Contacts of the helix formed by residues 573 - 578 (chain H) in PDB entry 6X34
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 GLU 573 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534H ARG* 5.6 4.8 + - - -
538H ALA* 5.0 10.9 - - - +
541H SER* 4.5 13.9 + - - +
571H SER* 3.2 19.9 - - - +
572H PRO* 1.3 96.6 - - + +
574H VAL* 1.3 62.3 + - + +
576H ASN* 3.4 18.4 + - - +
577H ILE* 4.2 4.0 + - - +
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Residues in contact with VAL 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537H CYS 4.3 6.5 - - - +
540H PHE 5.3 0.7 - - - +
541H SER* 3.7 29.6 - - - -
544H LEU* 3.8 33.4 - - + -
567H VAL* 4.3 17.9 - - + +
568H LEU* 3.7 25.6 - - + -
571H SER* 3.9 17.2 + - - +
572H PRO 3.2 0.8 - - - -
573H GLU* 1.3 76.6 - - - +
575H LEU* 1.3 62.4 + - - +
577H ILE* 3.1 22.6 - - + +
578H ILE* 3.2 7.6 - - + +
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Residues in contact with LEU 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568H LEU* 4.9 6.1 - - + +
572H PRO* 3.3 17.5 + - + +
573H GLU 3.2 0.8 - - - -
574H VAL* 1.3 78.0 - - - +
576H ASN* 1.3 62.9 + - - +
578H ILE* 3.2 28.9 - - + +
605H SER 4.0 7.4 - - - +
606H LEU* 3.2 47.8 - - + +
607H CYS 4.9 0.4 - - - -
608H VAL 4.4 5.2 - - - +
609H CYS* 3.6 22.4 - - - -
614H VAL* 3.7 37.9 - - + -
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Residues in contact with ASN 576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572H PRO 4.0 2.1 + - - +
573H GLU* 3.4 14.4 + - - +
574H VAL 3.2 1.0 - - - -
575H LEU* 1.3 83.1 - - - +
577H ILE* 1.3 60.2 + - - +
578H ILE* 3.3 4.2 + - - +
2170H GLN* 4.3 17.8 - - - +
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Residues in contact with ILE 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541H SER* 4.3 23.1 - - - +
542H ASN 4.8 7.9 - - - +
544H LEU* 4.1 22.2 - - + -
573H GLU 4.2 2.9 + - - +
574H VAL* 3.1 25.5 - - + +
576H ASN* 1.3 76.1 - - - +
578H ILE* 1.3 67.7 + - - +
579H GLN* 3.0 27.4 + - - +
582H HIS* 4.5 1.3 + - - +
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Residues in contact with ILE 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544H LEU* 4.6 5.4 - - + -
568H LEU* 5.4 0.9 - - + -
574H VAL* 3.2 20.9 - - + +
575H LEU* 3.2 25.1 - - + +
576H ASN 3.3 4.2 - - - +
577H ILE* 1.3 80.8 - - - +
579H GLN* 1.3 66.4 + - - +
582H HIS* 3.5 22.9 - - + -
583H ILE* 6.6 0.4 - - + -
606H LEU* 3.8 41.5 - - + -
616H SER* 5.9 2.7 - - - +
617H ASN* 4.0 21.8 - - + -
620H LEU* 6.3 2.5 - - + -
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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
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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