Contacts of the helix formed by residues 388 - 410 (chain A) in PDB entry 6DMY
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 388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A TYR* 3.7 16.1 + - - -
386A ASN* 3.4 23.0 + - - +
387A TRP* 1.3 87.5 - - - +
389A GLU* 1.3 60.2 + - - +
390A ASP* 3.1 11.4 - - + +
391A LYS* 2.8 38.3 + - + +
392A ALA* 3.3 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PRO* 3.6 28.7 - - + +
370A LYS* 4.2 21.9 - - - +
373A TYR* 3.5 31.9 - - + -
388A ASN* 1.3 71.3 - - - +
390A ASP* 1.3 66.9 + - - +
391A LYS 3.3 0.4 - - - -
392A ALA* 3.7 10.2 - - - +
393A ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASN* 3.1 8.4 + - + +
389A GLU* 1.3 82.1 - - - +
391A LYS* 1.3 60.9 + - + +
393A ALA* 3.4 6.2 + - - +
394A ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 4.7 0.2 - - - +
193A TYR* 3.3 44.2 + - + +
385A ILE* 4.2 16.7 - - + +
386A ASN* 3.3 33.0 - - - +
387A TRP* 4.7 6.5 - - + -
388A ASN* 2.8 23.5 + - + +
390A ASP* 1.3 79.8 - - + +
392A ALA* 1.3 56.4 + - - +
394A ALA* 3.2 5.8 + - - +
395A ILE* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PRO* 4.1 15.9 - - + +
372A MET* 3.9 24.1 - - + +
373A TYR 4.5 2.0 - - - +
387A TRP* 4.2 13.4 - - + -
388A ASN 3.3 3.4 + - - +
389A GLU* 4.0 15.5 - - - +
391A LYS* 1.3 78.5 - - - +
393A ALA* 1.3 58.4 + - - +
395A ILE* 3.2 12.4 + - - +
396A LEU* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PRO* 3.7 25.7 - - + +
389A GLU 2.9 19.6 + - - +
390A ASP* 3.8 7.0 - - - +
391A LYS 3.3 0.4 - - - -
392A ALA* 1.3 76.5 - - - +
394A ALA* 1.3 57.6 + - - +
396A LEU* 3.9 2.6 - - - +
397A GLU* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 3.7 24.0 - - + +
193A TYR* 5.1 0.7 - - - +
390A ASP 3.0 18.1 + - - +
391A LYS* 3.5 7.2 - - - +
393A ALA* 1.3 74.8 - - - +
395A ILE* 1.3 59.6 + - - +
397A GLU* 3.7 8.6 - - - +
398A ALA* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 5.3 4.6 - - + +
192A MET* 3.7 23.3 - - + -
193A TYR* 4.5 5.6 - - + -
197A TRP* 3.7 66.2 - - + -
202A LEU* 4.2 17.5 - - + -
372A MET* 4.2 2.9 - - + -
387A TRP* 3.9 17.9 - - + -
391A LYS 2.9 21.7 + - - +
392A ALA* 3.2 8.5 + - - +
394A ALA* 1.3 76.1 - - - +
396A LEU* 1.3 57.9 + - - +
398A ALA* 3.4 3.2 + - - +
399A TRP* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 5.8 1.8 - - - +
202A LEU* 3.8 37.2 - - + +
366A LEU* 4.3 14.8 - - + -
367A MET* 3.3 27.6 - - + +
368A THR 4.0 0.2 - - - -
369A PRO* 3.7 34.8 - - + -
372A MET* 4.1 13.2 - - - -
392A ALA 2.9 17.6 + - - +
393A ALA* 4.0 4.0 - - - +
395A ILE* 1.3 75.2 - - - +
397A GLU* 1.3 57.4 + - - +
399A TRP* 3.8 3.9 - - - +
400A GLN* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA 2.9 20.1 + - - +
394A ALA* 3.7 8.7 - - - +
395A ILE 3.2 0.2 - - - -
396A LEU* 1.3 76.8 - - - +
398A ALA* 1.3 63.6 + - - +
400A GLN* 3.2 10.3 + - - +
401A ARG* 2.7 61.7 + - - +
425A THR* 4.2 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 4.5 18.6 - - + -
192A MET* 4.8 8.7 - - + -
394A ALA 3.0 17.2 + - - +
395A ILE 3.9 3.1 - - - +
397A GLU* 1.3 76.4 - - - +
399A TRP* 1.3 54.3 + - - +
401A ARG* 3.5 8.2 + - - +
402A THR* 2.7 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN* 4.5 10.3 - - + -
185A ALA 4.2 5.8 - - - -
188A VAL* 3.3 47.2 + - + +
190A VAL* 4.0 23.9 - - + +
197A TRP* 4.7 5.6 - - + -
198A LYS 4.9 0.4 - - - -
199A LEU* 3.7 36.9 - - + +
202A LEU* 3.5 26.6 - - + +
364A PHE* 4.7 7.9 - + + -
366A LEU* 3.6 30.3 - - + -
395A ILE* 3.0 18.5 + - + +
396A LEU 3.8 3.1 - - - +
398A ALA* 1.3 76.5 - - - +
400A GLN* 1.3 64.3 + - + +
402A THR* 3.5 2.7 + - - -
403A TYR* 2.9 51.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 4.4 8.1 - - - +
156A GLN* 3.0 41.7 + - + +
366A LEU* 4.2 7.0 - - + +
396A LEU* 2.9 29.4 + - - +
397A GLU* 3.2 6.8 + - - +
399A TRP* 1.3 83.7 - - + +
401A ARG* 1.3 65.1 + - - +
403A TYR* 3.3 7.8 + - - +
404A VAL* 3.0 28.3 + - - +
423A THR* 4.0 10.5 + - - +
424A THR* 3.3 12.6 - - - +
425A THR* 2.4 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLU* 2.7 49.7 + - + +
398A ALA* 4.0 5.8 - - - +
400A GLN* 1.3 76.3 - - - +
402A THR* 1.3 64.4 + - - +
404A VAL* 3.2 7.3 + - - +
405A GLU* 3.1 37.7 + - - +
425A THR* 4.2 15.4 - - + +
429A ASP* 3.1 34.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
188A VAL* 4.5 15.3 - - + -
189A HIS 5.0 10.5 - - - +
190A VAL* 4.5 8.8 - - + +
398A ALA* 2.7 23.8 + - - +
399A TRP* 3.8 7.0 - - - -
401A ARG* 1.3 75.9 - - - +
403A TYR* 1.3 57.2 + - - +
405A GLU* 3.5 6.4 + - - +
406A VAL* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN* 3.7 18.0 + - + -
158A MET* 3.3 33.3 - - + +
185A ALA* 3.5 38.1 - - + -
188A VAL* 4.9 6.2 - - - +
364A PHE* 3.7 17.5 - + - -
399A TRP* 2.9 34.9 + + + +
400A GLN* 3.3 10.5 - - - +
402A THR* 1.3 77.9 - - - +
404A VAL* 1.3 61.8 + - + +
406A VAL* 3.9 3.6 - - - +
407A VAL* 2.9 35.3 + - + +
421A SER* 3.9 15.9 - - - -
423A THR* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLN 3.0 15.5 + - - +
401A ARG* 3.2 9.1 + - - +
403A TYR* 1.3 79.8 - - + +
405A GLU* 1.3 63.1 + - + +
407A VAL* 3.3 11.2 - - + +
408A HIS* 3.0 26.1 + - + +
421A SER* 4.8 13.7 - - - +
423A THR* 3.4 22.9 - - + +
426A THR* 4.1 22.4 - - + -
786A ARG* 4.6 3.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
401A ARG* 3.1 24.1 + - - +
402A THR* 4.2 5.3 - - - +
404A VAL* 1.3 83.1 - - + +
406A VAL* 1.3 58.9 + - + +
408A HIS* 3.1 10.2 + - + +
409A GLN* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLN* 3.3 40.5 - - + +
185A ALA* 4.5 1.3 - - - +
188A VAL* 3.7 19.3 - - + -
402A THR* 2.9 30.7 + - + +
403A TYR* 4.0 1.8 - - - +
405A GLU* 1.3 74.4 - - + +
407A VAL* 1.3 61.4 + - - +
409A GLN* 3.0 30.2 + - + +
410A SER* 3.7 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 4.2 25.4 - - + -
181A SER* 4.6 13.9 - - - +
184A GLN* 6.4 0.2 - - - -
185A ALA* 4.7 9.0 - - + +
403A TYR* 2.9 21.4 + - + +
404A VAL* 3.3 17.5 - - + +
406A VAL* 1.3 78.3 - - - +
408A HIS* 1.3 60.4 + - - +
410A SER* 3.2 22.8 + - - +
411A VAL* 4.2 2.6 - - - +
419A VAL* 4.6 12.8 - - + +
421A SER* 3.3 26.9 - - - +
786A ARG* 3.8 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 3.0 15.1 + - + +
405A GLU* 3.3 12.8 - - - +
406A VAL 3.1 0.2 - - - -
407A VAL* 1.3 77.6 - - - +
409A GLN* 1.3 74.7 + - - +
410A SER 3.2 1.2 + - - -
411A VAL* 3.4 19.0 + - + +
786A ARG* 3.1 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLN* 5.2 2.0 - - - +
405A GLU* 3.0 22.3 + - + +
406A VAL* 3.0 18.5 + - + +
408A HIS* 1.3 90.3 - - - +
410A SER* 1.3 57.2 + - - +
411A VAL 3.5 1.3 + - - -
412A ALA* 4.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLN* 2.5 34.9 + - - -
180A ASP* 4.5 6.3 - - - -
181A SER* 3.3 25.6 + - - -
184A GLN* 3.3 28.9 - - - -
406A VAL 3.7 3.6 + - - -
407A VAL* 3.2 18.7 + - - -
408A HIS 3.2 1.4 - - - -
409A GLN* 1.3 76.6 - - - +
411A VAL* 1.3 54.5 + - - +
412A ALA* 3.4 4.8 + - - +
419A VAL* 4.5 1.5 - - - +
----------------------------------------------------------
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