Contacts of the helix formed by residues 583 - 589 (chain A) in PDB entry 7ACN
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 LEU 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A MET* 4.3 16.1 - - + +
539A GLN* 4.0 13.0 + - - +
541A LEU* 4.3 22.4 - - + -
544A PHE* 4.3 18.6 - - + -
581A GLY 4.0 2.6 + - - -
582A HIS* 1.3 70.9 + - - +
584A ASP* 1.3 62.3 + - - +
586A ILE* 3.6 7.8 - - + +
587A SER* 2.7 37.8 + - - +
646A HIS* 5.6 0.9 - - + -
649A LEU* 3.8 34.3 - - + +
650A GLU* 4.1 7.9 - - + +
653A HIS* 3.9 30.3 - - + -
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Residues in contact with ASP 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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539A GLN* 3.5 19.7 - - - +
582A HIS* 3.4 7.5 - - + +
583A LEU* 1.3 78.2 - - - +
585A ASN* 1.3 70.8 + - - +
587A SER* 3.4 5.0 + - - -
588A ASN* 5.5 0.5 + - - -
621A ARG* 2.8 49.2 + - - -
653A HIS* 2.8 33.3 + - + +
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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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536A GLN* 3.0 47.0 + - - +
576A TRP* 3.6 12.0 - - - -
579A PHE* 3.7 29.5 - - + -
582A HIS* 3.1 28.3 + - + +
584A ASP* 1.3 86.7 + - - +
586A ILE* 1.3 61.8 + - - +
588A ASN* 3.3 26.1 + - - +
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Residues in contact with ILE 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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571A SER* 4.4 6.5 - - - +
572A ALA 5.1 1.1 - - - +
576A TRP* 3.7 21.4 - - + +
579A PHE* 3.5 27.1 - - + +
580A ARG* 3.2 35.0 - - - -
582A HIS 3.0 17.0 + - - +
583A LEU* 3.6 12.6 - - + +
585A ASN* 1.3 72.6 - - - +
587A SER* 1.4 59.5 + - - +
588A ASN 2.8 11.7 + - - -
589A ASN* 3.0 37.3 + - - +
646A HIS* 4.2 17.5 - - + -
650A GLU* 3.8 19.7 - - + +
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Residues in contact with SER 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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583A LEU* 2.7 24.0 + - - +
584A ASP 3.6 7.6 - - - -
585A ASN 3.3 0.6 - - - -
586A ILE* 1.4 73.1 - - - +
588A ASN* 1.3 61.1 + - - +
589A ASN 3.1 1.9 + - - -
590A LEU* 3.3 17.9 + - - +
617A PRO* 3.7 2.4 - - - +
621A ARG* 4.0 6.5 - - - -
650A GLU* 3.6 27.5 - - - +
653A HIS* 3.1 24.1 + - - +
654A LEU* 3.7 20.9 - - - +
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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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576A TRP* 3.5 19.8 - - + -
584A ASP* 3.9 2.8 + - - -
585A ASN* 3.3 27.8 + - - +
586A ILE 2.8 1.8 + - - -
587A SER* 1.3 76.8 - - - +
589A ASN* 1.3 56.4 + - - +
590A LEU 3.5 0.4 - - - -
592A ILE* 4.3 2.8 - - - +
617A PRO* 3.3 22.8 - - + +
618A ASP* 5.7 0.7 - - - +
621A ARG* 2.7 37.8 + - - +
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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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569A HIS 4.9 0.2 - - - +
570A ILE 3.6 3.8 - - - +
571A SER* 3.6 16.8 + - - +
572A ALA* 3.3 27.5 + - + +
576A TRP* 3.5 39.1 - - + +
586A ILE* 3.0 18.2 + - - +
588A ASN* 1.3 77.0 - - - +
590A LEU* 1.3 65.0 + - - +
591A LEU 3.1 3.6 + - - -
592A ILE* 3.2 27.7 + - + +
650A GLU* 2.5 36.2 + - - -
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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