Contacts of the helix formed by residues 746 - 751 (chain A) in PDB entry 4N78
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 TYR 746 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A LYS* 4.2 4.9 - - - +
661A MET* 3.7 27.1 - - + -
706A LEU* 4.1 4.9 - - + -
709A GLN* 2.6 49.6 + - + +
710A ILE* 3.6 29.4 - - + -
713A TYR* 3.8 36.3 - + + +
714A TYR* 4.6 7.8 + + + +
744A ASN* 3.1 40.7 + - + -
745A ARG* 1.3 73.2 - - - +
747A GLU* 1.3 68.9 + - - +
748A THR 3.3 2.7 - - - -
749A LEU* 3.0 9.3 + - + +
750A LEU* 2.9 32.0 + - + +
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Residues in contact with GLU 747 (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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662A GLU* 5.1 0.2 - - - +
714A TYR* 4.4 6.9 + - - -
744A ASN 3.5 7.2 - - - +
745A ARG* 3.1 46.6 + - - +
746A TYR* 1.3 97.9 + - - +
748A THR* 1.3 63.8 + - + +
750A LEU* 3.2 13.4 + - - +
751A LYS* 3.0 41.9 + - - +
815A TYR* 3.8 33.8 + - + -
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Residues in contact with THR 748 (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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662A GLU* 3.4 48.4 - - + +
745A ARG* 4.6 8.5 + - - +
747A GLU* 1.3 77.8 - - + +
749A LEU* 1.3 66.5 + - - +
751A LYS* 3.2 23.5 + - + +
752A GLN* 3.4 24.7 + - - +
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Residues in contact with LEU 749 (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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661A MET* 3.6 37.7 - - + +
662A GLU* 5.7 0.4 - - - -
664A VAL* 3.8 16.6 - - + -
665A LEU* 3.7 35.0 - - + -
702A PHE* 4.5 0.4 - - + -
706A LEU* 3.6 38.8 - - + -
710A ILE* 5.4 0.9 - - + -
746A TYR* 3.0 12.4 + - + +
748A THR* 1.3 84.4 + - - +
750A LEU* 1.3 65.3 + - + +
751A LYS 3.0 1.3 + - - -
752A GLN* 3.2 20.0 + - - +
764A LEU* 3.7 24.1 - - + +
765A ASN 4.9 0.5 + - - -
768A ILE* 4.9 0.9 - - - -
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Residues in contact with LEU 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ILE* 3.6 30.7 - - + -
714A TYR* 4.3 14.6 - - + +
746A TYR* 2.9 31.5 + - + +
747A GLU* 3.2 8.0 + - - +
749A LEU* 1.3 75.6 - - - +
751A LYS* 1.3 57.8 + - - +
752A GLN 3.4 0.2 - - - -
765A ASN* 2.6 36.3 + - - +
768A ILE* 3.8 24.2 - - + -
812A LEU* 6.1 1.1 - - + -
815A TYR* 3.9 41.0 - - + +
816A LEU* 3.9 16.8 - - + -
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Residues in contact with LYS 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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747A GLU* 3.0 39.1 + - - +
748A THR* 3.6 15.7 - - + +
749A LEU 3.0 1.2 - - - -
750A LEU* 1.3 81.1 - - + +
752A GLN* 1.3 63.8 + - - +
753A ARG* 3.1 19.3 + - - +
765A ASN* 5.0 0.4 - - - +
815A TYR* 4.9 15.0 - - + -
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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