Contacts of the helix formed by residues 581 - 587 (chain A) in PDB entry 1F9O
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 ARG 581 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP* 3.0 19.4 + - - -
161A TRP* 4.4 7.4 - - + -
162A TYR* 3.0 32.8 + - + -
188A THR 4.2 2.0 + - - -
189A TRP 5.0 0.2 + - - -
191A THR* 3.4 19.2 + - - +
193A PRO* 3.3 24.5 - - + +
555A VAL* 5.3 0.4 - - - +
567A ASN* 5.7 0.2 - - - +
569A ASP* 4.0 1.3 - - - -
577A PHE* 3.1 69.1 + - - +
578A ILE* 3.2 9.8 + - - +
580A ILE* 1.3 96.3 - - + +
582A SER* 1.3 60.6 + - - +
583A LYS* 3.0 8.6 + - - -
584A TYR* 3.0 34.8 + - + +
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Residues in contact with SER 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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567A ASN* 3.1 10.4 + - - -
569A ASP* 2.7 33.9 + - - -
578A ILE* 3.3 13.8 + - - -
579A ASP* 4.7 2.5 - - - -
581A ARG* 1.3 75.7 - - - +
583A LYS* 1.3 61.0 + - - +
584A TYR 3.1 0.4 - - - -
585A LYS* 3.2 32.6 + - - +
586A GLN* 4.0 4.6 + - - -
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Residues in contact with LYS 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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160A ASN 4.7 3.0 + - - -
161A TRP* 3.0 65.8 + - + +
162A TYR 5.9 0.2 - - - -
163A GLY* 6.0 0.4 - - - -
567A ASN* 3.9 29.6 - - + +
581A ARG* 3.0 2.3 + - - -
582A SER* 1.3 71.7 + - - +
584A TYR* 1.3 57.5 + - - +
585A LYS 2.9 11.7 + - - -
586A GLN* 2.9 31.6 + - + +
587A ASP 4.1 1.6 + - - -
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Residues in contact with TYR 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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40A THR 3.9 4.3 - - - -
41A LEU* 3.6 38.8 - - + -
42A MET 3.1 21.8 + - - -
43A VAL* 3.7 2.1 - - - +
47A ASP 2.8 28.7 + - - -
48A TYR* 3.5 15.5 - + - -
161A TRP* 3.6 25.3 - + - -
550A PHE* 3.8 24.9 - + - -
577A PHE* 4.0 14.8 - + - -
578A ILE* 3.7 13.2 - - + -
581A ARG* 3.0 20.5 + - + +
583A LYS* 1.3 77.8 - - - +
585A LYS* 1.3 57.4 + - - +
586A GLN 3.2 1.3 - - - -
587A ASP* 3.3 23.3 + - + +
590A TRP* 3.3 19.7 - - + -
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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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551A LEU* 6.4 0.4 - - - -
578A ILE* 4.2 23.7 - - + +
579A ASP* 5.7 3.2 + - - -
582A SER* 3.2 21.6 + - - +
583A LYS 2.9 1.4 + - - -
584A TYR* 1.3 78.8 - - - +
586A GLN* 1.3 68.5 + - - +
587A ASP 3.3 2.9 + - - +
590A TRP* 3.6 44.7 - - + +
591A GLN* 5.3 4.5 + - - -
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Residues in contact with GLN 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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582A SER 4.0 6.3 + - - -
583A LYS* 2.9 30.4 + - + +
585A LYS* 1.3 87.6 - - - +
587A ASP* 1.3 65.4 + - - +
588A PRO* 3.5 6.4 - - - +
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Residues in contact with ASP 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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40A THR* 2.5 33.0 + - - -
41A LEU* 3.5 23.1 + - + +
48A TYR* 4.8 1.6 - - - -
583A LYS 4.1 1.2 + - - -
584A TYR* 3.3 24.4 + - + +
585A LYS 3.3 2.5 - - - +
586A GLN* 1.3 80.4 - - - +
588A PRO* 1.3 75.7 - - - +
589A GLU* 3.0 32.9 + - - +
590A TRP* 3.0 22.3 + - + +
591A GLN* 4.7 1.7 + - - +
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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