Contacts of the helix formed by residues 370 - 388 (chain D) in PDB entry 1G3I
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 THR 370 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D ALA 4.7 0.2 - - - +
369D PHE* 1.3 76.3 - - - +
371D THR* 1.3 56.9 + - - +
372D ASP* 3.7 8.6 + - - +
373D ALA* 2.7 42.1 + - - +
374D VAL* 3.0 6.4 + - - +
420D ASN* 3.8 20.0 - - - +
421D ILE 3.0 19.9 + - - +
422D ASP* 3.6 21.2 - - + +
423D ALA 4.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D PHE 4.1 0.6 + - - -
370D THR* 1.3 69.4 - - - +
372D ASP* 1.3 63.2 + - - +
373D ALA 2.7 12.0 + - - -
374D VAL* 2.8 19.8 + - - +
375D LYS* 2.9 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D THR* 3.4 7.6 + - - +
371D THR* 1.3 82.9 - - - +
373D ALA* 1.3 56.2 + - - +
375D LYS* 3.6 18.0 - - - +
376D LYS* 2.8 29.5 + - - +
423D ALA* 4.2 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D PHE* 4.5 6.7 - - + -
370D THR* 2.7 29.6 + - - +
372D ASP* 1.3 69.6 - - - +
374D VAL* 1.3 51.4 + - - +
376D LYS* 3.0 6.3 + - - +
377D ILE* 2.6 40.9 + - - +
421D ILE* 3.0 33.4 - - + +
422D ASP 3.9 5.4 - - - -
423D ALA 4.1 6.7 - - - +
426D VAL* 4.0 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D GLU* 3.8 16.8 - - + +
345D LEU* 3.5 35.2 - - + -
346D THR* 4.0 20.9 - - + -
353D THR* 4.4 6.7 - - + -
369D PHE* 4.1 20.4 - - + +
370D THR 3.0 10.6 + - - +
371D THR* 2.8 12.9 + - - +
373D ALA* 1.3 68.2 - - - +
375D LYS* 1.3 71.2 + - - +
377D ILE* 2.9 7.6 + - + -
378D ALA* 2.8 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D GLU* 3.6 38.4 + - - +
371D THR* 2.9 18.2 + - + +
372D ASP* 3.6 21.3 - - - +
374D VAL* 1.3 76.3 - - - +
376D LYS* 1.3 53.2 + - - +
378D ALA* 3.5 1.6 + - - +
379D GLU* 2.8 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D ASP 2.8 20.3 + - - +
373D ALA* 3.0 7.8 + - - +
375D LYS* 1.3 73.2 - - - +
377D ILE* 1.3 65.6 + - - +
379D GLU* 3.3 9.9 + - + +
380D ALA* 2.8 28.5 + - + +
423D ALA* 4.3 13.0 - - + +
426D VAL* 3.7 23.3 - - + -
427D ALA* 3.9 26.1 - - + +
430D LEU* 6.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D LEU* 3.7 17.9 - - + -
353D THR* 5.5 0.9 - - + -
369D PHE* 4.2 18.4 - - + -
373D ALA 2.6 24.1 + - - +
374D VAL* 3.5 9.2 - - + +
376D LYS* 1.3 71.0 - - - +
378D ALA* 1.3 59.3 + - - +
380D ALA* 2.9 11.0 - - - +
381D ALA* 2.9 25.3 + - - +
396D LEU* 5.1 3.1 - - + -
399D VAL* 4.0 21.1 - - + +
400D MET* 3.9 26.5 - - + -
403D LEU* 3.4 24.5 - - + -
426D VAL* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ALA* 4.0 2.7 - - - +
341D PHE* 3.6 14.2 - - + -
342D GLU* 3.5 39.7 - - + +
345D LEU* 3.8 9.6 - - + +
374D VAL 2.8 19.9 + - - +
375D LYS 3.7 1.8 - - - +
377D ILE* 1.3 68.6 - - - +
379D GLU* 1.3 68.4 + - - +
380D ALA 2.9 2.2 + - - -
381D ALA* 2.9 15.9 + - - +
382D PHE* 3.0 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ALA* 4.2 19.0 - - + +
342D GLU* 3.8 11.4 - - - +
375D LYS* 2.8 54.6 + - - +
376D LYS* 3.7 10.2 + - + +
378D ALA* 1.3 72.1 - - - +
380D ALA* 1.3 51.4 - - - +
382D PHE* 3.6 6.6 + - - +
383D ARG* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D LYS* 2.8 16.5 + - + +
377D ILE 2.9 13.5 - - - +
378D ALA 2.9 0.2 - - - -
379D GLU* 1.3 74.8 - - - +
381D ALA* 1.3 63.5 + - - +
383D ARG* 3.1 21.4 - - - +
384D VAL* 3.1 13.0 - - - +
399D VAL* 4.6 4.9 - - + -
430D LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D PHE* 3.8 7.4 - - + -
377D ILE 2.9 11.6 + - - +
378D ALA 2.9 5.2 + - - +
380D ALA* 1.3 70.0 - - - +
382D PHE* 1.3 64.7 + - - +
384D VAL* 3.1 16.5 - - - +
385D ASN* 3.1 8.3 + - - +
395D ARG* 3.4 30.0 - - + +
396D LEU* 3.1 35.7 - - + -
399D VAL* 3.8 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D LEU 4.2 7.6 - - - -
337D SER* 3.6 14.6 - - - -
338D ALA* 3.0 41.3 - - + -
341D PHE* 3.3 20.7 - + + -
378D ALA 3.0 5.0 + - - +
379D GLU 3.7 8.1 - - - +
381D ALA* 1.3 78.5 - - - +
383D ARG* 1.3 68.8 + - - +
385D ASN* 3.2 6.8 + - + +
386D GLU* 2.9 47.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D GLU 2.8 20.5 + - - +
380D ALA* 3.1 16.1 + - - +
382D PHE* 1.3 78.7 - - - +
384D VAL* 1.3 65.0 + - - +
386D GLU* 3.2 5.8 + - - +
387D LYS* 3.1 56.7 + - + +
433D VAL* 5.2 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D ALA 3.1 11.9 - - - +
381D ALA* 3.1 19.5 - - - +
383D ARG* 1.3 73.8 - - - +
385D ASN* 1.3 68.4 + - - +
387D LYS* 2.5 22.6 + - - +
388D THR* 2.7 32.0 + - + +
395D ARG* 3.3 32.8 - - + +
399D VAL* 4.7 5.4 - - + -
402D ARG* 5.4 8.5 - - - +
433D VAL* 5.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 385 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D PHE* 4.0 10.9 - - - -
381D ALA 3.1 7.1 + - - +
382D PHE* 3.4 11.2 - - + +
384D VAL* 1.3 81.5 - - - +
386D GLU* 1.3 63.7 + - - +
388D THR 3.2 18.2 - - - +
390D ASN* 3.4 36.9 + - - +
391D ILE 3.3 8.4 + - - -
392D GLY* 2.8 38.0 + - - +
395D ARG* 2.8 35.5 + - - +
68J GLN* 3.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D PHE* 2.9 36.5 + - + +
383D ARG* 3.5 9.9 + - - +
384D VAL 2.8 0.6 + - - -
385D ASN* 1.3 78.9 - - - +
387D LYS* 1.3 83.5 + - + +
390D ASN* 4.8 1.7 - - - +
68J GLN* 3.9 8.2 + - - +
70J HIS* 3.0 37.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 387 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D ARG* 3.1 52.7 + - + +
384D VAL* 2.5 18.2 + - - +
386D GLU* 1.3 96.2 + - + +
388D THR* 1.3 67.7 + - + +
433D VAL* 4.6 18.4 - - + -
436D ASN* 4.1 22.0 + - - +
70J HIS* 4.5 8.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 388 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 2.7 36.6 + - + +
385D ASN 3.2 1.5 - - - +
386D GLU 3.3 0.2 - - - -
387D LYS* 1.3 87.1 - - + +
389D GLU* 1.3 62.9 + - - -
390D ASN 3.2 0.8 + - - -
395D ARG* 3.5 4.7 + - - -
433D VAL* 5.3 8.3 - - + -
434D VAL 5.5 6.3 - - - +
435D GLU 5.5 3.8 - - - +
436D ASN* 5.9 0.7 - - - +
68J GLN* 2.7 29.6 - - - +
70J HIS* 4.2 6.8 + - - -
----------------------------------------------------------
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