Contacts of the helix formed by residues 588 - 597 (chain B) 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 SER 588 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584B GLU 5.5 0.7 - - - -
585B CYS* 4.7 12.8 - - - -
586B GLU 3.4 5.3 + - - -
587B LEU* 1.3 73.1 - - - +
589B THR* 1.3 63.1 + - - +
590B PHE 3.3 2.7 - - - -
591B ILE* 3.2 22.7 - - - +
592B ASN* 3.2 22.9 - - - +
626B THR* 4.6 11.4 - - - +
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Residues in contact with THR 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B PRO* 3.6 20.7 - - - +
587B LEU* 5.1 5.9 - - - +
588B SER* 1.3 83.1 + - - +
590B PHE* 1.3 64.4 + - - +
592B ASN* 3.9 6.1 + - - +
593B TRP* 3.4 20.4 + - - +
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Residues in contact with PHE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B LEU* 5.4 9.0 - - + -
543B HIS* 6.3 0.2 - - - -
560B LEU* 5.1 1.3 - - + -
561B LEU* 4.0 23.6 - - + +
562B ALA 3.7 14.1 - - - -
563B PRO* 3.4 40.8 - - + -
576B ILE* 5.3 5.6 - - + -
581B PHE* 3.6 39.9 - + + -
582B ILE* 6.3 1.3 - - + -
587B LEU* 4.5 17.0 - - + +
588B SER* 3.3 1.0 - - - +
589B THR* 1.3 78.7 + - - +
591B ILE* 1.3 65.9 + - + +
592B ASN 3.1 4.5 - - - -
593B TRP* 3.1 28.3 + + - +
594B LEU* 3.4 36.4 + - + +
621B LEU* 5.5 1.1 - - + -
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Residues in contact with ILE 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B PHE* 6.5 0.4 - - + -
582B ILE 4.7 10.5 - - - +
583B CYS* 5.4 5.6 - - - -
584B GLU 4.6 11.0 - - - +
587B LEU 3.9 11.6 + - - +
588B SER* 3.2 33.2 - - - +
590B PHE* 1.3 86.0 - - + +
592B ASN* 1.3 59.6 + - - +
594B LEU* 4.4 8.9 + - - +
595B ASN* 4.1 15.4 + - - +
621B LEU* 4.7 29.9 - - + +
624B LEU* 6.1 6.1 - - + -
625B SER 5.8 0.9 - - - +
626B THR* 3.8 29.2 - - + -
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Residues in contact with ASN 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B SER* 3.2 21.0 + - - +
589B THR* 3.9 7.3 + - - +
590B PHE 3.1 0.4 - - - -
591B ILE* 1.3 79.2 - - + +
593B TRP* 1.3 61.8 - - - +
595B ASN* 3.6 6.2 + - - +
596B HIS* 3.5 19.4 + - - +
626B THR* 5.8 5.2 - - + +
1O NAG 3.2 23.0 + - - +
2O FUC 3.3 37.6 + - - +
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Residues in contact with TRP 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B LEU* 5.8 2.2 - - + -
543B HIS* 4.3 26.5 - + - -
563B PRO* 4.6 9.9 - - + -
564B ASN 4.0 19.8 + - - -
565B PRO* 5.0 4.3 + - + +
566B ASP 5.2 1.1 - - - -
567B VAL* 3.7 39.4 - - + +
574B LEU* 5.8 10.5 - - + -
589B THR 3.4 12.1 + - - +
590B PHE* 3.1 24.3 + + - +
592B ASN* 1.3 75.7 - - - +
594B LEU* 1.3 91.1 + - + +
595B ASN 2.8 10.9 + - - -
596B HIS* 3.1 21.1 + + + +
597B THR* 3.2 35.0 + - + +
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Residues in contact with LEU 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B LEU* 5.9 2.7 - - + -
576B ILE* 4.6 29.4 - - + -
581B PHE* 5.0 0.2 - - + -
590B PHE* 3.4 37.5 + - + +
591B ILE* 4.7 7.0 - - - +
592B ASN 3.6 0.2 - - - -
593B TRP* 1.3 103.4 - - + +
595B ASN* 1.3 57.3 + - - +
597B THR* 2.7 22.0 + - - +
598B ASN 4.6 3.1 - - - +
601B ILE 5.1 0.4 - - - +
602B ALA* 5.3 1.4 - - - +
621B LEU* 3.4 34.1 - - + -
622B PHE* 3.4 26.0 - - + -
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Residues in contact with ASN 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B ILE 4.1 12.3 + - - +
592B ASN* 3.6 10.9 + - - +
593B TRP 2.8 2.2 + - - -
594B LEU* 1.3 76.9 - - - +
596B HIS* 1.3 60.0 + - - +
597B THR 3.0 5.8 + - - -
598B ASN* 3.2 14.0 + - - +
622B PHE* 4.1 19.3 - - + -
1O NAG 1.5 71.7 + - - +
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Residues in contact with HIS 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B ASN 3.5 8.1 + - - +
593B TRP* 3.1 14.6 + + + +
595B ASN* 1.3 74.3 - - - +
597B THR* 1.3 57.6 + - + +
598B ASN* 2.9 17.0 + - - +
1O NAG 5.5 1.8 - - - -
2O FUC 3.5 31.7 + - - +
1P NAG 3.1 59.6 + - + +
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Residues in contact with THR 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B VAL* 5.8 4.0 - - + -
593B TRP* 3.2 50.5 - - + +
594B LEU* 2.7 28.9 + - - +
596B HIS* 1.3 77.0 - - + +
598B ASN* 1.4 73.5 + - - +
601B ILE* 3.1 47.2 + - + +
1P NAG 3.7 15.3 - - + -
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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