Contacts of the helix formed by residues 754 - 759 (chain B) in PDB entry 5MJ6
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 ASN 754 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B LYS* 3.7 19.5 - - - +
750B PHE 3.7 10.9 + - - +
751B ASP* 3.2 19.5 + - - +
752B LEU 3.0 1.0 - - - -
753B ILE* 1.3 80.7 - - - +
755B TYR* 1.3 57.5 + - - +
756B LEU 3.2 2.1 + - - -
757B GLY* 4.2 4.2 + - - -
794B ARG* 6.1 0.7 - - - -
798B LEU* 4.2 20.9 - - - +
1024B TRP* 5.4 5.9 - - - -
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Residues in contact with TYR 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B ILE* 6.5 0.2 - - + -
716B LEU* 3.8 57.4 - - + +
717B LYS* 4.2 17.8 - - + +
720B PRO* 4.3 9.6 - - + -
728B ARG* 3.4 14.1 - - + +
732B ILE* 4.1 16.1 - - + +
752B LEU* 3.2 26.1 + - + +
753B ILE* 3.0 1.9 - - - -
754B ASN* 1.3 75.0 - - - +
756B LEU* 1.3 77.0 + - + +
757B GLY 2.8 12.8 + - - -
758B ASN* 3.0 19.7 + - + +
759B GLU* 2.8 34.3 + - + -
764B PRO* 3.4 19.4 - - - +
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Residues in contact with LEU 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B ILE* 4.3 7.4 - - + -
753B ILE* 3.1 32.3 + - + +
754B ASN 3.2 0.6 - - - -
755B TYR* 1.3 108.4 - - + +
757B GLY* 1.3 57.9 + - - +
758B ASN 3.1 1.3 + - - -
759B GLU* 3.5 19.6 + - + +
764B PRO 4.8 4.0 - - - +
765B ILE* 5.0 3.8 - - + -
768B ALA* 3.4 30.5 - - + -
795B VAL* 6.1 1.3 - - + -
798B LEU* 4.1 15.0 - - + -
799B LEU* 3.4 27.6 - - + +
802B GLN* 2.8 23.6 + - - -
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Residues in contact with GLY 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754B ASN 4.2 5.1 + - - -
755B TYR 2.8 3.0 + - - -
756B LEU* 1.3 78.9 - - - +
758B ASN* 1.3 67.2 + - - +
759B GLU 3.5 0.4 + - - -
798B LEU* 3.6 20.4 + - - +
801B ASN* 4.7 12.9 + - - +
802B GLN* 3.4 15.4 + - - +
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Residues in contact with ASN 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B LYS* 5.3 7.3 + - - +
720B PRO* 4.6 14.8 - - + +
721B TYR* 3.0 24.1 + - + -
755B TYR* 3.0 13.8 + - - +
757B GLY* 1.3 84.6 - - - +
759B GLU* 1.3 55.8 + - - +
760B ASN* 5.0 0.9 - - - -
1P NAG 5.5 3.4 - - - +
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Residues in contact with GLU 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B PRO* 5.4 0.3 - - - +
721B TYR* 4.8 1.3 - - - -
728B ARG* 2.7 46.4 + - - -
755B TYR* 2.8 23.4 + - + -
756B LEU* 3.5 28.0 + - + +
757B GLY 3.5 3.2 - - - -
758B ASN* 1.3 78.7 - - - +
760B ASN* 1.3 64.2 + - - +
761B HIS* 3.0 23.9 + - - +
764B PRO* 3.6 13.1 - - + +
765B ILE* 3.8 25.3 - - + +
802B GLN* 2.9 27.1 + - - +
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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
------------------------------------------------------------
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