Contacts of the helix formed by residues 573 - 584 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A PRO* 3.7 26.5 - - + +
272A ARG* 2.9 38.6 + - - +
273A PHE* 3.6 13.6 - - + -
348A CYS* 4.3 8.0 - - - +
440A TRP* 4.7 11.8 + - - -
539A TYR* 4.3 7.4 + - - -
540A PHE* 5.6 0.5 - - - +
568A MET* 3.1 24.3 + - + +
571A THR* 2.8 31.9 + - - +
572A LEU* 1.3 78.1 - - - +
574A TYR* 1.3 58.6 - - - +
575A PRO* 3.4 1.7 - - - -
576A ASN 3.5 3.0 + - - -
577A MET* 2.9 29.8 + - - +
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Residues in contact with TYR 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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563A HIS* 4.5 9.9 + + - -
564A LEU 3.7 19.8 + - - -
565A ALA* 3.5 24.5 - - + -
568A MET* 3.0 25.5 + - - +
569A HIS* 3.3 42.7 + + - +
573A GLU* 1.3 78.2 - - - +
575A PRO* 1.3 69.0 - - + +
577A MET* 3.6 3.1 - - - +
578A MET* 2.9 60.8 + - + +
591B ASP* 4.6 8.3 + - - -
608B TRP* 3.8 28.0 + + - -
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Residues in contact with PRO 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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262A ALA 5.0 5.6 - - - +
263A GLU* 3.4 38.6 - - + +
569A HIS* 5.7 0.9 - - - +
572A LEU* 3.8 15.0 - - - +
573A GLU 3.6 2.7 - - - -
574A TYR* 1.3 96.3 - - + +
576A ASN* 1.3 60.8 + - - +
578A MET* 3.4 2.4 + - - +
579A ARG* 3.1 32.6 + - - +
608B TRP* 3.6 30.4 - - + -
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Residues in contact with ASN 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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265A GLY 5.4 0.8 + - - -
266A GLU* 2.9 22.1 + - - -
270A PRO* 5.8 0.6 - - - +
273A PHE* 3.5 35.5 - - + -
274A TYR* 3.5 21.8 + - - -
572A LEU 5.4 2.6 + - - -
573A GLU 3.5 3.0 + - - -
575A PRO* 1.3 75.3 - - - +
577A MET* 1.3 59.5 + - - +
579A ARG* 3.0 18.2 + - - +
580A ARG* 2.9 29.5 + - - +
612B SER* 3.7 15.0 + - - +
624B ARG* 2.9 25.3 + - - -
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Residues in contact with MET 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.6 27.1 - - - +
273A PHE* 3.3 7.2 - - + -
543A PRO* 3.9 37.5 - - + +
547A GLU* 3.4 26.5 - - + +
568A MET* 3.6 25.8 - - + -
573A GLU 2.9 18.7 + - - +
574A TYR* 3.6 5.2 - - - +
575A PRO 3.3 0.2 - - - -
576A ASN* 1.3 77.3 - - - +
578A MET* 1.3 73.2 + - + +
580A ARG* 3.2 9.7 + - + +
581A LEU* 3.0 44.6 + - + +
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Residues in contact with MET 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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564A LEU* 4.5 8.5 - - + -
565A ALA* 4.1 17.3 - - + -
574A TYR* 2.9 64.7 + - + +
575A PRO 3.8 2.0 - - - +
577A MET* 1.3 84.3 - - + +
579A ARG* 1.3 64.4 + - - +
581A LEU* 3.4 21.5 + - + +
582A HIS* 3.0 25.3 + - - +
588A GLU* 4.0 23.1 - - - +
591B ASP* 5.8 1.1 - - - +
608B TRP* 3.5 31.8 - - + +
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Residues in contact with ARG 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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263A GLU* 2.6 45.6 + - - -
575A PRO* 3.1 20.1 + - - +
576A ASN* 3.0 24.5 + - - +
577A MET 3.3 0.2 - - - -
578A MET* 1.3 77.0 - - - +
580A ARG* 1.3 55.6 - - - +
582A HIS* 3.4 2.3 + - - +
583A GLU* 3.0 31.9 + - - +
607B ILE 4.8 3.4 + - - -
608B TRP* 3.4 39.6 - - + +
610B ASP* 3.3 41.5 + - - +
611B GLY 3.7 0.9 - - - -
612B SER* 3.6 14.4 - - - -
624B ARG* 3.6 31.1 - - - +
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Residues in contact with ARG 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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272A ARG* 5.5 2.8 + - - +
273A PHE* 4.1 26.3 - - + -
547A GLU* 2.8 53.5 + - + +
551A THR* 5.7 0.2 - - - -
576A ASN 2.9 18.1 + - - +
577A MET* 3.5 13.2 - - + +
579A ARG* 1.3 74.4 - - - +
581A LEU* 1.3 64.5 + - - +
583A GLU* 3.1 25.3 + - - +
584A LEU* 3.1 41.2 + - + +
612B SER* 2.9 22.1 + - - -
613B LYS* 3.2 29.9 - - - +
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Residues in contact with LEU 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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543A PRO* 3.6 36.8 - - + +
546A ALA* 4.2 3.6 - - + -
547A GLU* 4.1 14.4 - - + +
558A ILE* 4.4 12.6 - - + -
564A LEU* 4.5 1.8 - - + -
577A MET* 3.0 27.6 + - + +
578A MET* 3.8 26.7 - - + +
580A ARG* 1.3 76.0 - - - +
582A HIS* 1.3 61.1 + - - +
584A LEU* 3.5 2.5 + - + -
585A HIS 3.3 3.3 + - - -
586A VAL* 2.9 49.8 + - + +
588A GLU* 3.7 26.0 - - - +
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Residues in contact with HIS 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 MET 3.0 17.3 + - - +
579A ARG 3.7 4.7 + - - +
581A LEU* 1.3 77.2 - - - +
583A GLU* 1.3 62.6 + - - +
585A HIS* 3.1 26.6 + - - +
586A VAL 5.1 2.9 - - - +
588A GLU* 5.5 0.4 + - - -
606B ASN* 3.8 33.7 + - - +
608B TRP* 3.9 12.3 + - + +
609B GLY* 3.9 26.3 + - - -
629B SER* 4.4 13.8 - - - -
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Residues in contact with GLU 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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579A ARG 3.0 14.9 + - - +
580A ARG* 3.1 25.2 + - - +
582A HIS* 1.3 81.7 - - - +
584A LEU* 1.3 65.9 + - + +
585A HIS* 3.6 16.2 + - - -
610B ASP 5.9 0.4 - - - +
611B GLY* 3.7 9.2 - - - -
612B SER* 2.5 46.3 + - - -
613B LYS* 4.9 4.2 + - - +
625B ASP* 5.7 0.2 - - - +
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Residues in contact with LEU 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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547A GLU* 3.8 22.7 - - + +
550A ALA* 3.8 24.8 - - + +
551A THR* 3.5 37.0 - - + +
580A ARG* 3.1 43.6 + - + +
581A LEU* 4.1 5.2 - - - +
582A HIS 3.2 0.4 - - - -
583A GLU* 1.3 82.0 - - + +
585A HIS* 1.3 72.0 + - - +
586A VAL* 3.4 4.4 + - + -
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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