TYR* 2.8 69.9 + - + +
575B PRO 3.8 2.0 - - - +
577B MET* 1.3 80.5 - - + +
579B ARG* 1.3 56.3 + - - +
581B LEU* 3.5 21.7 + - + +
582B HIS* 3.0 29.8 + - - +
588B GLU* 4.0 26.2 - - - +
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Residues in contact with ARG 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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607A ILE 4.8 4.0 + - - -
608A TRP* 3.5 40.0 - - - +
610A ASP* 3.3 42.4 + - - +
611A GLY 3.6 11.2 - - - -
612A SER* 3.6 14.1 - - - -
624A ARG* 3.4 18.7 - - - +
263B GLU* 2.8 43.5 + - - -
575B PRO* 3.1 22.8 + - - +
576B ASN* 3.1 20.1 + - - +
577B MET 3.3 0.2 - - - -
578B MET* 1.3 75.1 - - - +
580B ARG* 1.3 58.3 + - - +
582B HIS* 3.3 2.3 + - - +
583B GLU* 2.9 33.4 + - - +
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Residues in contact with ARG 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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612A SER* 3.1 29.4 + - - -
613A LYS* 3.9 25.8 - - - +
272B ARG* 5.4 3.8 + - - +
273B PHE* 4.1 27.0 - - + -
436B GLY* 6.3 0.6 - - - -
547B GLU* 2.9 53.4 + - + +
551B THR* 5.8 0.4 - - - -
576B ASN 2.9 13.9 + - - +
577B MET* 3.2 17.5 + - + +
579B ARG* 1.3 77.8 - - - +
581B LEU* 1.3 63.8 + - - +
583B GLU* 3.3 13.6 + - - +
584B LEU* 3.0 40.5 + - + +
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Residues in contact with LEU 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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543B PRO* 3.6 39.5 - - + +
546B ALA* 3.9 7.9 - - + -
547B GLU* 3.9 10.3 - - + +
558B ILE* 4.4 11.0 - - + -
564B LEU* 4.7 1.8 - - + -
577B MET* 3.0 23.4 + - + +
578B MET* 3.9 25.4 - - + +
580B ARG* 1.3 74.2 - - - +
582B HIS* 1.3 62.4 + - - +
584B LEU* 3.2 2.6 + - + -
585B HIS 3.1 4.7 + - - -
586B VAL* 3.0 52.3 + - + +
588B GLU* 3.8 24.7 - - - +
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Residues in contact with HIS 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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606A ASN* 4.1 30.7 - - - +
608A TRP* 3.9 17.6 + - + +
609A GLY* 3.9 23.2 + - - -
628A THR* 6.0 2.0 - - - -
629A SER* 4.5 12.8 - - - -
578B MET 3.0 19.4 + - - +
579B ARG 3.7 3.5 + - - +
581B LEU* 1.3 77.3 - - - +
583B GLU* 1.4 66.9 + - - +
585B HIS* 3.0 21.2 + - - +
586B VAL 5.1 2.7 - - - +
588B GLU* 5.2 0.8 + - - -
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Residues in contact with GLU 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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610A ASP 5.2 1.6 - - - +
611A GLY* 3.4 11.2 - - - -
612A SER* 2.6 49.4 + - - +
613A LYS* 4.5 4.0 + - - +
625A ASP* 5.0 4.2 - - - +
579B ARG 2.9 25.9 + - - +
580B ARG* 3.3 19.1 + - - +
582B HIS* 1.4 78.3 + - - +
584B LEU* 1.3 65.6 + - + +
585B HIS* 3.2 18.5 + - - -
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Residues in contact with LEU 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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547B GLU* 3.6 29.4 - - + +
550B ALA* 4.0 23.5 - - + +
551B THR* 3.5 43.3 - - + +
554B HIS 5.7 0.2 - - - +
580B ARG* 3.0 31.5 + - + +
581B LEU* 3.7 4.9 - - - +
582B HIS 3.1 0.4 - - - -
583B GLU* 1.3 82.5 - - + +
585B HIS* 1.3 70.7 + - - +
586B VAL* 3.4 3.9 + - + -
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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