Contacts of the helix formed by residues 574 - 586 (chain A) in PDB entry 4HBN
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 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A LEU* 1.3 76.3 - - - +
575A GLU* 1.3 64.6 + - - +
576A PRO* 3.4 17.2 - - - +
577A LEU* 3.4 22.4 + - - +
578A ARG* 3.0 30.6 + - - +
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Residues in contact with GLU 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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574A SER* 1.3 72.2 - - - +
576A PRO* 1.3 75.0 - - + +
578A ARG* 2.5 45.0 + - - +
579A GLU* 3.0 56.3 + - - +
609A THR* 3.3 24.1 + - - +
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Residues in contact with PRO 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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574A SER* 3.4 15.3 - - - +
575A GLU* 1.3 97.0 - - + +
577A LEU* 1.3 60.9 + - + +
579A GLU* 3.7 11.4 + - - +
580A GLU* 3.3 23.7 + - - +
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Residues in contact with LEU 577 (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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573A LEU* 4.0 32.8 - - + -
574A SER* 3.4 22.1 + - - +
575A GLU 3.2 0.6 - - - -
576A PRO* 1.3 77.4 - - + +
578A ARG* 1.3 67.1 + - - +
579A GLU 2.9 1.8 - - - -
580A GLU* 2.8 34.0 + - - +
581A ILE* 2.9 21.0 + - + +
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Residues in contact with ARG 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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570A LEU* 3.0 53.7 + - + +
571A GLY* 4.2 6.3 + - - -
573A LEU* 2.9 36.9 + - + -
574A SER* 3.0 13.8 + - - +
575A GLU* 2.5 43.1 + - - +
577A LEU* 1.3 76.8 - - - +
579A GLU* 1.3 57.5 + - + +
581A ILE* 3.5 11.0 + - - +
582A ILE* 2.9 30.1 + - - +
609A THR* 5.6 3.1 + - - +
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Residues in contact with GLU 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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575A GLU* 3.0 56.4 + - - +
576A PRO* 3.8 10.4 - - - +
577A LEU 2.9 0.6 - - - -
578A ARG* 1.3 74.9 - - - +
580A GLU* 1.3 61.5 + - - +
582A ILE* 3.3 8.2 - - - +
583A ASN* 2.9 38.5 + - - +
605A THR* 3.4 33.0 - - + +
606A SER* 5.7 1.0 - - - -
609A THR* 4.2 6.4 + - - +
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Residues in contact with GLU 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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576A PRO 3.3 13.1 + - - +
577A LEU* 2.8 31.5 + - + +
579A GLU* 1.3 80.3 - - - +
581A ILE* 1.3 58.3 + - + +
583A ASN* 3.7 4.2 - - - +
584A PHE* 2.8 31.8 + - - +
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Residues in contact with ILE 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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566A GLU* 6.0 1.3 - - - +
570A LEU* 4.9 13.2 - - + -
573A LEU* 3.5 30.5 - - + -
577A LEU* 2.9 26.6 + - + +
578A ARG* 3.6 8.7 - - - +
580A GLU* 1.3 74.3 - - + +
582A ILE* 1.3 67.4 + - + +
584A PHE* 3.1 6.6 + - - +
585A ASN* 2.8 42.7 + - - +
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Residues in contact with ILE 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 ARG 2.9 21.1 + - - +
579A GLU* 3.3 14.6 - - + +
581A ILE* 1.3 75.3 - - + +
583A ASN* 1.3 68.8 + - - +
585A ASN* 3.1 6.5 + - + +
586A CYS* 3.0 50.4 + - - +
605A THR 5.2 1.6 - - - +
608A LEU* 3.5 44.6 - - + +
609A THR* 4.8 12.8 - - - +
611A LEU* 5.6 1.6 - - + +
682A TYR* 4.6 15.7 - - + +
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Residues in contact with ASN 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 GLU* 2.9 25.4 + - - +
580A GLU* 3.7 4.9 - - - +
582A ILE* 1.3 76.7 - - - +
584A PHE* 1.3 66.7 + - - +
586A CYS 3.2 9.9 + - - -
587A ARG* 3.4 14.9 + - - +
590A VAL* 5.0 4.3 - - - +
601A PRO 5.2 0.5 - - - +
604A VAL* 5.0 3.1 - - - +
605A THR* 2.9 39.2 + - - +
608A LEU* 3.2 22.2 - - - +
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Residues in contact with PHE 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 GLU 2.8 21.9 + - - +
581A ILE* 3.6 5.6 - - - +
583A ASN* 1.3 71.8 - - - +
585A ASN* 1.3 76.1 + - - +
586A CYS 3.2 0.9 + - - -
587A ARG* 2.9 76.6 + - - +
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Residues in contact with ASN 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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566A GLU* 5.6 4.2 + - - -
581A ILE* 2.8 36.9 + - - +
582A ILE* 3.1 8.8 + - + +
584A PHE* 1.3 94.3 - - - +
586A CYS* 1.3 65.0 + - - +
587A ARG 3.5 1.0 + - - -
588A LYS 5.3 0.3 + - - -
636A GLN* 4.3 11.8 - - - +
682A TYR* 4.9 5.5 + - - +
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Residues in contact with CYS 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 ILE* 3.0 43.0 + - - +
583A ASN 3.2 3.1 + - - +
584A PHE 3.2 0.4 - - - -
585A ASN* 1.3 82.6 - - - +
587A ARG* 1.3 58.7 + - - +
588A LYS 3.3 2.2 - - - -
589A LEU* 3.1 19.0 + - + +
590A VAL* 2.8 38.0 + - + +
608A LEU* 4.0 20.4 - - + -
611A LEU* 5.6 0.7 - - - -
636A GLN* 5.5 0.9 - - - -
682A TYR* 3.8 27.4 - - - -
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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