Contacts of the helix formed by residues 389 - 405 (chain A) in PDB entry 5XJY
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 389 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PRO* 3.3 13.1 + - - +
388A ASP* 1.3 74.6 - - - +
390A PRO* 1.3 66.8 - - + +
391A ALA* 3.2 5.8 - - + +
392A THR* 2.8 19.4 + - - +
393A ARG* 2.7 31.3 + - - +
542A THR 3.3 16.5 + - - +
543A PRO* 3.4 13.3 - - - +
544A GLY 3.4 42.4 - - - +
545A SER* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASP 4.5 2.9 - - - +
389A THR* 1.3 89.1 - - + +
391A ALA* 1.3 56.9 + - - +
393A ARG* 3.2 21.4 + - + +
394A GLN* 2.9 29.3 + - - +
543A PRO* 5.9 1.8 - - + -
545A SER* 4.3 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.2 4.6 - - + +
390A PRO* 1.3 77.7 - - - +
392A THR* 1.3 60.4 + - - +
394A GLN* 2.8 40.1 + - - +
395A VAL* 3.2 8.2 + - - +
545A SER* 4.3 16.8 + - - +
546A ILE 4.5 2.9 - - - +
547A GLU* 3.3 41.7 - - + +
548A LEU* 5.1 1.8 - - + -
607A VAL* 4.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A TYR* 2.8 33.9 + - + +
387A PRO* 3.6 14.5 + - + +
389A THR* 2.8 20.8 + - - +
391A ALA* 1.3 78.1 - - - +
393A ARG* 1.3 57.0 + - - +
395A VAL* 3.1 12.3 + - + +
396A MET 3.0 20.4 + - - -
538A PHE* 3.5 38.1 - - + -
540A GLY* 5.9 3.4 - - - -
547A GLU 4.9 0.7 + - - -
548A LEU* 4.7 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A TYR* 4.0 4.5 - - + +
388A ASP* 2.7 48.0 + - + +
389A THR 2.7 15.1 + - - +
390A PRO* 3.3 23.4 - - + +
391A ALA 3.2 0.2 - - - -
392A THR* 1.3 75.0 - - - +
394A GLN* 1.3 58.9 + - - +
396A MET* 3.8 6.5 - - + +
397A ALA* 2.9 27.2 + - - +
512A PRO* 3.8 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A PRO 2.9 16.3 + - - +
391A ALA* 2.8 22.2 + - - +
393A ARG* 1.3 73.7 - - - +
395A VAL* 1.3 63.3 + - - +
397A ALA* 3.2 8.1 + - - +
398A GLU* 3.0 32.2 + - - +
547A GLU* 5.5 1.9 - - - +
607A VAL* 3.7 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA 3.2 9.4 + - - +
392A THR* 3.1 17.6 + - + +
394A GLN* 1.3 75.7 - - - +
396A MET* 1.3 79.8 + - + +
398A GLU* 3.1 3.7 + - - +
399A VAL* 3.1 22.0 + - - +
538A PHE* 3.9 9.2 - - + -
548A LEU* 4.3 12.6 - - + -
600A VAL* 5.2 3.4 - - + +
603A ALA* 4.0 13.8 - - + +
604A ILE* 3.8 34.3 - - + -
607A VAL* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 5.0 9.2 - - + -
385A TYR* 3.4 57.2 - - + -
392A THR 3.0 10.1 + - - +
393A ARG* 4.1 6.3 - - - +
395A VAL* 1.3 94.4 - - + +
397A ALA* 1.3 64.7 + - - +
399A VAL* 3.3 21.8 - - + +
400A ASN* 3.0 17.5 + - - +
510A LEU* 3.3 35.3 - - + +
512A PRO* 6.0 1.8 - - + -
536A ILE* 5.2 8.5 - - + -
538A PHE* 4.8 6.5 - - + -
600A VAL* 5.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG 2.9 18.8 + - - +
394A GLN* 3.2 9.6 + - - +
396A MET* 1.3 77.0 - - - +
398A GLU* 1.3 61.3 + - + +
400A ASN* 3.1 8.9 + - - +
401A LYS* 2.9 25.1 + - - +
2302A NAG 5.0 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLN* 3.0 19.4 + - - +
395A VAL* 3.1 3.5 + - - +
397A ALA* 1.3 78.7 - - + +
399A VAL* 1.3 64.6 + - - +
400A ASN 3.1 0.7 - - - -
401A LYS* 3.1 24.1 + - + +
402A THR* 3.1 23.4 + - - -
603A ALA* 3.4 20.2 - - + +
606A ARG* 3.3 55.4 + - - +
607A VAL* 3.7 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 4.9 9.0 - - + -
395A VAL 3.1 14.3 + - - +
396A MET* 3.3 39.3 - - + +
398A GLU* 1.3 76.0 - - - +
400A ASN* 1.3 64.5 + - - +
402A THR* 3.1 2.4 + - - -
403A PHE* 3.0 39.6 + - + -
510A LEU* 4.5 5.2 - - + -
596A LEU* 5.7 1.6 - - + -
599A VAL* 3.6 29.4 - - + -
600A VAL* 4.6 13.5 - - + -
603A ALA* 4.2 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A MET 3.0 17.1 + - - +
397A ALA* 3.1 12.3 + - - +
399A VAL* 1.3 78.7 - - - +
401A LYS* 1.3 57.9 + - - +
403A PHE* 3.4 6.4 + - - +
404A GLN* 2.9 29.2 + - - +
507A LEU 4.0 7.6 - - - +
510A LEU* 3.6 23.4 - - + +
2302A NAG 1.4 73.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA 2.9 12.2 + - - +
398A GLU* 3.1 27.8 + - + +
400A ASN* 1.3 76.9 - - - +
402A THR* 1.3 57.9 + - - +
404A GLN* 3.1 17.0 + - - +
405A GLU* 3.0 35.9 + - - +
606A ARG* 5.8 9.3 - - - +
1579A ARG* 4.2 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 3.8 27.6 - - + +
66A THR* 5.6 3.3 - - - -
398A GLU 3.1 13.1 + - - -
399A VAL 3.1 7.5 + - - -
401A LYS* 1.3 77.5 - - - +
403A PHE* 1.3 63.3 + - - +
405A GLU* 3.9 23.3 + - - +
406A LEU* 4.7 1.7 + - - +
599A VAL* 3.8 31.8 + - + +
606A ARG* 4.6 9.0 + - - -
613A LYS* 4.5 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 5.5 13.2 - + - -
378A LEU* 5.3 7.0 - - + -
383A ILE* 5.1 5.8 - - + -
399A VAL* 3.0 47.7 + - + -
400A ASN* 3.4 13.4 + - - +
402A THR* 1.3 80.9 - - - +
404A GLN* 1.3 57.9 + - - +
405A GLU 3.1 1.8 - - - -
406A LEU* 3.0 31.9 + - + +
407A ALA 4.0 0.7 + - - -
507A LEU* 4.4 27.4 - - + +
509A LYS* 4.4 30.5 - - + -
510A LEU* 5.5 4.3 - - + -
533A TRP* 3.4 37.2 - + - -
596A LEU* 5.8 0.9 - - + -
599A VAL* 4.8 11.2 - - + -
2302A NAG 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASN* 2.9 23.0 + - - +
401A LYS* 3.1 23.4 + - + +
403A PHE* 1.3 73.8 - - - +
405A GLU* 1.3 56.6 + - - +
406A LEU 3.0 4.5 - - - -
407A ALA* 3.0 28.2 + - + +
1572A ARG* 4.8 9.5 + - - -
1576A SER* 4.6 5.9 + - - -
1579A ARG* 3.8 32.3 + - - +
2302A NAG 3.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO 5.3 2.8 - - - +
65A GLY* 5.7 1.0 - - - -
66A THR* 3.6 24.7 + - + +
401A LYS* 3.0 24.7 + - + +
402A THR* 4.0 21.7 + - - +
403A PHE 3.1 1.0 - - - -
404A GLN* 1.3 76.1 - - - +
406A LEU* 1.3 54.6 + - - +
407A ALA 3.4 0.2 - - - -
408A VAL* 6.1 0.4 - - - -
613A LYS* 5.5 10.2 + - - +
1579A ARG* 4.1 33.7 - - + +
1580A PHE* 3.1 30.9 - - - +
1582A THR* 5.0 2.9 + - - +
1583A GLY* 4.1 22.4 - - - +
----------------------------------------------------------
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