Contacts of the helix formed by residues 417 - 434 (chain D) in PDB entry 2G1T
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 SER 417 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D ILE* 3.7 19.4 - - - +
409D GLU* 4.7 3.5 + - - +
415D LYS* 5.5 9.3 + - - -
416D PHE* 1.3 76.7 - - - +
418D ILE* 1.3 65.0 + - - +
419D LYS* 3.2 19.8 + - - +
420D SER* 2.7 28.4 + - - -
421D ASP* 3.1 11.1 + - - -
480D PRO* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU* 5.6 0.7 - - + -
355D GLU* 3.7 47.6 - - + +
358D ASN* 4.5 6.1 - - - +
359D PHE 3.5 39.3 - - - +
360D ILE* 4.0 11.3 - - + +
417D SER* 1.3 74.2 - - - +
419D LYS* 1.3 63.3 + - + +
421D ASP* 2.9 25.8 + - - +
422D VAL* 2.9 14.7 + - + +
486D PHE* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D GLU* 5.2 1.2 + - - -
417D SER* 3.1 11.2 + - - +
418D ILE* 1.3 84.5 - - + +
420D SER* 1.3 60.2 + - - +
422D VAL* 3.1 10.3 + - + +
423D TRP 3.1 13.0 + - - -
480D PRO* 3.4 42.6 - - + +
481D SER* 4.5 10.5 + - - +
483D ARG* 2.7 47.4 + - + +
484D PRO 3.0 19.3 + - - +
485D SER* 3.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D ILE* 5.1 0.2 - - - +
405D TRP 4.9 1.6 - - - +
407D ALA* 3.8 12.7 + - - +
409D GLU* 3.9 5.6 + - - -
410D SER* 3.3 23.7 + - - -
415D LYS 4.7 0.2 - - - -
416D PHE* 3.5 13.7 - - - +
417D SER* 2.7 37.2 + - - -
419D LYS* 1.3 77.0 - - - +
421D ASP* 1.3 65.9 + - - +
423D TRP* 3.3 3.9 + - - +
424D ALA* 3.1 20.4 + - - +
483D ARG* 3.9 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D MET* 3.9 8.9 - - + +
359D PHE 4.3 2.4 - - - +
360D ILE* 3.5 10.4 - - - +
361D HIS* 2.8 33.5 + - - +
362D ARG* 2.9 27.8 + - - -
364D LEU* 3.7 5.6 - - + +
417D SER 3.1 12.2 + - - +
418D ILE* 2.9 16.6 + - - +
420D SER* 1.3 80.2 + - - +
422D VAL* 1.3 55.8 + - - +
424D ALA* 3.2 8.5 + - - +
425D PHE* 2.9 24.3 + - - +
486D PHE* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D ILE* 2.9 19.8 + - + +
419D LYS* 3.1 18.1 + - + +
421D ASP* 1.3 78.5 - - - +
423D TRP* 1.3 63.2 + - - +
425D PHE* 3.1 11.1 + - - +
426D GLY 3.1 9.4 + - - -
475D CYS* 3.5 32.2 - - - +
483D ARG* 4.0 10.1 - - + -
484D PRO* 3.6 29.4 - - + +
485D SER* 4.9 1.1 - - - -
486D PHE* 3.5 33.2 - - + +
489D ILE* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D LYS 4.9 1.6 + - - -
405D TRP 3.7 17.5 + - - -
406D THR 3.9 7.3 + - - -
407D ALA* 3.7 21.5 - - + -
408D PRO* 3.6 25.6 - - + -
419D LYS 3.1 5.3 + - - -
420D SER 3.5 8.3 - - - +
421D ASP 3.3 0.2 - - - -
422D VAL* 1.3 76.7 - - - +
424D ALA* 1.3 64.1 + - - +
426D GLY 3.0 10.6 + - - -
427D VAL* 3.3 19.6 + - + +
440D TYR* 4.3 6.4 + - - -
452D LEU* 3.8 28.9 - - + +
457D ARG* 3.8 20.6 - - - -
475D CYS 3.4 13.2 + - - +
476D TRP* 3.1 59.4 + + + -
477D GLN 3.7 5.6 - - - -
478D TRP* 4.7 0.4 - - - -
483D ARG* 3.6 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D LEU* 3.6 34.1 - - + +
405D TRP* 3.7 24.5 - - + +
420D SER 3.1 9.8 + - - +
421D ASP* 3.5 10.3 - - - +
423D TRP* 1.3 80.7 - - - +
425D PHE* 1.3 57.8 + - - +
427D VAL* 3.0 8.1 + - - +
428D LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D ALA* 4.1 5.2 - - - -
347D ILE* 3.4 35.2 - - + -
348D SER* 4.0 13.9 - - - -
351D MET* 4.7 0.2 - - + -
364D LEU* 3.8 11.9 - - + +
421D ASP 2.9 13.4 + - - +
422D VAL 3.1 8.9 + - - +
424D ALA* 1.3 75.4 - - - +
426D GLY* 1.3 58.1 + - - +
428D LEU* 3.1 9.1 + - + +
429D LEU* 2.8 64.8 + - + +
432D ILE* 6.2 0.4 - - + -
475D CYS* 4.0 14.8 - - - -
486D PHE* 3.7 22.4 - + + -
489D ILE* 3.4 33.2 - - + -
493D PHE* 3.8 6.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D VAL 3.1 6.1 + - - -
423D TRP 3.0 9.5 + - - -
425D PHE* 1.3 79.2 - - - +
427D VAL* 1.3 60.7 + - - +
429D LEU* 3.3 10.1 + - - +
430D TRP 3.3 13.9 + - - -
472D MET* 3.6 7.4 - - - +
475D CYS* 3.7 18.8 - - - -
476D TRP* 3.3 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D LYS 3.5 23.8 - - - +
405D TRP* 3.6 30.1 - - + +
423D TRP* 3.3 21.5 + - + +
424D ALA 3.0 6.4 + - - +
426D GLY* 1.3 74.2 - - - +
428D LEU* 1.3 66.0 + - - +
430D TRP* 2.9 8.4 + - + +
431D GLU* 2.9 19.7 + - + +
439D PRO* 3.7 22.2 - - + -
440D TYR* 5.0 2.5 - - - +
458D MET* 4.5 7.9 - - + -
476D TRP* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LEU* 4.4 2.2 - - + -
347D ILE* 3.7 30.3 - - + -
364D LEU* 3.9 17.9 - - + -
365D ALA* 4.6 5.4 - - - -
366D ALA* 3.4 37.0 - - + +
369D CYS* 3.8 18.6 - - - -
405D TRP* 4.8 0.4 - - - +
424D ALA 2.9 12.4 + - - +
425D PHE* 3.3 14.1 - - + +
427D VAL* 1.3 76.7 - - - +
429D LEU* 1.3 64.2 + - - +
431D GLU* 2.9 14.4 + - - +
432D ILE* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D ALA* 3.9 15.3 - - + -
425D PHE* 2.8 49.1 + - + +
426D GLY* 3.5 9.2 - - - +
427D VAL 3.2 0.2 - - - -
428D LEU* 1.3 75.9 - - - +
430D TRP* 1.3 57.6 + - - +
432D ILE* 3.3 12.7 + - + +
433D ALA* 2.8 30.8 + - - +
468D VAL* 4.4 10.1 - - + +
471D LEU* 4.4 5.8 - - + -
472D MET* 3.8 37.0 - - + +
475D CYS* 5.0 0.7 - - - -
493D PHE* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D GLY 3.3 9.5 + - - +
427D VAL 2.9 10.9 + - - +
429D LEU* 1.3 76.1 - - - +
431D GLU* 1.3 67.8 + - - +
433D ALA* 3.4 1.6 + - - +
434D THR* 2.9 54.0 + - + +
437D MET* 3.5 34.3 - - + -
438D SER 3.4 30.1 - - - -
439D PRO* 3.6 13.2 - - + -
441D PRO* 4.0 17.9 - - + -
458D MET* 3.5 41.4 - - + +
459D GLU 3.8 13.8 + - - -
461D PRO* 4.1 15.6 - - + +
472D MET* 3.9 23.9 - - - +
476D TRP* 4.4 0.7 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
324D LEU* 3.9 14.6 - - - +
327D LEU* 4.0 2.3 - - - +
366D ALA* 2.9 47.7 + - + +
367D ARG* 4.8 1.2 + - - -
405D TRP* 2.9 37.9 + - - +
427D VAL 2.9 12.8 + - - +
428D LEU* 2.9 14.7 + - + +
430D TRP* 1.3 78.7 - - + +
432D ILE* 1.3 61.2 + - - +
434D THR* 3.2 9.2 + - - -
436D GLY* 2.7 33.3 + - - -
437D MET 4.2 14.7 - - - +
439D PRO* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LEU* 4.1 18.2 - - + -
327D LEU* 3.6 10.7 - - + +
340D LEU* 3.8 50.5 - - + +
343D MET* 4.8 5.6 - - + -
344D ALA* 4.7 10.5 - - + +
347D ILE* 3.9 28.5 - - + -
425D PHE* 6.2 0.4 - - + -
428D LEU* 2.8 27.6 + - + +
429D LEU* 3.6 20.0 - - + +
431D GLU* 1.3 75.4 - - + +
433D ALA* 1.3 65.4 + - - +
435D TYR* 3.1 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D LEU* 4.5 10.6 - - - +
429D LEU 2.8 17.4 + - - +
430D TRP 3.4 2.0 + - - +
432D ILE* 1.3 77.5 - - - +
434D THR* 1.3 59.3 + - - +
435D TYR* 3.8 11.0 + - - -
461D PRO* 3.7 25.5 - - + +
462D GLU 4.4 12.6 - - - +
463D GLY 6.0 0.2 - - - -
464D CYS* 4.3 13.3 + - + +
468D VAL* 5.8 2.2 - - + -
472D MET* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D ARG* 4.5 3.8 + - - -
430D TRP* 2.9 49.5 + - + +
431D GLU* 3.2 9.5 + - - -
432D ILE 3.1 0.2 - - - -
433D ALA* 1.3 75.8 - - - +
435D TYR* 1.3 71.2 + - - +
436D GLY 3.4 0.2 + - - -
437D MET* 3.2 45.2 + - - +
461D PRO* 3.7 21.8 - - + -
----------------------------------------------------------
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