Contacts of the helix formed by residues 589 - 597 (chain A) in PDB entry 3J0A
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 THR 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A PRO* 3.6 19.7 - - - +
587A LEU* 5.1 6.6 - - - +
588A SER* 1.3 82.3 + - - +
590A PHE* 1.3 61.4 + - - +
592A ASN* 3.5 9.6 + - - +
593A TRP* 3.2 25.3 + - - +
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Residues in contact with PHE 590 (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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541A LEU* 5.1 8.7 - - + -
560A LEU* 5.2 2.0 - - + -
561A LEU* 4.2 22.7 - - + +
562A ALA 3.6 18.6 - - - -
563A PRO* 3.4 42.0 - - + -
576A ILE* 5.2 6.3 - - + -
581A PHE* 3.6 39.9 - + - -
582A ILE* 6.5 0.4 - - + -
587A LEU* 4.6 13.9 - - + -
588A SER* 3.4 1.0 - - - +
589A THR* 1.3 78.0 + - - +
591A ILE* 1.3 69.3 + - + +
592A ASN 3.0 5.6 + - - -
593A TRP* 3.2 29.5 + + - +
594A LEU* 3.4 31.0 + - + +
621A LEU* 5.5 0.4 - - + -
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Residues in contact with ILE 591 (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 4.8 11.0 - - - +
583A CYS* 5.6 5.2 - - + -
584A GLU 4.8 8.3 - - - +
587A LEU* 3.9 10.5 - - + +
588A SER* 3.2 33.9 - - - +
590A PHE* 1.3 84.5 - - + +
592A ASN* 1.3 58.5 + - - +
594A LEU* 4.3 9.3 + - - +
595A ASN* 3.8 17.7 + - - +
621A LEU* 4.6 32.1 - - + +
622A PHE* 5.9 0.5 - - - -
624A LEU* 5.9 8.3 - - + -
625A SER 5.9 0.4 - - - +
626A THR* 3.7 29.4 - - + -
1H NAG 6.1 0.5 - - - +
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Residues in contact with ASN 592 (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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588A SER 3.1 20.3 + - - +
589A THR* 3.5 10.1 + - - +
590A PHE 3.0 0.6 - - - -
591A ILE* 1.3 79.5 - - - +
593A TRP* 1.3 64.1 + - - +
595A ASN* 3.5 5.8 + - - +
596A HIS* 3.2 22.9 + - - +
1H NAG 3.8 21.3 + - - +
2H FUC 3.8 27.2 + - - +
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Residues in contact with TRP 593 (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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541A LEU* 5.6 2.7 - - + -
543A HIS* 4.1 28.3 - + - -
563A PRO* 4.7 9.6 - - + -
564A ASN 3.9 20.0 + - - -
565A PRO* 4.9 3.5 + - + -
566A ASP 5.1 0.7 - - - -
567A VAL* 3.6 40.4 - - + +
574A LEU* 5.4 15.0 - - + -
589A THR 3.2 12.9 + - - +
590A PHE* 3.2 26.1 + + - +
592A ASN* 1.3 75.4 - - - +
594A LEU* 1.3 90.9 + - + +
595A ASN 3.1 1.6 - - - -
596A HIS* 3.0 17.8 + + - +
597A THR* 2.9 51.1 + - + +
601A ILE* 6.5 1.6 - - + -
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Residues in contact with LEU 594 (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 LEU* 5.7 2.7 - - + -
576A ILE* 4.4 28.5 - - + -
581A PHE* 5.0 2.2 - - + -
590A PHE* 3.4 36.0 + - + +
591A ILE* 4.5 7.6 - - - +
592A ASN 3.5 0.2 - - - -
593A TRP* 1.3 104.6 - - + +
595A ASN* 1.3 57.7 + - - +
597A THR* 2.7 20.7 + - - +
598A ASN 4.2 3.8 - - - +
601A ILE 6.0 1.6 - - - +
602A ALA* 6.3 2.2 - - + -
608A ILE* 6.3 0.4 - - + -
621A LEU* 3.6 33.0 - - + -
622A PHE* 3.1 29.9 - - + -
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Residues in contact with ASN 595 (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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591A ILE 3.8 13.6 + - - +
592A ASN* 3.5 10.0 + - - +
593A TRP 3.1 0.6 - - - -
594A LEU* 1.3 77.4 - - - +
596A HIS* 1.3 64.0 + - - +
597A THR 3.2 0.4 - - - -
598A ASN* 3.4 14.0 + - - +
622A PHE* 3.9 17.1 - - + -
1H NAG 1.5 72.3 + - - +
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Residues in contact with HIS 596 (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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592A ASN* 3.2 13.9 + - - +
593A TRP* 3.0 20.7 + + - +
595A ASN* 1.3 76.4 - - - +
597A THR* 1.3 52.2 + - + +
598A ASN* 3.0 12.0 + - - -
1H NAG 5.2 7.0 - - - +
2H FUC 3.9 29.3 + - - +
1I NAG 2.8 69.9 + - + -
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Residues in contact with THR 597 (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 VAL* 5.8 3.1 - - + -
593A TRP* 2.9 53.8 + - + +
594A LEU* 2.7 30.0 + - - +
596A HIS* 1.3 76.1 - - + +
598A ASN* 1.3 74.7 + - - +
601A ILE* 3.1 48.2 + - + +
602A ALA* 5.0 0.9 - - - +
1I NAG 3.5 14.4 - - + -
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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