Contacts of the helix formed by residues 729 - 731 (chain D) in PDB entry 5D4D
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 HIS 729 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637D LEU* 3.3 24.8 + - + +
638D LYS 3.3 24.7 - - - +
639D LEU* 3.5 16.7 + - + +
641D GLN 4.4 12.2 + - - +
642D CYS* 5.6 0.2 - - - +
716D PHE* 5.0 1.6 - - + -
728D LEU* 1.3 81.1 - - - +
730D PRO* 1.3 79.6 - - + +
731D LEU* 3.0 53.9 + - + +
732D VAL* 3.2 29.1 - - + +
733D CYS* 3.8 4.7 + - - -
932D ASP* 3.1 22.7 + - - -
935D LYS* 3.8 8.3 - - + +
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Residues in contact with PRO 730 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684C PHE* 3.9 30.9 - - + -
633D VAL* 4.0 15.7 - - + -
634D GLY 4.3 0.7 - - - -
635D PRO* 4.0 15.7 - - + -
728D LEU 3.7 4.2 - - - +
729D HIS* 1.3 101.3 - - + +
731D LEU* 1.3 62.8 + - + +
733D CYS* 3.1 23.7 + - - +
734D GLU 4.6 0.9 + - - -
782D SER* 5.4 1.3 + - - -
785D ILE* 4.7 7.2 - - + -
935D LYS* 4.5 2.7 - - + -
939D PHE* 3.8 34.1 - - + -
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Residues in contact with LEU 731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684C PHE* 6.4 0.2 - - + -
639D LEU* 4.0 13.9 - - + -
729D HIS* 3.0 29.0 + - + +
730D PRO* 1.3 76.9 - - + +
732D VAL* 1.3 60.0 + - - +
733D CYS 3.4 0.2 - - - -
734D GLU* 4.6 5.7 + - - +
735D ALA* 5.1 1.4 + - - +
778D LEU 4.5 2.1 - - - +
779D ALA* 3.7 26.2 - - + +
780D LYS 3.5 29.8 + - - +
781D PRO* 4.3 1.8 - - + -
782D SER* 5.1 1.8 - - - +
785D ILE* 3.7 27.6 - - + -
931D LEU* 3.6 49.6 - - + +
932D ASP* 4.7 0.4 - - - +
935D LYS* 4.6 2.2 - - + -
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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
------------------------------------------------------------
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