Contacts of the helix formed by residues 347 - 360 (chain A) in PDB entry 4P6Q
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 347 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ARG 5.0 3.4 - - - +
346A SER* 1.3 77.7 - - - +
348A ASP* 1.3 65.9 + - - +
349A THR* 3.8 6.4 + - - -
350A SER* 2.5 34.5 + - - +
351A LEU* 3.2 22.3 + - - +
377A ARG* 3.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A THR* 1.3 73.4 - - - +
349A THR* 1.3 59.6 + - - +
351A LEU* 3.2 3.8 + - - +
352A LYS* 2.9 29.8 + - - +
370A ILE* 3.5 38.2 - - + +
372A GLY* 4.9 7.4 + - - -
377A ARG* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A THR* 3.3 6.6 + - - -
348A ASP* 1.3 79.4 - - - +
350A SER* 1.3 63.7 + - - +
352A LYS* 3.2 9.0 + - + +
353A ASP* 3.0 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A SER* 4.5 9.1 - - - -
347A THR* 2.5 38.2 + - - +
349A THR* 1.3 76.3 - - - +
351A LEU* 1.3 58.1 + - - +
353A ASP* 3.5 5.0 + - - +
354A GLY* 2.9 26.3 + - - -
402A PHE* 3.9 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.9 19.1 - - + -
343A PRO* 4.1 13.7 - - + +
346A SER* 3.7 12.3 - - - +
347A THR 3.2 8.4 + - - +
348A ASP* 3.6 6.7 - - - +
350A SER* 1.3 77.1 - - - +
352A LYS* 1.3 57.3 + - - +
355A LEU* 2.7 40.8 + - + +
370A ILE* 4.0 13.5 - - + -
377A ARG* 3.5 49.1 - - - +
401A PHE* 4.2 10.5 - - + -
402A PHE* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP 2.9 17.3 + - - +
349A THR* 3.2 10.1 + - + +
351A LEU* 1.3 74.7 - - - +
353A ASP* 1.3 70.2 + - - +
355A LEU 3.5 0.2 + - - -
356A PHE* 3.0 23.9 + - + +
368A VAL* 3.5 42.7 + - + +
369A GLN* 5.6 0.4 - - - -
370A ILE* 3.8 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR* 3.0 34.0 + - - +
350A SER* 3.9 4.5 - - - +
352A LYS* 1.3 85.4 - - - +
354A GLY* 1.3 57.9 + - - +
356A PHE* 3.4 8.8 + - - +
357A HIS* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A SER 2.9 16.5 + - - -
351A LEU 3.6 2.2 - - - -
353A ASP* 1.3 76.5 - - - +
355A LEU* 1.3 55.8 + - - +
357A HIS* 3.3 5.8 + - - +
358A GLU* 2.8 31.2 + - - +
401A PHE* 3.6 8.0 - - - -
402A PHE* 4.0 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL* 4.0 18.8 - - + -
342A LEU* 4.6 9.4 - - + -
351A LEU 2.7 18.8 + - - +
352A LYS 3.9 3.6 - - - +
354A GLY* 1.3 70.6 - - - +
356A PHE* 1.3 57.6 + - - +
359A PHE* 2.8 59.8 + - + +
368A VAL* 4.1 11.9 - - + -
370A ILE* 3.8 28.7 - - + -
379A GLY* 3.8 19.5 - - - -
381A VAL* 4.1 12.3 - - + -
401A PHE* 3.5 28.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS* 3.0 18.3 + - + +
353A ASP* 3.6 7.9 - - - +
355A LEU* 1.3 78.0 - - - +
357A HIS* 1.3 66.7 + - + +
359A PHE* 5.4 0.2 - - - -
360A LYS* 3.0 72.2 + - + +
365A VAL* 3.8 41.9 - - + +
368A VAL* 4.1 14.0 - - + +
381A VAL* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP 2.9 16.6 + - - +
354A GLY* 3.7 6.2 + - - +
356A PHE* 1.3 80.4 - - + +
358A GLU* 1.3 66.4 + - - +
360A LYS* 3.9 19.6 - - + +
361A LYS* 3.8 18.6 - - - +
701A SO4 3.2 41.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLY 2.8 17.2 + - - +
355A LEU 3.9 3.1 - - - +
357A HIS* 1.3 81.8 + - - +
359A PHE* 1.3 68.8 + - + +
361A LYS* 3.3 47.4 + - - +
362A PHE* 4.3 5.0 - - - -
399A LYS* 3.1 37.8 + - + +
400A LEU 5.3 3.8 - - - +
401A PHE* 4.1 25.3 - - + -
701A SO4 4.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 3.4 28.9 - - + -
339A VAL* 4.1 9.6 - - + -
355A LEU* 2.8 51.6 + - + +
358A GLU* 1.3 81.3 - - + +
360A LYS* 1.3 59.9 + - - +
361A LYS 3.0 5.6 + - - -
362A PHE* 3.2 37.2 + + - -
365A VAL* 3.8 2.9 - - + -
381A VAL* 3.8 29.2 - - + -
383A PHE* 3.3 18.2 - - + -
392A ALA* 4.2 4.7 - - + -
396A SER* 4.4 12.1 - - - -
399A LYS* 4.3 13.5 - - + -
401A PHE* 5.2 0.7 - + - -
406A ILE* 4.1 23.8 - - + -
408A VAL* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 3.0 58.4 + - + +
357A HIS* 3.9 20.9 - - + +
359A PHE* 1.3 76.2 - - - +
361A LYS* 1.3 65.8 + - + +
362A PHE 3.1 0.7 - - - -
363A GLY* 2.9 25.1 + - - +
364A LYS* 5.9 0.4 - - - -
365A VAL* 3.6 12.3 - - + +
----------------------------------------------------------
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