Contacts of the helix formed by residues 339 - 353 (chain D) in PDB entry 3G1Q
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 MET 339 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D LEU* 5.1 0.2 - - + -
322D GLU* 3.3 11.7 - - + +
323D ILE* 4.2 6.7 - - + -
326D PHE* 3.6 22.2 - - + -
330D LEU* 5.4 0.7 - - - -
334D ASN* 3.5 9.9 - - - +
335D VAL* 3.8 39.7 + - - +
336D MET 5.2 0.2 - - - -
337D ASP 3.7 1.2 - - - -
338D GLU* 1.3 81.2 - - - +
340D PRO* 1.4 65.5 - - - +
341D PHE 3.4 2.0 - - - -
342D ALA* 3.1 32.0 + - + -
343D GLU* 3.2 21.0 + - - +
433D LYS* 3.4 34.5 + - + +
437D ALA* 4.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 6.5 0.9 - - + -
421B LYS* 4.0 28.5 - - - +
322D GLU* 3.3 10.1 - - - +
337D ASP 4.8 2.9 - - - +
338D GLU* 3.3 10.5 - - - +
339D MET* 1.4 90.9 - - - +
341D PHE* 1.3 57.0 + - + +
343D GLU* 3.3 7.8 + - + +
344D ARG* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D HIS* 3.2 50.3 - - + -
318D ALA* 3.9 14.4 - - + +
319D LEU* 3.6 23.3 - - + -
322D GLU* 3.0 20.8 + - + +
340D PRO* 1.3 79.5 - - + +
342D ALA* 1.3 58.0 + - - +
344D ARG* 3.1 16.0 + - - +
345D CYS* 2.9 49.9 + - - -
402D PRO* 4.0 16.4 - - + -
403D GLU* 3.4 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D LEU* 3.7 18.6 - - + -
322D GLU* 2.9 13.1 + - - +
339D MET* 3.1 37.7 - - + +
340D PRO 3.3 0.2 - - - -
341D PHE* 1.3 76.0 - - - +
343D GLU* 1.3 62.3 + - - +
345D CYS* 3.4 8.4 + - - +
346D ALA* 3.1 21.5 + - - +
433D LYS* 4.2 8.2 - - + +
436D LEU* 4.3 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D MET* 5.1 4.9 - - - +
339D MET 3.2 10.6 + - - +
340D PRO* 3.6 10.3 - - + +
341D PHE 3.2 0.2 - - - -
342D ALA* 1.3 76.0 - - - +
344D ARG* 1.3 59.0 + - - +
346D ALA* 3.2 4.6 + - - +
347D ARG* 2.6 61.1 + - - +
429D LEU* 4.2 17.3 - - + +
433D LYS* 2.7 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D PRO* 2.9 22.3 + - - +
341D PHE* 3.4 21.5 - - + +
343D GLU* 1.3 75.7 - - + +
345D CYS* 1.3 58.3 + - - +
347D ARG* 3.5 7.1 + - - +
348D GLU* 3.0 32.6 + - - +
402D PRO* 2.9 38.5 + - + +
403D GLU* 3.5 13.8 - - - +
404D ARG 3.0 20.2 + - - -
405D ASP* 2.5 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D SER* 4.0 3.4 - - - +
307D LEU* 4.1 21.1 - - + -
319D LEU* 5.2 1.6 - - - -
341D PHE* 2.9 46.1 + - - -
342D ALA* 3.4 12.6 - - - +
344D ARG* 1.3 77.0 - - - +
346D ALA* 1.3 62.6 + - - +
348D GLU 3.4 0.2 + - - -
349D SER* 3.0 26.3 + - - -
400D TRP* 3.7 33.5 - - + -
402D PRO* 3.9 6.0 - - - +
436D LEU* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D THR* 3.8 4.6 - - + +
303D SER* 3.5 11.2 - - - +
342D ALA 3.1 9.8 + - - +
343D GLU* 3.7 8.5 - - - +
345D CYS* 1.3 79.4 - - - +
347D ARG* 1.3 63.9 + - - +
349D SER* 3.2 5.2 + - - -
350D ILE* 3.2 25.3 + - - +
429D LEU* 3.8 18.6 - - + -
432D VAL* 3.6 29.6 - - + -
433D LYS* 5.2 1.6 - - + -
436D LEU* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLU* 2.6 55.7 + - + +
344D ARG* 3.9 7.0 - - - +
346D ALA* 1.3 77.7 - - - +
348D GLU* 1.3 50.7 + - - +
350D ILE* 3.2 10.5 + - - +
351D ARG* 2.6 34.9 + - - +
412D PHE* 3.5 32.4 - - + -
415D PHE* 4.6 10.1 - - + -
425D GLN* 3.2 26.7 + - - -
429D LEU* 3.9 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D ARG 3.0 17.5 + - - +
345D CYS 4.0 0.9 - - - +
347D ARG* 1.3 76.7 - - - +
349D SER* 1.3 53.3 + - - +
351D ARG* 2.8 53.4 + - - +
352D ARG* 2.7 33.6 + - - +
399D ARG 3.4 1.6 - - - +
400D TRP* 3.4 23.6 - - + +
401D ASP 2.9 29.7 + - - +
402D PRO* 3.8 10.3 - - + +
404D ARG* 2.9 25.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D THR* 4.3 5.8 - - - -
302D TRP* 3.8 22.7 - - - -
303D SER* 3.1 26.1 + - - -
306D HIS* 3.6 4.2 - - - -
345D CYS 3.0 14.7 + - - -
346D ALA 3.5 8.5 - - - -
347D ARG 3.2 0.4 - - - -
348D GLU* 1.3 78.6 - - - +
350D ILE* 1.3 55.7 + - - +
352D ARG* 3.4 2.0 + - - +
353D ASP* 3.0 33.8 + - - +
400D TRP* 3.1 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D THR* 3.4 33.0 - - + +
346D ALA 3.2 17.8 + - - +
347D ARG* 3.5 7.0 - - - +
349D SER* 1.3 71.4 - - - +
351D ARG* 1.3 68.5 + - - +
353D ASP 4.3 5.6 - - - -
354D PRO* 3.0 26.8 - - + +
355D PRO* 4.0 15.7 - - + -
388D HIS* 3.7 0.7 - - - -
412D PHE* 4.0 5.8 - - + -
414D GLY* 3.6 34.1 - - - +
415D PHE* 3.5 34.1 - - + -
429D LEU* 4.7 3.1 - - + -
480D HEM 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D ARG 2.6 19.9 + - - +
348D GLU* 2.8 53.8 + - - +
350D ILE* 1.3 77.0 - - - +
352D ARG* 1.3 81.5 + - - +
354D PRO* 3.7 1.4 - - - +
388D HIS* 3.0 62.7 + - + +
389D HIS* 4.1 4.2 - - - -
394D PHE* 3.5 37.8 - - + -
397D PRO* 2.6 39.1 + - - +
399D ARG 3.6 2.8 + - - -
404D ARG* 3.5 15.2 - - - +
412D PHE* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D TRP* 4.1 3.0 - - - -
306D HIS* 3.5 31.1 + - - -
348D GLU 2.7 20.2 + - - +
349D SER 4.0 1.8 - - - +
350D ILE 3.3 0.2 - - - -
351D ARG* 1.3 88.1 - - - +
353D ASP* 1.3 90.7 + - - +
354D PRO* 3.6 2.9 - - - +
385D LEU* 5.0 0.9 - - - +
389D HIS* 3.1 12.0 + - - -
397D PRO 4.0 11.9 - - - +
398D ARG* 2.8 81.4 + - - +
400D TRP* 3.9 17.9 - - + +
452D VAL* 4.1 17.8 - - - +
453D PRO 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D TRP* 3.4 48.4 + - + +
306D HIS* 4.1 1.9 + - - -
349D SER 3.0 13.3 + - - +
350D ILE* 3.5 2.4 - - - -
352D ARG* 1.3 111.5 + - - +
354D PRO* 1.3 69.4 - - - +
355D PRO* 3.4 7.4 - - - +
385D LEU* 5.6 1.3 - - - -
398D ARG* 2.9 27.5 + - - -
455D PRO* 3.5 15.6 - - + +
457D TYR* 4.7 1.8 + - - -
462D VAL* 4.8 3.9 - - + +
----------------------------------------------------------
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