Contacts of the helix formed by residues 744 - 751 (chain A) in PDB entry 7ACN
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 ALA 744 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ALA* 5.4 3.6 - - + -
188A ASP* 5.3 2.0 - - - +
674A LYS* 2.8 53.1 + - + +
738A TRP* 3.8 28.7 - - + +
743A SER* 1.3 67.7 - - - +
745A LEU* 1.3 59.1 + - - +
747A ARG* 3.1 4.7 + - - +
748A MET* 2.9 30.8 + - - +
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Residues in contact with LEU 745 (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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82A GLN* 3.5 47.6 - - + +
85A SER* 3.7 28.3 - - - +
86A SER* 4.4 18.8 - - - +
184A ALA* 6.2 1.3 - - + +
187A VAL* 4.5 13.5 - - + -
541A LEU* 4.9 4.9 - - + -
675A GLN* 6.1 1.1 - - - +
743A SER* 3.4 7.8 + - - +
744A ALA* 1.3 78.6 - - - +
746A ASN* 1.4 58.5 + - - +
748A MET* 3.3 13.6 + - + +
749A LYS* 3.0 36.1 + - + +
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Residues in contact with ASN 746 (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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543A PRO* 3.5 24.6 - - - +
544A PHE 2.9 28.3 + - - +
546A LYS* 3.6 14.4 + - - +
741A ALA 2.9 28.2 + - - +
742A GLY* 3.6 6.3 - - - -
743A SER* 3.2 22.0 + - - +
745A LEU* 1.4 79.9 - - - +
747A ARG* 1.3 58.1 + - - +
749A LYS* 3.5 8.5 + - - +
750A GLU* 3.1 29.5 + - - +
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Residues in contact with ARG 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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737A GLU* 3.5 63.3 + - + +
738A TRP* 4.1 9.0 - - + +
741A ALA* 3.8 8.3 - - + +
743A SER 3.2 9.5 + - - +
744A ALA* 3.2 12.8 - - - +
746A ASN* 1.3 77.1 - - - +
748A MET* 1.3 65.5 + - - +
749A LYS 3.2 0.2 - - - -
750A GLU* 3.0 40.0 + - - +
751A LEU* 3.1 46.2 + - - +
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Residues in contact with MET 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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86A SER* 4.0 26.5 - - - -
88A LEU* 4.7 2.5 - - + -
187A VAL* 4.0 19.7 - - + -
188A ASP* 3.8 23.6 - - - +
191A ALA* 4.3 23.3 - - + -
193A ILE* 4.6 15.5 - - + -
744A ALA 2.9 14.0 + - - +
745A LEU* 3.6 17.3 - - + +
747A ARG* 1.3 75.4 - - - +
749A LYS* 1.3 62.7 + - + +
751A LEU* 3.2 22.0 + - + +
752A GLN* 3.3 23.9 + - + +
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Residues in contact with LYS 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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85A SER* 3.1 27.0 + - - +
86A SER* 2.7 25.9 + - - +
87A GLY* 4.6 2.0 - - - -
745A LEU* 3.0 20.5 + - + +
746A ASN* 3.7 8.3 - - - +
747A ARG 3.2 0.2 - - - -
748A MET* 1.3 79.7 - - + +
750A GLU* 1.3 57.1 + - - +
752A GLN* 2.6 38.8 + - - +
754A LYS* 2.6 43.0 + - - +
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Residues in contact with GLU 750 (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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546A LYS* 2.6 30.5 + - - +
737A GLU* 4.8 1.6 - - - +
741A ALA* 3.6 16.0 - - - +
746A ASN 3.1 20.3 + - - +
747A ARG* 3.0 37.7 + - - +
749A LYS* 1.3 75.4 - - - +
751A LEU* 1.3 63.3 + - - +
752A GLN 2.9 1.6 + - - -
753A GLN* 3.3 7.6 + - - -
754A LYS 3.2 20.8 + - - +
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Residues in contact with LEU 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 ARG* 3.1 47.1 + - - +
748A MET* 3.2 13.4 + - + +
750A GLU* 1.3 75.8 - - - +
752A GLN* 1.3 56.2 + - + +
753A GLN* 2.9 9.5 + - - +
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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