Contacts of the helix formed by residues 419 - 438 (chain D) in PDB entry 3HN3
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 419 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D PRO* 4.9 4.0 + - - +
179D THR* 4.7 5.1 - - - +
416D GLN 2.9 27.9 + - - -
417D PHE* 4.0 1.4 - - - +
418D PHE* 1.3 75.1 - - - +
420D ASN* 1.3 57.8 + - - +
421D VAL* 3.2 12.5 + - - +
422D SER* 3.0 35.7 + - - -
423D LEU* 2.9 30.3 + - - +
462D TYR* 4.3 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D ASN* 1.3 76.1 - - - +
421D VAL* 1.3 62.0 + - + +
423D LEU* 3.4 13.0 + - - +
424D HIS* 3.0 67.0 + - - -
461D TYR* 6.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D THR* 3.8 21.5 - - + -
419D ASN* 3.2 8.6 + - - +
420D ASN* 1.3 77.4 - - + +
422D SER* 1.3 68.5 + - - +
424D HIS* 3.4 4.9 + - - +
425D HIS* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D PRO 4.3 11.9 - - - -
179D THR* 4.4 11.6 - - - +
181D LEU* 5.8 0.3 - - - +
417D PHE 2.7 29.5 + - - -
419D ASN* 3.0 32.2 + - - -
421D VAL* 1.3 76.0 - - - +
423D LEU* 1.3 57.6 + - - +
425D HIS* 3.3 7.3 + - - +
426D HIS* 2.9 31.7 + - - +
462D TYR* 3.5 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D ASN 2.9 19.8 + - - +
420D ASN* 3.6 17.5 - - - +
422D SER* 1.3 77.6 + - - +
424D HIS* 1.3 69.7 + - + +
426D HIS* 3.2 2.9 + - - +
427D MET* 3.0 32.3 + - + +
461D TYR* 3.9 30.5 - - + +
462D TYR* 3.5 31.6 - - + +
465D MET* 4.2 15.3 - - + -
466D VAL* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D ASN* 3.0 57.3 + - - +
421D VAL* 4.1 3.6 - - - +
423D LEU* 1.3 80.9 - - + +
425D HIS* 1.3 62.9 + - - +
427D MET* 3.3 29.3 + - + +
428D GLN* 3.1 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D GLU* 2.6 36.0 + - + -
144D GLY* 5.9 1.3 - - - -
179D THR* 3.3 24.8 + - - +
181D LEU* 3.8 30.7 - - + +
421D VAL* 3.0 21.0 + - + +
422D SER* 3.6 7.6 + - - +
424D HIS* 1.3 77.3 - - - +
426D HIS* 1.3 62.4 + - - +
428D GLN* 3.1 11.1 + - + +
429D VAL* 3.0 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LEU* 3.6 24.5 - - + +
407D CYS* 3.4 13.6 - - - -
409D GLY* 4.0 17.3 - - - -
412D LEU* 4.1 7.6 - - + -
422D SER 2.9 11.8 + - - +
423D LEU 3.5 5.4 - - - +
425D HIS* 1.3 75.7 - - - +
427D MET* 1.3 56.8 + - - +
429D VAL* 3.4 1.7 + - - +
430D MET* 2.9 26.4 + - + +
448D VAL* 2.8 29.8 + - + -
449D ALA* 4.6 3.4 - - + -
462D TYR* 2.6 43.1 + + + +
463D LEU* 5.6 0.4 - - + -
466D VAL* 3.6 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 3.0 33.8 + - + +
424D HIS* 3.5 38.4 - - + +
426D HIS* 1.3 78.5 - - - +
428D GLN* 1.3 58.1 + - + +
430D MET* 3.5 3.4 + - - +
431D GLU* 3.0 24.7 + - - +
465D MET* 4.8 7.9 - - + +
466D VAL* 4.4 9.9 - - + -
469D HIS* 3.2 65.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.0 38.3 + - - +
424D HIS* 3.1 19.2 + - + +
425D HIS* 3.1 13.0 + - + +
427D MET* 1.3 73.4 - - + +
429D VAL* 1.3 66.4 + - + +
431D GLU* 3.2 27.8 + - - +
432D GLU* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D GLU* 5.1 3.1 - - - +
144D GLY* 5.9 3.8 - - - -
147D LEU* 4.1 13.5 - - + -
181D LEU* 4.3 14.4 - - + -
407D CYS* 4.3 4.5 - - + -
408D PRO* 3.9 28.9 - - + -
425D HIS* 3.0 42.8 + - + +
426D HIS 3.4 7.6 + - - +
428D GLN* 1.3 73.5 - - + +
430D MET* 1.3 67.1 + - - +
432D GLU* 3.0 16.9 + - - +
433D VAL* 2.9 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D ASP 5.7 0.4 - - - +
407D CYS* 3.5 30.5 - - - -
426D HIS* 2.9 24.6 + - + +
427D MET* 3.8 6.3 - - - +
429D VAL* 1.3 75.0 - - - +
431D GLU* 1.3 57.2 + - - +
433D VAL* 3.2 7.9 + - + +
434D VAL* 2.9 41.7 + - + +
446D TRP* 4.2 17.3 - - + -
447D SER 4.5 2.2 - - - +
448D VAL* 4.2 13.2 - - + -
466D VAL* 3.8 18.4 - - + -
469D HIS* 5.0 4.7 - - + -
470D THR* 3.3 43.5 - - + +
473D LEU* 4.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU 4.1 14.6 + - - +
427D MET* 3.0 9.4 + - - +
428D GLN* 3.3 30.0 - - - +
430D MET* 1.3 77.0 - - - +
432D GLU* 1.3 58.4 + - + +
434D VAL* 3.8 1.8 - - - +
435D ARG* 2.9 29.1 + - - +
469D HIS* 2.8 39.5 + - - +
473D LEU* 3.3 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 6.5 2.9 - - + -
142D HIS* 2.7 35.8 + - - -
143D GLU 4.4 5.2 - - - +
147D LEU* 3.7 30.2 - - + +
148D PRO 4.1 6.8 - - - +
428D GLN* 3.0 15.6 + - - +
429D VAL* 3.0 18.9 + - - +
431D GLU* 1.3 72.8 - - - +
433D VAL* 1.3 66.2 + - - +
435D ARG* 3.4 30.0 + - - +
436D ARG* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LEU* 4.0 16.2 - - + -
387D PRO* 3.8 27.1 - - + -
405D ASP* 4.3 15.9 - - - +
407D CYS* 4.0 25.1 - - + +
429D VAL* 2.9 19.1 + - + +
430D MET* 3.2 15.0 + - + +
432D GLU* 1.3 75.0 - - - +
434D VAL* 1.3 58.5 + - - +
436D ARG* 3.3 3.5 + - - +
437D ASP* 3.0 30.3 + - - +
446D TRP* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D MET* 2.9 36.3 + - + +
431D GLU 3.9 3.4 - - - +
433D VAL* 1.3 73.0 - - - +
435D ARG* 1.3 67.3 + - - +
438D LYS* 2.8 42.1 + - + +
446D TRP* 4.0 27.8 - - + +
470D THR* 4.4 9.2 - - + -
473D LEU* 4.3 23.1 - - + +
474D ASP* 4.2 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.5 3.2 - - - +
24D GLN 3.1 29.7 + - - +
25D GLY 3.2 18.5 + - - -
26D GLY* 4.0 3.6 + - - -
27D MET* 3.3 59.5 - - + +
148D PRO 4.5 4.0 + - - -
230D ASP* 5.2 2.5 - - - +
431D GLU 2.9 19.0 + - - +
432D GLU* 3.6 34.3 + - - +
434D VAL* 1.3 78.4 - - - +
436D ARG* 1.3 62.2 + - - +
438D LYS* 3.6 29.7 - - - +
439D ASN* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET* 4.6 17.5 - - + +
146D TYR 3.7 7.7 + - - -
147D LEU* 4.3 6.6 - - + +
148D PRO* 3.6 32.3 - - + +
216D ARG* 3.5 18.6 - - - +
387D PRO* 3.6 16.3 - - - +
388D TYR 2.7 32.2 + - - +
390D GLU* 3.6 35.5 + - + +
393D MET* 4.2 9.3 - - - +
405D ASP* 5.1 0.2 + - - -
432D GLU 3.0 16.8 + - - +
433D VAL* 3.8 3.3 - - - +
435D ARG* 1.3 80.5 - - - +
437D ASP* 1.3 96.6 + - - +
438D LYS* 3.7 0.6 - - - +
439D ASN* 5.2 2.1 + - - +
440D HIS* 4.4 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D GLU* 5.0 1.2 - - - +
393D MET* 4.1 6.3 - - - +
405D ASP* 2.6 32.8 - - - +
433D VAL* 3.0 18.0 + - - +
436D ARG* 1.3 124.1 + - - +
438D LYS* 1.3 64.7 + - - +
439D ASN 3.0 5.0 + - - -
440D HIS* 3.1 38.3 + - + +
443D VAL* 4.4 4.0 - - + +
446D TRP* 4.0 9.8 - - + -
477D ARG* 4.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 6.1 0.7 - - - -
230D ASP* 2.9 30.2 + - - -
231D ILE 3.4 13.7 - - - -
232D THR* 2.5 37.2 + - + +
233D VAL 4.3 7.4 - - - +
234D THR* 6.0 0.2 - - - +
434D VAL* 2.8 33.3 + - + +
435D ARG* 3.6 24.1 - - - +
436D ARG 3.7 0.4 - - - -
437D ASP* 1.3 75.9 - - - +
439D ASN* 1.3 72.1 + - - +
440D HIS 3.5 0.4 - - - -
446D TRP* 4.1 4.2 - - - -
474D ASP* 5.5 3.4 - - - -
477D ARG* 3.0 33.2 + - - +
----------------------------------------------------------
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