Contacts of the helix formed by residues 591 - 603 (chain B) in PDB entry 5XA0
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 ALA 591 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B CYS* 5.7 3.6 - - - -
557B TYR* 4.9 9.1 - - - +
581B MET* 5.1 11.4 - - + +
584B GLN* 4.7 20.4 - - + -
585B ILE* 4.8 16.4 - - + +
588B ASP 4.9 0.8 + - - -
589B VAL 3.5 1.0 - - - -
590B LEU* 1.3 76.5 - - - +
592B GLU* 1.3 61.1 + - - +
593B ASP 3.5 0.2 + - - -
594B THR* 4.0 13.6 + - - -
595B ILE* 4.6 2.1 + - - +
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Residues in contact with GLU 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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585B ILE* 6.1 0.6 - - + +
589B VAL 3.8 7.5 + - - +
590B LEU 3.0 0.8 - - - -
591B ALA* 1.3 79.9 - - - +
593B ASP* 1.3 66.9 + - - +
595B ILE* 3.0 20.5 + - + +
596B THR* 3.5 8.1 + - - -
629B ARG 5.3 0.4 - - - +
630B PHE* 5.3 7.9 - - + +
633B TYR* 3.1 39.9 - - + -
634B LEU* 4.7 2.2 - - - +
637B LEU* 5.8 0.5 - - - +
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Residues in contact with ASP 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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589B VAL 4.4 2.5 + - - +
590B LEU* 3.0 18.1 + - - +
592B GLU* 1.3 76.2 - - - +
594B THR* 1.3 65.0 + - - +
596B THR* 3.1 17.5 + - - -
597B ALA* 3.2 11.9 + - - +
633B TYR* 5.4 0.2 - - - +
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Residues in contact with THR 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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557B TYR* 6.0 0.4 - - - -
561B ARG* 5.2 15.9 - - - -
590B LEU 4.4 1.4 + - - -
591B ALA 4.0 10.4 + - - -
592B GLU 3.2 0.4 - - - -
593B ASP* 1.3 77.4 - - - +
595B ILE* 1.3 52.4 + - - +
597B ALA* 3.0 9.6 + - - +
598B LEU* 2.4 38.7 + - - +
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Residues in contact with ILE 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 ALA 4.6 2.1 + - - +
592B GLU* 3.0 15.3 + - + +
594B THR* 1.3 76.4 - - - +
596B THR* 1.4 50.2 + - - +
598B LEU* 2.7 11.9 - - - +
599B LEU* 2.2 39.2 + - - +
637B LEU* 4.7 12.3 - - + -
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Residues in contact with THR 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 GLU 3.5 4.3 + - - -
593B ASP* 3.1 12.1 + - - -
595B ILE* 1.4 74.7 - - - +
597B ALA* 1.3 66.8 + - - +
599B LEU* 2.9 10.2 + - - +
600B HIS* 2.8 22.7 + - - +
633B TYR 5.7 0.7 - - - -
636B ASP* 5.0 4.9 - - - -
637B LEU* 4.0 24.8 - - - +
639B VAL* 5.5 0.5 - - - +
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Residues in contact with ALA 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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593B ASP 3.2 8.9 + - - +
594B THR* 3.0 10.0 + - - +
596B THR* 1.3 76.5 - - - +
598B LEU* 1.3 64.6 + - - +
600B HIS* 2.9 10.8 + - - +
601B ASN* 2.8 23.1 + - - +
602B ASN 3.8 0.3 + - - -
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Residues in contact with LEU 598 (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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594B THR 2.4 25.0 + - - +
595B ILE* 2.7 21.5 - - - +
597B ALA* 1.3 70.7 - - - +
599B LEU* 1.3 60.0 + - - +
601B ASN 2.9 0.7 + - - -
602B ASN* 2.0 59.5 + - + +
606B LEU* 6.3 2.7 - - + -
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Residues in contact with LEU 599 (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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595B ILE 2.2 26.0 + - - +
596B THR* 2.9 10.3 + - - +
598B LEU* 1.3 67.1 - - - +
600B HIS* 1.3 65.5 + - - +
602B ASN 4.4 0.4 - - - -
603B ARG* 2.9 29.4 - - - +
637B LEU* 3.2 29.6 - - + +
638B CYS* 4.8 1.3 - - - -
639B VAL* 4.1 16.3 - - + +
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Residues in contact with HIS 600 (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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596B THR 2.8 14.1 + - - +
597B ALA* 2.9 13.6 + - - +
599B LEU* 1.3 76.3 - - - +
601B ASN* 1.3 60.5 + - + +
603B ARG* 4.2 5.2 - - - +
639B VAL* 4.6 9.5 - - + +
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Residues in contact with ASN 601 (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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597B ALA 2.8 14.4 + - - +
598B LEU 3.0 0.4 - - - -
600B HIS* 1.3 74.9 - - + +
602B ASN* 1.3 55.9 + - - +
603B ARG* 3.1 9.7 + - - +
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Residues in contact with ASN 602 (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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598B LEU* 2.0 53.6 + - + +
599B LEU* 4.4 0.6 - - - -
601B ASN* 1.3 67.7 - - - +
603B ARG* 1.3 67.0 + - - +
604B LYS 3.5 1.0 + - - -
605B LEU* 3.8 14.7 + - + +
606B LEU* 4.5 6.2 + - - +
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Residues in contact with ARG 603 (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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598B LEU 2.8 4.6 + - - -
599B LEU* 2.9 23.5 + - - +
600B HIS 4.2 6.3 - - - +
601B ASN 3.1 5.4 - - - +
602B ASN* 1.3 83.9 - - - +
604B LYS* 1.3 69.1 + - + +
605B LEU* 3.6 1.9 + - - +
639B VAL 6.1 0.4 - - - +
640B SER* 5.2 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