Contacts of the helix formed by residues 750 - 756 (chain A) in PDB entry 3H0G
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 LYS 750 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A GLU* 3.6 33.7 + - + +
741A HIS* 5.4 1.6 - - - +
743A LEU* 3.1 38.3 + - + +
744A LYS 4.0 5.8 - - - +
745A ASP* 3.5 25.4 + - - +
747A ASN* 3.1 23.6 - - - +
748A ASN 2.7 7.9 + - - -
749A VAL* 1.3 77.1 - - + +
751A GLN* 1.3 58.4 + - - +
753A VAL* 3.5 6.2 + - + +
754A ALA* 3.1 23.4 + - - +
764A ILE* 5.1 9.2 - - + -
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Residues in contact with GLN 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ARG* 3.0 39.5 - - - +
539A LYS* 3.5 27.9 + - - +
668A PHE* 3.0 32.3 - - + -
745A ASP 4.4 7.1 + - - +
746A SER* 4.3 17.1 - - - +
747A ASN 3.3 3.2 + - - +
748A ASN* 3.1 25.2 - - - +
750A LYS* 1.3 76.7 - - - +
752A MET* 1.3 66.5 + - - +
753A VAL 3.0 2.2 - - - -
754A ALA* 3.8 6.9 - - - +
755A ALA* 3.0 25.5 + - - +
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Residues in contact with MET 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ALA* 5.1 5.8 - - + -
668A PHE* 3.1 40.8 - - + -
670A ILE* 3.3 30.1 - - + -
749A VAL* 3.8 19.9 - - - +
750A LYS 3.4 0.2 - - - -
751A GLN* 1.3 82.8 - - - +
753A VAL* 1.3 61.3 + - + +
755A ALA* 3.9 3.3 - - - +
756A GLY 3.6 1.0 + - - -
757A SER* 2.7 48.7 + - - +
758A LYS* 3.7 17.9 + - + +
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Residues in contact with VAL 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A VAL* 3.1 23.3 - - + +
750A LYS* 3.5 6.9 + - + +
751A GLN 3.0 0.4 - - - -
752A MET* 1.3 77.6 - - + +
754A ALA* 1.3 69.8 + - - +
755A ALA 3.0 1.3 - - - -
756A GLY* 2.8 17.1 + - - +
758A LYS 3.8 5.8 - - - +
759A GLY 3.5 33.9 - - - +
760A SER* 4.0 19.3 - - - +
761A PHE 4.5 3.1 - - - +
763A ASN* 6.1 0.9 - - + -
764A ILE* 5.1 10.8 - - + -
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Residues in contact with ALA 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ARG* 4.2 18.4 - - - +
624A ASP* 4.1 12.0 - - - +
626A LYS* 5.6 2.4 - - - -
750A LYS 3.1 14.5 + - - +
751A GLN* 3.2 5.8 + - - +
753A VAL* 1.3 81.7 - - - +
755A ALA* 1.3 65.6 + - - +
756A GLY* 4.2 0.3 - - - -
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Residues in contact with ALA 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A LEU* 4.1 7.4 - - + +
535A ALA* 3.9 28.0 - - - +
538A ARG* 4.1 19.2 - - + +
624A ASP* 3.5 10.3 - - - +
625A LYS* 3.0 29.5 + - - +
626A LYS* 6.0 0.2 - - - +
751A GLN 3.0 16.2 + - - +
752A MET 3.9 6.3 - - - +
753A VAL 3.0 0.2 - - - -
754A ALA* 1.3 80.2 - - - +
756A GLY* 1.3 57.6 + - - +
757A SER 3.4 4.0 - - - +
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Residues in contact with GLY 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A LEU* 4.2 2.0 - - - -
625A LYS* 3.5 32.7 + - - -
752A MET 4.1 0.7 - - - -
753A VAL 2.8 20.8 + - - -
754A ALA 4.2 0.9 - - - -
755A ALA* 1.3 73.6 - - - +
757A SER* 1.3 68.5 + - - +
758A LYS* 2.9 6.8 + - - -
759A GLY 5.0 2.8 + - - +
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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