Contacts of the helix formed by residues 783 - 791 (chain A) in PDB entry 4PE5
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 GLY 783 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A ASN* 1.3 80.0 + - - +
784A PHE* 1.3 59.2 + - - -
785A MET 3.6 1.1 - - - -
786A GLU* 3.8 14.8 - - - +
787A ASP* 2.9 35.6 + - - +
698D ASN* 5.3 2.4 - - - +
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Residues in contact with PHE 784 (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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461A ASP* 5.1 3.8 - - + -
462A LEU* 4.8 4.3 - - + -
465A LYS* 3.5 31.6 - - + -
779A SER* 3.3 29.4 - - - +
782A ASN* 2.8 20.3 + - - +
783A GLY* 1.3 75.6 - - - +
785A MET* 1.3 63.8 + - - +
787A ASP* 3.2 8.5 + - - +
788A LEU* 2.9 61.3 + - + +
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Residues in contact with MET 785 (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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458A PHE* 4.3 7.6 - - - -
462A LEU* 3.8 23.1 - - + -
533A PHE* 3.9 21.8 - - + +
776A ILE* 4.0 4.5 - - + -
779A SER* 3.4 37.5 + - - +
780A HIS* 3.5 43.1 - - + +
782A ASN 4.9 1.3 + - - +
784A PHE* 1.3 76.0 - - - +
786A GLU* 1.3 59.4 + - - +
788A LEU* 3.6 22.4 - - - +
789A ASP* 2.9 41.0 + - - +
759D SER* 4.6 6.3 - - - +
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Residues in contact with GLU 786 (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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782A ASN 5.2 1.7 + - - +
783A GLY* 3.8 19.8 + - - +
784A PHE 3.1 0.2 - - - -
785A MET* 1.3 79.6 - - - +
787A ASP* 1.3 60.4 + - - +
789A ASP* 3.3 6.5 + - - +
790A LYS* 2.9 30.6 + - - +
757D PHE* 6.1 2.7 - - + -
758D ALA 5.6 8.1 - - - +
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Residues in contact with ASP 787 (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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783A GLY 2.9 18.4 + - - +
784A PHE* 3.2 6.9 + - - +
786A GLU* 1.3 77.1 - - - +
788A LEU* 1.3 59.1 + - + +
790A LYS* 3.4 7.1 + - - +
791A THR* 2.7 41.2 + - + +
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Residues in contact with LEU 788 (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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458A PHE* 3.5 28.0 - - + +
461A ASP* 4.4 22.4 - - + +
462A LEU* 4.6 13.9 - - + -
784A PHE* 2.9 49.1 + - + +
785A MET* 3.6 25.6 - - - +
786A GLU 3.3 0.2 - - - -
787A ASP* 1.3 80.5 - - + +
789A ASP* 1.3 60.6 + - - +
791A THR* 3.7 3.4 - - - +
792A TRP* 3.0 40.9 + - + +
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Residues in contact with ASP 789 (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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458A PHE* 3.4 22.5 - - - -
785A MET* 2.9 21.8 + - - +
786A GLU* 3.7 6.3 - - - +
787A ASP 3.2 0.2 - - - -
788A LEU* 1.3 73.0 - - - +
790A LYS* 1.3 54.9 + - - +
791A THR 3.1 5.2 - - - -
793A VAL* 2.9 29.6 + - + +
794A ARG* 2.4 37.2 + - + +
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Residues in contact with LYS 790 (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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786A GLU 2.9 18.0 + - - +
787A ASP* 3.4 9.6 + - - +
789A ASP* 1.3 75.6 - - - +
791A THR* 1.3 63.8 + - + +
794A ARG* 3.7 14.9 - - + +
795A TYR* 4.4 9.9 + - - +
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Residues in contact with THR 791 (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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425A THR* 5.3 17.9 - - + +
787A ASP* 2.7 25.0 + - + +
788A LEU* 3.7 2.9 - - - +
789A ASP 3.1 0.2 - - - -
790A LYS* 1.3 84.1 - - + +
792A TRP* 1.3 91.1 + - - +
795A TYR* 4.3 10.3 - - - +
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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