Contacts of the helix formed by residues 752 - 759 (chain D) 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 MET 752 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528B LEU* 3.5 36.8 - - + +
529B THR 4.2 1.3 - - - +
530B PRO* 3.6 25.6 - - + +
535B LEU* 6.2 0.9 - - + -
2D 486 4.2 11.0 - - - -
564D ASN* 6.1 2.7 - - + +
568D GLY* 6.5 0.7 - - - -
751D GLU* 1.3 87.6 - - - +
753D LEU* 1.3 67.0 + - - +
754D ALA* 3.1 2.8 + - - +
755D GLU* 3.4 17.3 + - - +
756D ILE* 3.7 11.7 - - - +
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Residues in contact with LEU 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D 486 3.0 39.5 - - + +
564D ASN* 4.7 9.1 - - - +
600D TRP* 6.1 1.6 - - + -
739D THR* 6.2 2.0 - - + -
752D MET* 1.3 75.8 - - - +
754D ALA* 1.3 58.7 + - - +
755D GLU 3.3 0.2 - - - -
756D ILE* 3.5 7.6 + - - +
757D ILE* 3.0 45.8 + - + +
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Residues in contact with ALA 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B LEU* 4.4 9.9 - - + -
582C PRO* 5.8 1.3 - - + -
740D PHE* 3.3 35.0 - - + -
751D GLU* 3.3 31.9 - - + -
752D MET 3.1 0.8 - - - +
753D LEU* 1.3 76.7 - - - +
755D GLU* 1.3 62.0 + - - +
757D ILE* 4.6 0.2 - - - +
758D THR* 2.9 29.9 + - - -
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Residues in contact with GLU 755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C PRO* 4.9 15.0 - - + -
583C GLY* 5.6 3.6 + - - +
586C ASN* 5.7 0.5 - - - +
751D GLU* 4.3 10.7 + - - +
752D MET 3.4 12.8 + - - +
753D LEU 3.3 0.6 - - - -
754D ALA* 1.3 80.5 - - - +
756D ILE* 1.3 65.9 + - + +
758D THR* 3.4 12.0 + - - -
759D ASN* 3.5 14.2 + - - +
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Residues in contact with ILE 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D 486 4.9 12.6 - - - -
571D VAL* 5.4 11.7 - - + -
600D TRP* 3.8 40.4 - - + +
752D MET 3.7 17.0 - - - +
753D LEU* 3.5 9.3 + - - +
754D ALA 3.4 0.2 - - - -
755D GLU* 1.3 82.3 - - + +
757D ILE* 1.3 59.7 + - + +
758D THR 3.5 0.2 - - - -
759D ASN* 3.3 8.3 + - + +
760D GLN* 3.1 35.1 + - + +
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Residues in contact with ILE 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D TRP* 6.1 3.8 - - + -
736D CYS* 3.3 37.5 - - + +
737D PHE* 3.9 19.2 - - + -
739D THR* 4.1 15.7 - - + +
740D PHE* 3.6 34.3 - - + -
753D LEU* 3.0 37.8 + - + +
754D ALA 3.3 3.3 + - - +
756D ILE* 1.3 77.6 - - + +
758D THR* 1.3 65.2 + - - +
760D GLN* 3.5 5.8 + - - +
761D ILE* 3.3 23.7 + - + +
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Residues in contact with THR 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C PRO* 4.9 2.8 + - - +
583C GLY* 4.5 10.9 + - - -
685C LEU* 3.4 17.8 - - - +
688C ALA* 3.9 27.2 - - + +
689C ILE* 4.1 16.4 - - + +
692C THR* 3.8 12.6 - - + +
740D PHE* 3.6 25.6 - - + -
754D ALA 2.9 16.6 + - - -
755D GLU* 3.4 9.4 + - - -
757D ILE* 1.3 74.1 - - - +
759D ASN* 1.3 55.9 + - - +
760D GLN 3.1 5.2 + - - -
761D ILE 3.7 15.4 + - - +
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Residues in contact with ASN 759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C GLY* 6.2 1.1 - - - -
586C ASN* 5.3 14.6 - - + +
685C LEU* 4.2 12.3 - - + -
597D GLN* 4.2 16.9 + - - +
755D GLU 3.5 16.4 + - - +
756D ILE* 3.3 9.8 + - - +
757D ILE 3.3 0.8 - - - -
758D THR* 1.3 76.1 - - - +
760D GLN* 1.3 62.9 + - - +
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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