Contacts of the helix formed by residues 383 - 397 (chain J) in PDB entry 5A31
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 383 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378J TYR* 2.9 30.3 + - + +
381J THR* 3.9 11.6 - - - +
382J ASN* 1.3 78.7 - - - +
384J SER* 1.3 58.0 + - - +
385J LYS 3.4 2.7 - - - -
386J LEU* 3.5 34.0 + - + +
387J ALA* 3.0 27.0 + - - +
385R THR 5.3 6.9 + - - -
386R SER* 6.1 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379J GLY* 5.4 2.9 - - - -
382J ASN* 3.3 9.6 + - - -
383J ASN* 1.3 71.4 - - - +
385J LYS* 1.3 70.3 + - - +
387J ALA* 3.6 7.1 - - - +
388J GLU* 2.8 35.7 + - - +
411J VAL* 4.5 15.6 - - - +
414J GLN* 6.2 3.6 - - - -
415J ASN* 5.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383J ASN 3.4 0.4 - - - -
384J SER* 1.3 89.7 + - - +
386J LEU* 1.3 63.4 + - + +
388J GLU* 3.3 7.2 + - + +
389J ARG* 3.0 35.6 + - + +
415J ASN* 5.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753F THR* 5.3 10.1 - - - +
754F HIS* 5.7 2.7 - - + +
757F LEU* 3.5 31.0 - - + -
378J TYR* 3.6 33.0 - - + -
383J ASN* 3.8 33.2 - - + +
384J SER 3.3 0.4 - - - -
385J LYS* 1.3 80.6 - - + +
387J ALA* 1.3 67.5 + - - +
389J ARG* 3.2 7.4 + - - +
390J PHE* 3.1 33.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375J GLY* 3.2 28.2 - - - +
378J TYR* 3.9 4.8 - - + +
379J GLY* 3.6 16.2 - - - +
383J ASN 3.0 15.8 + - - +
384J SER* 3.6 7.0 - - - +
386J LEU* 1.3 78.2 - - - +
388J GLU* 1.3 62.7 + - - +
390J PHE* 3.3 4.0 + - - +
391J PHE* 3.0 36.4 + - + -
411J VAL* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384J SER 2.8 21.3 + - - +
385J LYS* 3.5 8.3 - - + +
387J ALA* 1.3 73.0 - - - +
389J ARG* 1.3 60.7 + - + +
391J PHE* 3.3 11.3 + - - +
392J SER* 2.9 41.2 + - - +
408J VAL* 4.5 18.8 - - - +
411J VAL* 4.0 23.8 - - + +
412J ALA 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751F GLY 3.5 24.0 + - - -
752F GLN* 3.7 17.8 - - - +
753F THR* 4.9 8.6 + - - +
754F HIS* 3.8 39.6 + - + +
385J LYS* 3.0 24.0 + - + +
386J LEU* 3.2 7.8 + - - +
388J GLU* 1.3 80.0 - - + +
390J PHE* 1.3 56.5 + - - +
392J SER* 2.5 26.4 + - - -
393J GLN* 3.0 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 390 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754F HIS* 3.2 41.7 - - + -
757F LEU* 4.5 3.1 - - + -
758F MET* 4.4 7.4 - - + -
358J PHE* 3.9 22.7 - + - -
371J MET* 3.7 26.4 - - + +
374J ILE* 3.7 21.1 - - + -
375J GLY* 3.9 6.5 - - - +
378J TYR* 3.5 29.6 - + - -
386J LEU* 3.1 30.1 + - + -
387J ALA 3.8 4.3 - - - +
389J ARG* 1.3 74.1 - - - +
391J PHE* 1.3 62.3 + - - +
393J GLN* 3.0 23.5 + - - +
394J ALA* 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J LEU* 3.3 46.7 - - + -
375J GLY* 3.2 26.2 - - - -
376J LEU* 3.4 4.9 - - + -
379J GLY* 6.0 0.4 - - - -
387J ALA* 3.0 28.5 + - + -
388J GLU* 3.7 10.3 - - - +
390J PHE* 1.3 75.9 - - - +
392J SER* 1.3 59.3 + - - +
394J ALA* 3.3 4.1 + - - +
395J LEU* 2.8 32.4 + - - +
404J VAL* 4.0 7.5 - - + +
407J GLU* 3.3 29.8 - - + -
408J VAL* 4.3 18.8 - - + -
411J VAL* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 392 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754F HIS* 5.9 0.2 - - - -
388J GLU* 2.9 23.8 + - - -
389J ARG* 2.5 34.0 + - - -
391J PHE* 1.3 74.1 - - - +
393J GLN* 1.3 55.9 + - - +
395J LEU* 3.3 8.0 + - - +
396J SER* 2.8 27.9 + - - -
408J VAL* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754F HIS* 3.2 28.5 + - + +
755F LEU* 3.4 29.3 - - - +
758F MET* 3.7 12.1 - - - +
371J MET* 3.9 18.4 - - + +
389J ARG 3.0 11.1 + - - +
390J PHE* 3.0 25.9 + - - +
392J SER* 1.3 74.1 + - - +
394J ALA* 1.3 63.6 + - - +
396J SER* 3.0 26.9 - - - +
397J ILE* 3.4 11.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368J HIS* 3.9 32.4 - - + +
371J MET* 4.0 13.6 - - + +
372J LEU* 4.1 9.9 - - + +
390J PHE 2.8 17.1 + - - +
391J PHE* 3.8 4.3 - - - +
393J GLN* 1.3 73.7 - - - +
395J LEU* 1.3 60.5 + - - +
397J ILE* 3.3 15.1 + - - +
398J ALA 3.5 10.7 - - - +
404J VAL* 3.8 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391J PHE 2.8 18.5 + - - +
392J SER* 3.5 8.5 - - - +
394J ALA* 1.3 71.8 - - - +
396J SER* 1.3 57.7 + - - +
397J ILE 2.7 20.0 - - - +
398J ALA 4.2 3.4 - - - -
399J PRO* 3.5 32.5 - - + +
404J VAL* 3.7 25.1 - - + +
405J MET* 4.4 11.0 - - + -
408J VAL* 4.5 16.8 - - + -
424J TRP* 4.5 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 396 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J GLN* 5.9 0.7 + - - -
392J SER 2.8 13.1 + - - -
393J GLN* 3.0 21.5 - - - -
395J LEU* 1.3 71.1 - - - +
397J ILE* 1.3 65.5 + - - +
399J PRO* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 397 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177J THR* 3.3 27.1 - - + +
210J LYS* 5.0 2.5 - - - +
366J GLY* 4.4 15.5 - - - +
367J CYS 4.5 5.8 - - - +
368J HIS* 4.0 22.0 - - + +
371J MET* 3.6 38.4 - - + -
393J GLN* 3.4 6.7 + - + +
394J ALA 3.3 10.0 + - - +
395J LEU 2.7 11.8 - - - +
396J SER* 1.3 81.5 - - - +
398J ALA* 1.3 85.8 + - + +
399J PRO* 2.8 6.1 - - - +
----------------------------------------------------------
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