Contacts of the helix formed by residues 347 - 353 (chain A) in PDB entry 5H65
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 PRO 347 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ARG 3.6 8.1 - - - +
346A THR* 1.4 90.7 - - + +
348A LEU* 1.3 65.6 + - - +
349A CYS* 4.1 11.2 - - - -
350A ALA* 3.1 26.0 + - + +
351A ILE* 3.3 5.1 + - - +
550A ASP* 3.4 9.9 - - - +
552A THR* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A THR 3.7 0.6 + - - +
347A PRO* 1.3 67.7 - - - +
349A CYS* 1.3 65.5 + - - +
351A ILE* 3.1 15.1 + - + +
352A LEU* 3.0 30.8 + - + +
362A ILE* 4.1 29.4 - - + -
364A ALA* 4.2 4.0 - - + -
548A LEU* 3.6 22.0 - - + +
549A ASP 4.1 0.2 - - - -
550A ASP* 3.0 46.6 + - + +
552A THR* 3.2 0.8 + - - +
553A GLY* 3.5 23.8 - - - +
554A VAL* 4.5 1.8 - - - +
555A LEU* 4.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 4.1 10.3 - - - -
348A LEU* 1.3 75.8 - - - +
350A ALA* 1.3 74.7 + - - +
352A LEU* 3.6 14.9 + - - +
353A LYS* 3.5 28.3 + - - +
552A THR* 3.1 43.8 + - - +
553A GLY 4.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A THR* 4.0 13.7 - - + -
347A PRO* 3.1 23.3 + - + +
349A CYS* 1.3 82.3 - - - +
351A ILE* 1.3 64.7 + - - +
353A LYS* 3.2 24.6 + - - +
354A GLN* 3.5 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A THR* 3.7 10.3 - - + -
347A PRO 3.3 9.1 + - - +
348A LEU* 3.1 15.7 + - + +
350A ALA* 1.3 77.2 - - - +
352A LEU* 1.3 61.4 + - - +
354A GLN* 3.1 22.2 + - - +
360A TYR* 3.6 49.9 + - + -
362A ILE* 3.4 33.0 - - + -
555A LEU* 4.0 8.5 - - + -
607A ILE* 4.0 8.1 - - + -
622A TYR* 3.5 32.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.0 23.8 + - + +
349A CYS* 4.0 9.6 - - - +
350A ALA 3.3 0.4 - - - -
351A ILE* 1.3 75.2 - - - +
353A LYS* 1.3 60.5 + - + +
354A GLN 3.3 4.4 + - - +
553A GLY* 4.5 2.9 - - - -
554A VAL 3.6 35.7 - - - +
555A LEU* 4.3 15.7 - - + -
620A ILE* 5.9 1.4 - - - +
622A TYR* 3.9 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A CYS* 3.5 24.3 - - + +
350A ALA* 3.2 15.9 + - - +
351A ILE 3.2 1.0 - - - -
352A LEU* 1.3 77.4 - - + +
354A GLN* 1.3 61.7 + - + +
355A LYS* 5.5 1.7 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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