Contacts of the helix formed by residues 723 - 727 (chain D) in PDB entry 3T6A
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 723 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599D ILE* 4.4 2.5 - - + -
603D ASN* 3.5 17.0 - - - +
711D MET* 4.2 19.3 - - + -
715D THR* 4.4 13.9 - - + -
721D ALA 3.9 1.9 + - - +
722D VAL* 1.3 82.1 - - - +
724D PHE* 1.3 64.4 + - - +
725D GLU 3.3 1.2 + - - -
726D GLY* 3.3 10.2 + - - -
727D THR* 2.8 43.5 + - - +
728D ASP* 4.8 1.3 - - + +
729D MET* 3.7 15.1 - - + +
801D TYR* 3.7 8.0 - - - +
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Residues in contact with PHE 724 (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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603D ASN* 3.3 13.6 + - + +
607D ILE* 3.4 35.2 - - + -
652D LYS* 2.9 31.0 + - - +
656D MET* 3.5 36.3 - - + -
723D THR* 1.3 71.5 - - - +
725D GLU* 1.3 98.7 + - + +
726D GLY 3.3 0.7 + - - -
727D THR* 3.5 5.7 + - - -
801D TYR* 3.2 42.9 - - + -
804D PHE 4.0 1.8 - - - -
805D ASN* 3.6 18.4 - - + -
808D LEU* 3.8 20.4 - - + -
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Residues in contact with GLU 725 (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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652D LYS* 5.4 0.6 - - - -
656D MET* 4.0 7.7 - - - +
657D PRO* 2.9 30.2 - - - +
658D GLN* 2.7 39.1 + - - +
723D THR 3.3 1.8 + - - -
724D PHE* 1.3 106.4 - - + +
726D GLY* 1.3 62.7 + - - +
727D THR* 3.0 13.6 + - + +
801D TYR* 5.4 1.2 - - - +
805D ASN* 3.1 15.7 - - - +
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Residues in contact with GLY 726 (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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723D THR* 3.3 15.2 + - - -
724D PHE 3.2 2.6 - - - -
725D GLU* 1.3 76.9 - - - +
727D THR* 1.3 61.6 + - - +
729D MET* 3.2 28.2 + - - +
731D GLU* 4.4 6.9 - - - +
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Residues in contact with THR 727 (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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652D LYS* 2.9 44.7 + - + -
723D THR* 2.8 25.0 + - - +
724D PHE 3.5 2.3 + - - +
725D GLU* 3.7 16.2 - - + +
726D GLY* 1.3 73.4 - - - +
728D ASP* 1.3 81.6 + - - +
729D MET 3.0 3.9 + - - -
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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