Contacts of the helix formed by residues 752 - 758 (chain A) in PDB entry 1EJ9
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 PHE 752 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A ASP* 4.4 10.8 - - - -
444A TYR* 5.2 0.9 - + - -
720A LYS 3.8 19.3 - - - -
721A LEU* 3.8 18.2 - - + -
724A LEU 4.6 2.7 - - - -
726A PRO* 3.3 39.9 - - + -
744A TYR* 3.5 44.6 - + + -
748A GLN* 2.7 33.6 + - + +
749A ARG 3.5 1.6 - - - -
751A LYS* 1.3 98.5 - - + +
753A ALA* 1.3 51.9 + - - +
754A TRP* 3.1 12.8 - - - +
755A ALA* 2.8 8.8 + - + +
756A ILE* 2.7 37.0 + - + -
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Residues in contact with ALA 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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206A TRP* 3.8 17.6 - - + -
749A ARG 2.7 20.6 + - - +
750A GLU* 3.7 12.8 - - - +
751A LYS 3.3 3.4 + - - -
752A PHE* 1.3 72.2 - - - +
754A TRP* 1.3 54.1 + - - +
756A ILE* 3.5 9.5 - - + +
757A ASP* 2.7 36.2 + - - +
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Residues in contact with TRP 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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205A TRP* 4.0 21.5 - + + -
206A TRP* 3.8 39.6 - - + -
437A GLY* 4.5 10.6 + - - -
440A ASP* 4.7 7.6 + - - +
441A TRP* 3.5 57.2 - + + -
444A TYR* 4.3 11.2 - + - -
726A PRO* 3.5 31.4 - - + -
727A ARG* 3.8 26.0 - - + -
751A LYS 3.4 24.4 + - - -
752A PHE* 3.7 10.1 - + - +
753A ALA* 1.3 78.3 - - - +
755A ALA* 1.3 78.8 + - + +
757A ASP* 3.5 0.7 - - - +
758A MET* 2.8 35.1 + - + +
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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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726A PRO* 3.3 40.2 - - + +
727A ARG* 3.8 19.7 - - + +
730A VAL* 3.7 4.1 - - + +
752A PHE* 2.8 8.7 + - + +
754A TRP* 1.3 91.7 - - + +
756A ILE* 1.3 66.7 + - - +
758A MET* 3.5 2.8 + - - -
759A ALA* 3.2 25.1 - - - +
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Residues in contact with ILE 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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730A VAL* 3.6 20.3 - - + +
734A LYS* 3.7 19.2 + - - -
740A ILE* 3.7 35.0 - - + -
744A TYR* 4.6 4.5 - - + -
749A ARG* 3.8 42.2 - - + +
752A PHE* 2.7 23.2 + - + +
753A ALA* 3.6 9.6 - - + +
755A ALA* 1.3 78.3 - - - +
757A ASP* 1.3 62.4 + - + +
758A MET 3.3 0.3 + - - -
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Residues in contact with ASP 757 (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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204A LYS* 4.0 14.4 - - - +
206A TRP* 3.2 33.8 + - + +
207A GLU* 3.3 15.2 - - - +
734A LYS* 5.1 1.9 + - - -
753A ALA 2.7 21.3 + - - +
754A TRP 2.9 0.4 + - - -
756A ILE* 1.3 75.3 - - + +
758A MET* 1.3 59.1 + - - +
759A ALA 3.7 1.6 + - - -
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Residues in contact with MET 758 (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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206A TRP* 4.1 28.0 - - + +
441A TRP* 3.4 43.5 - - + -
727A ARG* 4.7 14.0 - - - -
754A TRP* 2.8 46.2 + - + +
755A ALA* 4.3 1.1 - - - +
756A ILE 3.3 0.6 - - - -
757A ASP* 1.3 76.2 - - - +
759A ALA* 1.3 60.8 + - - +
763A TYR* 6.1 0.2 - - - -
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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