Contacts of the helix formed by residues 756 - 760 (chain K) in PDB entry 6R1U
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 ARG 756 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660K GLU* 3.6 6.1 - - - -
721K VAL* 3.0 34.3 + - - +
722K ARG* 4.4 9.3 + - - +
724K LEU 2.8 22.1 + - - -
725K ASP* 3.4 12.5 - - - +
726K ASP* 2.8 28.6 + - - +
729K VAL* 3.6 12.6 - - - +
754K VAL* 3.9 13.2 + - - +
755K THR* 1.3 80.4 + - - +
757K TRP* 1.3 66.0 + - - +
758K SER* 3.1 3.8 - - - -
759K THR* 3.0 26.0 + - - +
760K ASP* 3.2 10.8 + - - +
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Residues in contact with TRP 757 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416K ARG* 3.7 14.1 - - - -
419K GLY 3.4 26.2 - - - -
420K ARG* 3.7 10.8 - - + -
422K TRP* 3.9 17.9 - + + -
434K ARG* 2.9 25.5 + - + -
435K GLY* 3.7 23.3 - - - -
658K ILE* 3.9 7.4 - - + -
659K ILE 4.2 1.1 - - - -
660K GLU* 2.9 24.0 + - - +
755K THR* 3.5 15.8 - - + -
756K ARG* 1.3 76.4 - - - +
758K SER* 1.3 63.4 + - - +
759K THR 3.0 1.4 + - - -
760K ASP* 3.1 22.5 + - + +
763K ILE* 3.6 31.1 - - + +
764K GLN* 3.2 17.8 + - - -
765K MET 3.7 14.8 - - - +
901K FAD 3.5 26.1 - - + +
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Residues in contact with SER 758 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658K ILE* 3.8 21.0 - - - +
660K GLU* 2.9 17.9 + - - -
718K VAL* 5.1 7.6 - - - +
756K ARG* 3.1 1.1 - - - -
757K TRP* 1.3 77.7 - - - +
759K THR* 1.3 65.7 + - - +
764K GLN* 3.5 26.4 + - - +
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Residues in contact with THR 759 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722K ARG* 6.5 1.6 - - + -
756K ARG* 3.0 24.0 + - - +
757K TRP 3.0 0.6 - - - -
758K SER* 1.3 87.3 - - - +
760K ASP* 1.3 63.4 + - - +
761K PRO* 3.2 12.7 - - - +
764K GLN* 5.2 0.9 - - - -
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Residues in contact with ASP 760 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K LYS* 2.9 39.4 + - - -
416K ARG* 4.6 0.9 + - - -
422K TRP* 5.4 4.0 - - - -
756K ARG 3.2 8.6 + - - +
757K TRP* 3.1 25.6 + - + +
759K THR* 1.3 76.0 - - - +
761K PRO* 1.3 69.6 - - - +
762K TRP* 3.3 11.1 + - - +
763K ILE* 3.0 18.8 + - + +
764K GLN* 2.8 31.8 + - - +
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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