Contacts of the helix formed by residues 579 - 584 (chain B) in PDB entry 4HXG
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 GLY 579 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 4.7 1.2 + - - -
577B ALA* 3.1 3.4 - - - +
578B HIS* 1.3 78.4 - - - +
580B HIS* 1.3 60.5 + - - +
581B SER* 2.9 6.8 + - - -
582B ILE* 3.2 11.5 + - - +
583B ARG* 2.8 40.3 + - - +
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Residues in contact with HIS 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B GLU* 5.0 1.0 + - - -
489B ASN* 2.9 30.0 + - - -
541B ILE* 4.0 21.3 - - + -
542B HIS 4.4 0.7 - - - -
543B SER* 3.1 28.5 + - - -
573B PHE* 4.4 7.6 - + - -
576B GLY* 3.9 14.1 - - - -
577B ALA 2.9 21.2 + - - +
578B HIS 3.8 5.8 - - - -
579B GLY* 1.3 76.2 - - - +
581B SER* 1.3 67.6 + - - +
583B ARG* 4.3 2.0 - - - -
584B GLY* 2.7 33.1 + - - +
588B HIS* 3.1 37.3 + - + -
589B ARG* 3.6 3.8 - - - +
592B ARG* 4.4 11.6 - - - -
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Residues in contact with SER 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LYS* 5.3 1.0 + - - -
399B GLU* 4.6 3.4 + - - -
465B ILE* 3.7 20.8 - - - +
488B GLU* 4.8 0.7 - - - -
579B GLY* 2.9 4.6 + - - -
580B HIS* 1.3 84.9 - - - +
582B ILE* 1.3 75.7 + - - +
588B HIS* 5.5 0.2 - - - -
589B ARG* 2.8 26.4 + - - +
592B ARG* 3.4 47.1 + - - +
593B TYR* 3.8 10.1 + - - -
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Residues in contact with ILE 582 (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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41B TYR* 3.7 2.4 + - - -
397B LYS* 5.7 6.5 - - + +
399B GLU* 5.9 3.1 - - - +
579B GLY* 3.4 13.5 - - - +
581B SER* 1.3 92.0 + - - +
583B ARG* 1.3 76.2 + - + +
584B GLY 3.6 0.7 - - - -
589B ARG* 3.2 34.5 + - - +
593B TYR* 4.8 4.0 - - - +
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Residues in contact with ARG 583 (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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41B TYR* 4.1 9.4 - - - -
143B ASN* 3.4 35.3 + - - +
577B ALA* 6.1 1.4 - - - +
579B GLY* 2.8 32.3 + - - +
580B HIS* 4.3 1.8 - - - -
582B ILE* 1.3 89.4 - - + +
584B GLY* 1.3 66.1 + - - +
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Residues in contact with GLY 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 2.6 32.4 + - - -
576B GLY* 5.5 4.0 - - - -
580B HIS* 2.7 31.8 + - - -
582B ILE 3.6 1.6 - - - -
583B ARG* 1.3 74.9 - - - +
585B SER* 1.3 62.5 + - - +
588B HIS* 4.4 10.5 - - - -
589B ARG* 3.4 4.5 - - - +
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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
------------------------------------------------------------
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