Contacts of the helix formed by residues 384 - 396 (chain H) in PDB entry 4D1Q
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 PHE 384 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373H GLU* 5.6 13.2 - - + +
374H LEU* 4.6 7.4 - - + -
380H PRO* 3.8 18.2 - - + -
381H SER* 2.6 23.4 + - - +
383H CYS* 1.3 97.3 - - - +
385H VAL* 1.3 66.4 + - - +
386H VAL 3.1 2.2 - - - -
387H PRO* 3.1 15.8 - - + +
388H SER* 2.9 29.7 + - - +
436H TYR* 3.4 33.2 - + - -
540H VAL* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H SER* 3.4 30.5 - - - +
374H LEU* 4.4 7.2 - - + -
381H SER 3.8 0.6 + - - -
382H LEU* 3.2 31.9 + - + +
384H PHE* 1.3 78.2 - - - +
386H VAL* 1.3 66.9 + - + +
388H SER* 3.1 12.8 + - - -
389H ILE* 3.2 14.2 + - - +
421H TRP* 3.7 21.5 - - + +
425H LEU* 4.1 10.5 - - + -
429H HIS* 3.7 16.6 - - + -
566H ALA* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 386 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382H LEU 4.6 0.6 + - - -
383H CYS 4.6 0.6 + - - -
385H VAL* 1.3 76.8 - - - +
387H PRO* 1.3 64.1 - - + +
389H ILE* 2.8 29.0 + - + +
390H LEU* 3.0 22.6 + - + +
425H LEU* 4.6 7.4 - - + -
429H HIS* 4.0 27.1 - - + +
430H TYR* 3.9 29.8 - - + -
433H PHE* 3.5 30.1 - - + -
442H MET* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 387 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H CYS 3.4 13.9 - - - +
384H PHE* 3.1 26.9 - - + +
386H VAL* 1.3 92.3 - - + +
388H SER* 1.3 50.5 + - - +
390H LEU* 3.2 17.1 + - + +
391H LYS* 2.7 31.7 + - - +
433H PHE* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 388 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H ILE* 3.9 22.3 - - - +
373H GLU* 5.8 1.6 - - - +
374H LEU* 3.7 15.5 - - - +
384H PHE* 2.9 15.5 + - - +
385H VAL* 3.2 9.9 - - - -
387H PRO* 1.3 72.4 - - - +
389H ILE* 1.3 56.3 + - - +
391H LYS* 2.6 29.1 + - - +
392H VAL* 2.7 19.6 + - - +
421H TRP* 3.6 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H VAL* 3.3 15.3 - - + +
386H VAL* 2.8 9.2 + - + +
388H SER* 1.3 77.5 - - - +
390H LEU* 1.3 66.8 + - + +
392H VAL* 3.8 3.6 - - - +
393H LYS* 3.2 38.8 + - - +
417H VAL* 3.5 20.2 - - + -
421H TRP* 3.5 44.8 - - + -
422H GLU* 3.8 18.2 - - + +
425H LEU* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H VAL* 3.0 35.0 + - + +
387H PRO* 3.4 15.0 - - + +
388H SER 3.0 0.2 - - - -
389H ILE* 1.3 82.5 - - + +
391H LYS* 1.3 58.1 + - - +
393H LYS* 3.4 12.0 + - + +
394H GLU* 2.9 28.2 + - - +
433H PHE* 5.1 3.8 - - + -
441H HIS* 4.4 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H GLY* 5.8 2.7 - - - +
370H ILE* 3.7 20.6 - - + -
387H PRO 2.7 13.7 + - - +
388H SER* 2.6 15.1 + - - +
390H LEU* 1.3 68.1 - - - +
392H VAL* 1.3 67.6 + - - +
394H GLU* 2.7 52.6 + - - +
395H ILE* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 392 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H LEU* 4.9 4.7 - - + -
273H VAL* 5.8 0.2 - - + -
367H PHE* 4.0 22.0 - - + -
370H ILE* 4.1 12.1 - - + +
388H SER 2.7 19.3 + - - +
389H ILE 3.8 5.8 - - - +
391H LYS* 1.3 72.7 - - - +
393H LYS* 1.3 64.3 + - - +
395H ILE* 2.9 19.3 + - - +
396H CYS* 3.1 12.6 + - - -
413H ILE* 3.5 22.4 - - + -
414H ILE* 5.4 0.4 - - - +
417H VAL* 3.3 28.9 - - + -
421H TRP* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389H ILE* 3.2 17.6 + - + +
390H LEU* 3.5 14.8 - - + +
391H LYS 3.1 0.6 - - - -
392H VAL* 1.3 80.3 - - - +
394H GLU* 1.3 61.7 + - - +
395H ILE 3.3 0.7 + - - -
396H CYS* 3.3 11.8 + - - +
397H SER* 3.4 10.6 + - - -
414H ILE* 4.4 26.1 - - + +
417H VAL* 3.9 20.9 - - + -
418H ARG* 4.3 12.9 - - - +
422H GLU* 2.9 40.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 394 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390H LEU 2.9 13.2 + - - +
391H LYS* 2.7 56.2 + - - +
393H LYS* 1.3 69.0 - - - +
395H ILE* 1.3 65.6 + - - +
397H SER* 3.2 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H ASN 5.9 0.7 - - - +
363H ILE* 4.0 44.0 - - + +
366H GLY* 5.2 11.0 - - - -
367H PHE* 4.5 6.5 - - + -
370H ILE* 5.3 2.5 - - + -
391H LYS* 2.8 62.8 + - + +
392H VAL* 3.2 11.0 - - - +
394H GLU* 1.3 77.7 - - + +
396H CYS* 1.3 69.8 - - - +
397H SER* 2.8 17.6 + - - +
399H ASP* 4.1 4.3 - - - +
410H LYS* 3.8 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 396 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H ILE* 5.4 0.7 - - - -
367H PHE* 4.7 1.6 - - - -
392H VAL* 3.1 16.2 + - - +
393H LYS 3.3 4.2 + - - +
395H ILE* 1.3 82.5 - - - +
397H SER* 1.3 64.3 + - - +
398H PRO* 3.3 6.8 - - - +
410H LYS* 3.6 35.1 - - + +
413H ILE* 3.6 40.2 - - - -
414H ILE* 3.4 33.1 - - + +
----------------------------------------------------------
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