Contacts of the helix formed by residues 321 - 336 (chain J) in PDB entry 5GJQ
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 ASN 321 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318J PRO* 5.6 1.6 - - - +
319J PRO 3.5 12.7 - - - +
320J PRO* 1.3 69.7 - - - +
322J GLU* 1.3 56.9 + - - +
323J GLU* 3.4 9.9 - - - +
324J ALA* 3.9 21.1 - - - +
325J ARG* 2.5 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321J ASN* 1.3 77.3 - - - +
323J GLU* 1.3 52.2 + - - +
325J ARG* 3.7 8.4 - - - +
326J LEU* 2.5 41.0 + - + +
345J ARG* 4.5 12.6 - - + +
348J ALA* 3.9 24.5 - - + +
349J GLU* 4.2 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321J ASN* 3.4 10.3 - - + +
322J GLU* 1.3 76.9 - - - +
324J ALA* 1.3 54.7 + - - +
326J LEU* 2.8 16.2 + - + +
327J ASP* 2.5 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J GLY 4.4 1.1 - - - +
153J GLY* 4.1 26.2 - - - +
320J PRO* 4.2 9.9 - - + -
321J ASN* 3.9 28.3 + - - +
322J GLU 3.6 0.2 - - - -
323J GLU* 1.3 75.5 - - - +
325J ARG* 1.3 52.1 + - - +
327J ASP* 3.1 9.4 + - - +
328J ILE* 2.5 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J PRO* 5.7 0.6 - - - +
320J PRO* 1.7 63.2 + - + +
321J ASN* 2.5 45.0 + - - +
322J GLU* 3.7 5.8 - - - +
324J ALA* 1.3 68.3 - - - +
326J LEU* 1.3 57.2 + - - +
328J ILE* 2.9 8.3 + - - -
329J LEU* 2.2 41.8 + - - +
348J ALA* 3.8 14.6 + - + -
351J MET* 3.5 49.7 + - - +
352J PRO* 4.1 5.7 - - - +
353J GLY* 4.0 16.3 - - - +
354J ALA* 4.1 10.4 + - - -
359J VAL* 4.5 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322J GLU* 2.5 25.3 + - + +
323J GLU* 2.8 15.3 + - + +
325J ARG* 1.3 70.3 - - - +
327J ASP* 1.3 64.0 + - - +
329J LEU* 3.3 11.0 + - - +
330J LYS* 2.8 66.8 + - - +
344J LEU* 4.0 6.3 - - + -
345J ARG* 3.0 57.2 - - + +
348J ALA* 4.2 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 327 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J GLY* 4.5 17.9 - - - -
153J GLY 5.1 1.7 + - - -
323J GLU* 2.5 23.9 + - - +
324J ALA* 3.4 10.9 - - - +
326J LEU* 1.3 83.8 - - - +
328J ILE* 1.3 64.6 + - - +
330J LYS* 2.9 28.1 + - - +
331J ILE* 3.0 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J GLY 3.6 9.4 - - - +
153J GLY 5.7 0.7 - - - +
194J THR 5.0 1.3 - - - +
320J PRO* 4.4 15.0 - - + -
324J ALA* 2.5 27.8 + - + +
325J ARG* 3.5 5.4 - - - +
327J ASP* 1.3 71.3 - - - +
329J LEU* 1.3 61.9 + - - +
331J ILE* 3.0 11.3 + - + +
332J HIS* 3.0 48.7 + - + +
355J SER 4.8 0.9 - - - +
356J GLY* 4.2 16.6 - - - +
359J VAL* 4.1 15.0 - - + -
501J ADP 3.0 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325J ARG* 2.2 34.4 + - + +
326J LEU* 3.4 9.0 - - - +
328J ILE* 1.3 68.7 - - - +
330J LYS* 1.3 50.7 + - - +
333J SER* 2.4 37.9 + - - +
344J LEU* 3.3 62.4 - - + +
347J ILE* 4.2 6.7 - - + -
348J ALA* 4.2 12.6 - - + +
351J MET* 4.9 8.1 - - + -
359J VAL* 3.7 17.9 - - + -
363J CYS* 3.9 20.0 - - - -
383J PHE* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326J LEU* 2.8 56.8 + - - +
327J ASP* 2.9 20.7 + - - +
329J LEU* 1.3 70.9 - - - +
331J ILE* 1.3 59.8 + - + +
333J SER* 3.4 6.9 + - - -
334J ARG* 3.0 30.4 + - - +
344J LEU* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 331 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J GLU 5.0 0.9 - - - +
150J MET* 3.9 28.7 - - + -
151J ILE* 3.6 25.8 - - - +
152J GLY* 3.6 14.6 - - - +
327J ASP* 3.0 18.8 + - + +
328J ILE* 3.0 15.7 + - - +
330J LYS* 1.3 78.0 - - + +
332J HIS* 1.3 72.3 + - + +
334J ARG* 3.4 18.7 + - - +
335J LYS* 3.6 15.6 - - - +
501J ADP 4.3 6.1 - - + +
173R ASP* 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 332 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328J ILE* 3.0 32.6 + - + +
331J ILE* 1.3 75.5 - - + +
333J SER* 1.3 63.2 + - - +
334J ARG 3.0 4.9 - - - -
335J LYS* 2.8 58.6 + - + +
336J MET* 3.9 7.1 + - - +
356J GLY 3.6 11.1 + - - -
359J VAL* 4.3 2.0 - - + -
360J LYS* 3.4 40.8 - - + +
363J CYS* 4.0 20.8 - - + +
501J ADP 3.5 36.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329J LEU* 2.4 31.0 + - - -
330J LYS* 3.4 11.3 + - - -
332J HIS* 1.3 77.5 - - - +
334J ARG* 1.3 59.7 + - - +
335J LYS 3.2 0.2 - - - -
336J MET* 3.2 29.8 + - - +
338J LEU* 2.9 42.4 - - - +
344J LEU* 3.8 8.2 - - - +
363J CYS* 3.9 2.8 - - - -
383J PHE* 4.0 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 334 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J LYS 3.0 23.8 + - - +
331J ILE* 3.4 11.1 - - - +
332J HIS 3.0 0.8 - - - -
333J SER* 1.3 77.2 - - - +
335J LYS* 1.3 53.8 + - - +
336J MET 3.4 5.1 - - - +
135R GLY* 6.0 0.2 - - - -
139R ASP* 3.8 9.3 + - - -
173R ASP* 2.6 45.7 - - - +
175R ASP* 3.1 38.3 - - + +
176R ARG* 2.7 51.2 - - - +
179R ARG* 6.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J MET* 6.5 1.3 - - - -
331J ILE* 3.6 14.4 - - - +
332J HIS* 2.8 53.9 + - + +
334J ARG* 1.3 78.0 - - - +
336J MET* 1.3 60.9 + - + +
360J LYS* 3.5 21.2 - - + +
501J ADP 4.9 0.8 + - - -
195K GLY* 4.9 2.7 - - - -
172R GLY 4.5 6.6 - - - +
173R ASP* 3.0 31.5 - - + +
174R TRP* 3.5 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 336 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332J HIS 3.9 9.6 - - - +
333J SER* 3.2 21.5 + - - +
334J ARG* 3.4 6.8 - - - +
335J LYS* 1.3 80.9 - - + +
337J ASN* 1.3 61.7 + - - +
338J LEU* 3.2 6.8 + - + -
363J CYS* 3.5 31.9 - - + +
364J THR* 5.5 2.0 - - - +
366J ALA* 4.2 2.2 - - + -
367J GLY* 3.3 39.9 - - - +
378J VAL* 4.1 21.8 - - + -
383J PHE* 4.1 11.9 - - + -
194K ILE 4.5 2.5 - - - +
195K GLY* 3.6 23.6 - - - +
174R TRP* 4.2 3.5 - - - +
175R ASP* 4.6 3.1 + - - +
----------------------------------------------------------
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