Contacts of the helix formed by residues 587 - 590 (chain C) 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 587 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583C LEU 3.5 17.9 - - - +
584C GLU* 2.7 17.3 + - - +
586C ILE* 1.3 76.4 - - - +
588C LEU* 1.3 69.5 + - - +
713C LEU* 5.1 0.7 - - + -
717C MET* 4.4 1.1 - - - -
747C ALA* 3.8 15.0 - - + +
748C ARG* 6.2 0.4 - - - -
750C MET* 3.6 20.0 - - + -
751C ALA* 4.0 13.4 - - + +
736D SER* 3.8 2.3 + - - -
737D CYS* 3.0 52.4 + - - +
738D GLU 4.7 0.5 + - - -
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Residues in contact with LEU 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579C VAL* 4.8 15.0 - - + -
584C GLU* 3.6 22.0 - - + +
585C LEU* 3.2 22.7 + - + +
587C THR* 1.3 90.0 - - - +
589C PRO* 1.3 74.4 - - + +
590C HIS* 3.2 10.3 - - + +
591C GLY 3.0 6.0 + - - +
595C ARG* 2.7 27.7 + - - -
735D GLN 3.4 4.0 - - - -
736D SER* 6.0 0.9 - - - +
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Residues in contact with PRO 589 (chain C).
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* 1.3 88.8 - - + +
590C HIS* 1.3 68.4 + - + +
591C GLY 2.9 5.9 + - - -
592C HIS* 3.1 18.0 + - - +
595C ARG* 3.2 8.6 + - - +
732D LYS 3.8 17.7 - - - +
733D ASN* 3.6 40.2 - - - +
735D GLN* 3.1 21.7 - - - +
736D SER* 4.2 11.2 - - - -
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Residues in contact with HIS 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C LEU* 4.4 18.6 - - + +
588C LEU* 3.2 7.0 - - + +
589C PRO* 1.3 85.3 - - + +
591C GLY* 1.3 56.0 + - - +
592C HIS* 3.1 7.2 + - - +
593C GLN* 4.5 5.7 + - - +
733D ASN* 4.8 17.5 + - - -
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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