Contacts of the helix formed by residues 578 - 589 (chain A) in PDB entry 3F7F
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 ASP 578 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A GLU* 5.5 1.0 + - - -
576A SER 4.4 0.4 + - - -
577A PHE* 1.3 70.2 - - - +
579A ILE* 1.3 63.7 + - - +
580A PRO* 2.7 15.0 - - - +
581A VAL* 2.7 53.4 + - + +
582A VAL* 3.4 10.4 + - + +
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Residues in contact with ILE 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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509A TYR* 4.6 16.4 - - + +
574A LEU* 4.4 26.0 - - + +
577A PHE* 2.9 24.9 + - + +
578A ASP* 1.3 71.7 - - - +
580A PRO* 1.3 69.7 - - + +
582A VAL* 3.2 7.8 + - - -
583A LEU* 2.9 39.2 + - + +
637A PHE* 5.4 0.2 - - + -
642A LEU* 4.5 28.7 - - + -
647A PHE* 3.6 26.7 - - + -
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Residues in contact with PRO 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASP* 3.1 19.1 - - - +
579A ILE* 1.3 88.3 - - + +
581A VAL* 1.3 62.6 + - + +
583A LEU* 4.0 2.1 - - + +
584A ASN* 3.1 26.2 + - - +
646A ILE* 5.7 4.9 - - + -
647A PHE* 3.8 29.2 - - + -
650A HIS* 4.4 5.0 + - - +
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Residues in contact with VAL 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASP* 2.7 44.7 + - + +
580A PRO* 1.3 76.4 - - + +
582A VAL* 1.3 65.6 + - + +
584A ASN* 3.3 7.3 + - - +
585A ASP* 3.2 21.8 + - + +
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Residues in contact with VAL 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A GLU* 4.4 22.4 - - + -
506A LEU* 3.3 33.1 - - + +
509A TYR* 3.5 30.5 - - + -
577A PHE* 4.7 10.1 - - + -
578A ASP* 3.4 21.0 + - + +
579A ILE* 3.2 9.6 + - - +
581A VAL* 1.3 79.1 - - + +
583A LEU* 1.3 59.7 + - - +
585A ASP* 3.1 7.0 + - - +
586A LEU* 2.9 26.5 + - - +
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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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509A TYR* 3.6 22.7 - - + +
579A ILE* 2.9 38.1 + - + +
580A PRO 4.1 2.7 - - - +
582A VAL* 1.3 73.3 - - - +
584A ASN* 1.3 54.2 + - - +
586A LEU* 4.2 13.0 - - + -
587A ILE* 2.7 48.9 + - + +
633A VAL* 3.6 27.6 - - + -
637A PHE* 3.5 32.1 - - + -
647A PHE* 3.9 10.8 - - + -
650A HIS* 4.2 16.4 - - + -
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Residues in contact with ASN 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 PRO 3.1 19.1 + - - +
581A VAL* 3.4 8.3 - - - +
582A VAL 3.1 0.2 - - - -
583A LEU* 1.3 78.6 - - - +
585A ASP* 1.3 54.2 + - - +
588A ASN* 2.7 66.1 + - - +
589A ASN* 4.3 2.4 + - - -
650A HIS* 4.1 14.5 + - - +
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Residues in contact with ASP 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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493A TRP* 5.1 0.9 - - - -
506A LEU* 3.4 23.5 - - + +
581A VAL* 3.2 10.1 + - + +
582A VAL* 3.1 10.4 + - - +
584A ASN* 1.3 76.9 - - - +
586A LEU* 1.3 62.1 - - - +
589A ASN* 2.4 48.4 + - - +
590A GLN* 2.9 34.9 + - - +
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Residues in contact with LEU 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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490A VAL* 5.3 1.3 - - + -
493A TRP* 4.9 1.8 - - + -
506A LEU* 3.7 28.8 - - + +
509A TYR* 4.9 0.9 - - + -
510A LEU* 4.2 16.8 - - + -
582A VAL 2.9 16.1 + - - +
583A LEU* 3.7 15.9 - - + +
585A ASP* 1.3 78.7 - - - +
587A ILE* 1.3 62.5 + - + +
590A GLN* 3.5 7.1 + - + -
591A MET* 2.8 51.7 + - + +
629A ILE* 3.9 33.2 - - + -
633A VAL* 4.0 18.4 - - + -
654A LEU* 5.7 1.6 - - + -
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Residues in contact with ILE 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A LEU* 2.7 29.7 + - + +
584A ASN 4.5 0.4 - - - +
586A LEU* 1.3 82.1 - - + +
588A ASN* 1.3 67.2 + - - +
589A ASN 3.6 0.2 - - - -
591A MET* 4.5 7.4 - - - -
592A LYS* 3.3 28.0 + - + +
650A HIS* 3.4 37.7 - - + +
653A THR* 3.8 26.2 - - + -
654A LEU* 3.7 39.0 - - + -
657A LEU* 4.9 7.2 - - + -
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Residues in contact with ASN 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 ASN* 2.7 56.9 + - - +
587A ILE* 1.3 87.5 - - - +
589A ASN* 1.3 68.2 + - - +
592A LYS* 4.2 16.8 - - - +
650A HIS* 4.2 9.5 - - - -
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Residues in contact with ASN 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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584A ASN* 4.3 3.6 + - - -
585A ASP* 2.4 50.2 + - - +
587A ILE 3.6 0.2 - - - -
588A ASN* 1.3 90.4 - - - +
590A GLN* 1.3 76.6 + - - +
591A MET 3.8 0.2 - - - -
592A LYS 3.7 11.0 - - - +
593A PRO* 5.3 1.4 - - - +
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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