Contacts of the helix formed by residues 568 - 580 (chain B) in PDB entry 4UQJ
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 568 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569B ASN* 1.3 66.1 + - - +
570B GLU* 3.4 5.5 - - - +
571B PHE* 3.5 17.1 + - - +
572B GLY* 3.4 15.2 + - - -
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Residues in contact with ASN 569 (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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568B THR* 1.3 78.7 - - - +
570B GLU* 1.3 63.3 + - - +
572B GLY* 3.3 9.7 + - - -
573B ILE* 3.4 10.6 + - - +
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Residues in contact with GLU 570 (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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568B THR 3.4 3.0 - - - +
569B ASN* 1.3 74.7 - - - +
571B PHE* 1.3 59.8 + - - +
572B GLY 3.0 2.0 - - - -
573B ILE* 2.9 24.4 + - + +
574B PHE* 2.9 17.0 + - - +
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Residues in contact with PHE 571 (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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568B THR* 3.5 21.6 + - - +
569B ASN 3.3 0.4 - - - -
570B GLU* 1.3 79.4 - - - +
572B GLY* 1.3 58.9 + - - +
574B PHE* 4.1 6.0 - - - +
575B ASN* 3.4 22.3 + - - +
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Residues in contact with GLY 572 (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 PHE* 3.0 40.4 - - - -
568B THR 3.4 6.6 + - - -
569B ASN 3.3 7.9 + - - -
570B GLU 3.0 1.2 - - - -
571B PHE* 1.3 78.8 - - - +
573B ILE* 1.3 57.4 + - - +
575B ASN* 3.9 0.7 - - - -
576B SER* 3.0 14.6 + - - -
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Residues in contact with ILE 573 (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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569B ASN 3.4 10.7 + - - +
570B GLU* 2.9 13.3 + - + +
572B GLY* 1.3 76.9 - - - +
574B PHE* 1.3 59.1 + - - +
576B SER* 3.3 5.4 + - - -
577B LEU* 3.0 29.8 + - - +
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Residues in contact with PHE 574 (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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594A ARG* 5.5 2.4 - - - +
570B GLU 2.9 14.8 + - - +
571B PHE* 4.3 6.5 - - - +
573B ILE* 1.3 76.1 - - - +
575B ASN* 1.3 56.7 + - - +
577B LEU* 3.5 7.6 + - - +
578B TRP* 3.1 24.3 + - - +
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Residues in contact with ASN 575 (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 PHE* 4.1 13.0 - - + -
544B SER* 4.1 19.3 - - - +
571B PHE 3.4 18.3 + - - +
572B GLY* 4.0 3.6 - - - +
573B ILE 3.2 0.6 - - - -
574B PHE* 1.3 76.9 - - - +
576B SER* 1.3 59.9 + - - +
577B LEU 3.1 1.8 - - - -
578B TRP* 2.9 8.6 + - - +
579B PHE* 2.8 31.4 + - - +
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Residues in contact with SER 576 (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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537B SER* 5.4 2.2 - - - +
541B PHE* 3.8 19.0 - - - -
572B GLY 3.0 21.4 + - - -
573B ILE* 3.3 7.4 + - - -
575B ASN* 1.3 76.1 - - - +
577B LEU* 1.3 56.6 + - - +
579B PHE* 4.0 4.5 - - - +
580B SER* 3.2 25.5 + - - -
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Residues in contact with LEU 577 (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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594A ARG* 5.2 5.0 - - + +
596A LEU* 4.1 36.1 - - + +
573B ILE 3.0 16.7 + - - +
574B PHE* 3.8 7.9 - - - +
576B SER* 1.3 76.5 - - - +
578B TRP* 1.3 60.1 + - - +
580B SER* 3.7 8.2 + - - -
581B LEU* 3.2 22.2 + - - +
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Residues in contact with TRP 578 (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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594A ARG* 4.3 18.8 - - + -
574B PHE 3.1 13.7 + - - +
575B ASN* 2.9 12.6 + - - +
577B LEU* 1.3 77.1 - - - +
579B PHE* 1.3 59.7 + - - +
580B SER 3.2 0.4 - - - -
581B LEU* 3.2 8.3 + - - +
582B GLY* 2.9 22.5 + - - -
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Residues in contact with PHE 579 (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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537B SER* 3.4 33.7 - - - +
540B LEU* 4.4 12.8 - - + +
541B PHE* 4.4 15.0 - - + +
575B ASN 2.8 15.0 + - - +
576B SER 4.3 3.1 - - - +
578B TRP* 1.3 74.1 - - - +
580B SER* 1.3 58.4 + - - +
581B LEU 3.2 0.4 - - - -
582B GLY* 3.5 5.4 - - - +
583B ALA* 2.9 25.1 + - - +
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Residues in contact with SER 580 (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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596A LEU* 5.5 5.8 - - - -
533B TYR* 3.4 8.3 + - - -
537B SER* 4.4 6.3 - - - -
576B SER 3.2 20.7 + - - -
577B LEU* 3.8 9.6 - - - -
578B TRP 3.2 0.6 - - - -
579B PHE* 1.3 76.9 - - - +
581B LEU* 1.3 58.5 + - - +
583B ALA* 3.3 8.8 - - - +
584B PHE* 2.8 25.1 + - - +
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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