Contacts of the helix formed by residues 375 - 379 (chain A) in PDB entry 4X2N
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 THR 375 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ARG* 3.2 8.3 + - - +
333A ASP* 2.7 23.8 + - - +
335A LYS* 2.8 39.0 + - + +
374A GLY* 1.3 69.8 - - - -
376A LYS* 1.3 67.3 + - - +
377A ARG 4.4 2.5 - - - +
378A TYR* 3.2 28.4 + - + +
379A MET* 3.4 12.7 + - - +
601A SO4 4.1 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.5 9.3 + - - -
375A THR* 1.3 72.5 - - - +
377A ARG* 1.3 64.5 + - - +
378A TYR 3.2 0.7 + - - -
379A MET* 3.2 37.6 + - + +
384A LEU* 4.1 2.3 - - - +
435A ASP* 5.6 2.9 - - - +
436A PRO* 3.3 28.5 - - + +
437A SER* 4.2 4.7 - - - +
438A VAL* 3.8 32.1 - - + +
441A MET* 3.4 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR* 3.3 2.0 - - + +
376A LYS* 1.3 78.0 - - - +
378A TYR* 1.3 78.7 + - + +
379A MET 3.5 1.8 - - - +
402A TYR* 4.8 0.3 + - - -
406A LEU* 3.9 5.4 - - - +
426A LEU* 3.9 28.7 - - - +
427A PRO* 2.9 35.1 + - + +
428A TYR* 3.8 20.7 - - + -
429A TYR* 4.0 5.1 - - - +
432A VAL* 3.7 16.9 + - - +
433A PRO 3.4 21.2 + - - -
434A SER* 3.8 5.9 - - - +
436A PRO* 3.7 11.6 - - + +
441A MET* 3.5 27.3 - - - +
601A SO4 2.8 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASP* 5.8 0.7 - - - +
334A LEU 3.7 22.9 - - - +
335A LYS* 3.5 33.2 - - + -
336A SER* 3.3 14.4 + - - -
337A LYS 5.2 0.2 + - - -
375A THR* 3.2 21.3 + - + +
376A LYS 3.2 0.8 - - - -
377A ARG* 1.3 98.1 - - + +
379A MET* 1.3 63.0 + - - +
380A ALA 3.5 2.1 + - - -
399A ALA 5.0 0.9 - - - +
402A TYR* 3.6 14.8 - - - -
403A ALA* 3.9 16.4 - - + +
406A LEU* 3.9 21.8 - - + -
407A VAL* 4.0 6.7 - - + -
410A GLU* 2.6 33.1 + - - -
426A LEU* 3.5 12.9 - - + +
427A PRO* 4.0 12.8 - - + -
601A SO4 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ARG* 3.5 34.8 - - + -
373A VAL 3.5 18.8 - - - +
374A GLY* 3.4 24.7 - - - +
375A THR 3.4 9.4 + - - +
376A LYS* 3.2 38.9 + - + +
377A ARG 3.5 1.8 - - - +
378A TYR* 1.3 75.4 - - - +
380A ALA* 1.3 64.1 + - - +
381A PRO 3.9 0.2 - - - -
383A VAL* 3.8 14.6 - - + -
384A LEU* 3.6 34.3 - - + +
402A TYR* 3.4 12.3 + - - -
438A VAL* 4.3 2.9 - - + -
441A MET* 5.8 0.3 - - - +
445A VAL* 5.4 0.2 - - - +
----------------------------------------------------------
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