Contacts of the helix formed by residues 751 - 759 (chain A) in PDB entry 3H52
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 751 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A PHE* 3.2 33.7 + - + +
750A PRO* 1.3 71.8 - - - +
752A MET* 1.3 57.9 + - + +
753A LEU 3.4 0.2 - - - -
754A ALA* 3.7 6.9 - - + +
755A GLU* 2.5 63.8 + - - +
2260N ASN 5.7 2.4 + - - -
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Residues in contact with MET 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A 486 3.5 27.0 - - + -
564A ASN* 3.7 48.7 - - + +
565A MET* 5.2 1.3 - - - -
750A PRO* 3.2 2.2 - - + +
751A GLU* 1.3 77.0 - - - +
753A LEU* 1.3 59.1 + - + +
755A GLU* 3.2 28.9 - - - +
756A ILE* 3.2 34.8 + - - +
2261N LEU 5.7 0.9 - - - +
2266N ILE* 6.0 4.7 - - + -
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Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A 486 4.0 20.9 - - + +
560A MET* 5.1 10.1 - - + -
564A ASN* 5.5 8.3 - - - +
735A TYR* 5.1 2.2 - - + +
736A CYS* 4.3 27.9 - - - +
739A THR* 3.7 27.8 - - + +
740A PHE* 4.4 9.1 - - + +
743A LYS* 4.6 11.7 - - - +
750A PRO* 3.5 28.0 + - + +
751A GLU 3.4 0.2 - - - -
752A MET* 1.3 78.1 - - + +
754A ALA* 1.3 56.0 - - - +
756A ILE* 4.1 11.9 - - + +
757A ILE* 3.2 26.3 - - - +
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Residues in contact with ALA 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A PHE* 3.6 22.9 - - + -
749A PHE* 4.4 7.2 - - + -
750A PRO 3.0 17.5 + - - +
751A GLU* 3.7 11.0 - - + +
752A MET 3.2 0.2 - - - -
753A LEU* 1.3 76.5 - - - +
755A GLU* 1.3 60.7 + - + +
756A ILE 3.2 1.1 - - - -
757A ILE* 3.0 24.2 + - - +
758A THR* 3.3 12.1 + - - -
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Residues in contact with GLU 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A 486 5.1 2.3 - - - -
751A GLU* 2.5 52.6 + - + +
752A MET* 3.2 29.6 - - + +
754A ALA* 1.3 71.2 - - - +
756A ILE* 1.3 59.1 + - + +
757A ILE 3.0 0.4 - - - -
758A THR* 3.0 31.1 + - - +
759A ASN 3.4 5.7 + - - -
2260N ASN 5.3 3.1 + - - -
2261N LEU 3.7 17.5 + - - +
2262N GLY* 4.0 21.2 + - - -
2263N LEU* 3.9 22.6 + - + +
2266N ILE* 5.9 0.9 - - - +
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Residues in contact with ILE 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A 486 3.8 55.9 - - + -
600A TRP* 4.1 22.4 - - + -
601A MET* 4.7 0.9 - - + -
733A LEU* 4.2 23.5 - - + +
736A CYS* 4.4 12.8 - - - -
752A MET 3.2 18.9 + - - +
753A LEU* 4.2 11.9 - - + +
754A ALA 3.2 0.6 - - - -
755A GLU* 1.3 76.8 - - - +
757A ILE* 1.3 65.3 - - + +
759A ASN 4.5 0.2 - - - -
760A GLN* 3.3 25.5 + - - +
2263N LEU* 4.5 8.1 - - + -
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Residues in contact with ILE 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733A LEU* 4.8 6.3 - - + +
736A CYS* 4.2 20.6 - - + -
737A PHE* 4.0 40.6 - - + +
740A PHE* 5.2 9.9 - - + -
753A LEU 3.2 23.1 - - - +
754A ALA* 3.0 12.7 + - - +
756A ILE* 1.3 83.9 - - + +
758A THR* 1.3 57.6 + - - +
760A GLN 3.0 22.5 - - - +
761A ILE* 3.1 18.9 - - + +
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Residues in contact with THR 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ALA 3.3 11.3 + - - -
755A GLU* 3.0 16.6 + - - +
757A ILE* 1.3 78.9 - - - +
759A ASN* 1.3 64.7 + - + +
760A GLN 3.1 4.4 + - - -
761A ILE* 4.3 4.7 + - - +
2263N LEU* 5.8 2.9 - - - +
2264N GLU* 4.7 20.0 - - + +
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Residues in contact with ASN 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLN* 3.5 43.1 - - - +
598A TYR* 5.3 4.0 - - - -
600A TRP* 4.4 3.1 - - - +
755A GLU 3.4 3.2 + - - -
758A THR* 1.3 79.2 - - - +
760A GLN* 1.3 59.2 + - - +
761A ILE 4.2 0.7 - - - -
2263N LEU* 3.1 44.2 - - + -
2264N GLU* 4.3 6.5 - - + +
2267N ILE* 5.1 0.4 - - + -
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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