Contacts of the helix formed by residues 731 - 735 (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 GLU 731 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720C GLN* 4.0 25.1 + - - +
726D GLY 4.4 6.3 - - - +
729D MET* 3.0 34.8 + - - +
730D TRP* 1.3 78.0 - - - +
732D LYS* 1.3 84.6 + - + +
734D ASP* 3.2 20.8 + - - +
735D GLN* 4.1 7.2 - - - +
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Residues in contact with LYS 732 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589C PRO* 3.8 7.6 - - - +
731D GLU* 1.3 83.9 - - + +
733D ASN* 1.3 68.6 + - + +
735D GLN* 2.9 37.8 + - - +
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Residues in contact with ASN 733 (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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589C PRO* 3.6 30.0 - - + +
590C HIS* 4.8 15.9 + - - -
732D LYS* 1.3 86.5 - - + +
734D ASP* 1.3 62.9 + - - +
735D GLN 3.2 0.9 - - - -
736D SER* 4.1 6.8 - - - -
739D ILE* 4.3 7.6 - - - +
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Residues in contact with ASP 734 (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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692D HIS* 3.3 34.5 + - - -
728D ASP* 5.6 2.8 + - - -
729D MET 5.6 0.2 + - - -
730D TRP* 3.4 50.9 + - + -
731D GLU 3.4 14.2 + - - +
732D LYS 3.0 1.2 + - - -
733D ASN* 1.3 77.8 - - - +
735D GLN* 1.3 52.0 + - - +
736D SER* 2.7 20.9 + - - +
739D ILE* 4.5 11.8 - - + +
740D MET* 4.9 0.2 - - - +
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Residues in contact with GLN 735 (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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588C LEU 3.4 3.8 - - - -
589C PRO* 3.1 25.6 - - + +
592C HIS* 3.9 15.7 + - - +
595C ARG* 3.7 17.4 + - - +
717C MET* 3.4 36.7 + - + +
718C GLU* 3.1 31.9 + - - +
719C ARG 4.8 1.6 - - - +
730D TRP* 3.0 30.4 + - + +
731D GLU* 4.2 4.6 - - - +
732D LYS* 2.9 29.1 + - - +
733D ASN 3.2 0.2 - - - -
734D ASP* 1.3 71.7 - - - +
736D SER* 1.3 56.5 - - - +
740D MET* 5.3 2.9 - - - -
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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