Contacts of the helix formed by residues 370 - 386 (chain D) in PDB entry 4QGC
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 TYR 370 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 5.2 6.9 + - - -
334D MET* 3.9 15.4 + - + +
336D LYS 3.3 23.3 + - - -
337D LYS 3.4 26.7 - - - +
338D PRO* 3.5 26.0 - - + +
364D GLU 3.8 4.1 - - - +
368D GLY 3.3 0.6 - - - -
369D ASP* 1.3 99.5 - - + +
371D PRO* 1.3 64.5 - - - +
372D LEU 3.3 2.7 - - - -
373D GLU* 3.3 34.9 + - + +
374D ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ALA* 3.7 24.5 - - + +
55D SER* 4.4 6.1 - - - -
60D THR* 4.6 8.5 - - + -
64D MET* 4.8 4.5 - - - -
364D GLU 3.3 12.5 - - - +
365D THR* 3.7 30.4 - - - +
368D GLY 3.7 8.3 - - - +
369D ASP 3.5 8.5 - - - +
370D TYR* 1.3 89.0 - - - +
372D LEU* 1.3 63.6 + - + +
373D GLU* 5.0 0.2 - - - +
374D ALA 3.5 0.5 + - - -
375D VAL* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D THR* 5.0 4.7 - - + +
63D GLU* 3.5 39.7 - - + +
64D MET* 3.7 14.1 - - + +
67D SER* 3.2 24.7 - - - +
370D TYR 3.3 0.4 - - - -
371D PRO* 1.3 81.3 - - + +
373D GLU* 1.3 71.9 + - - +
375D VAL* 3.5 3.2 + - + +
376D ARG* 3.2 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D MET* 3.6 17.1 - - + +
338D PRO* 4.2 13.9 - - + +
370D TYR* 3.3 40.3 - - + +
371D PRO* 3.4 0.9 - - - +
372D LEU* 1.3 83.3 + - - +
374D ALA* 1.3 59.8 + - - +
376D ARG* 3.4 18.0 + - - +
377D MET* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D LEU* 3.8 4.4 - - + +
334D MET* 3.6 21.2 - - + +
361D LEU* 3.7 7.1 - - + +
364D GLU* 3.8 31.2 - - + +
365D THR* 4.2 4.7 - - + -
370D TYR 3.1 18.2 + - - +
371D PRO 3.7 5.6 - - - +
372D LEU 3.3 0.2 - - - -
373D GLU* 1.3 75.2 - - - +
375D VAL* 1.3 60.8 + - - +
377D MET* 3.4 1.4 + - - +
378D GLN* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 4.1 5.1 - - + +
49D CYS* 3.6 28.5 - - - -
64D MET* 3.7 41.1 - - + +
67D SER* 3.8 14.6 - - - -
68D GLY* 4.4 2.5 - - - -
69D MET 4.0 12.3 - - - +
361D LEU* 4.1 6.5 - - - -
365D THR* 3.8 4.7 - - + -
371D PRO 3.2 17.0 + - - +
372D LEU* 3.9 6.3 - - - +
374D ALA* 1.3 76.5 - - - +
376D ARG* 1.3 58.4 + - - +
378D GLN* 3.5 3.4 + - - +
379D HIS* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU* 4.2 11.3 + - - -
67D SER* 3.2 28.0 + - - +
372D LEU* 3.2 49.9 + - - +
373D GLU* 3.7 18.8 + - - +
374D ALA 3.3 0.2 - - - -
375D VAL* 1.3 78.2 - - - +
377D MET* 1.3 58.9 + - - +
379D HIS* 3.4 9.2 + - - +
380D LEU* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.8 28.7 - - - +
331D LEU* 4.3 3.4 - - + -
334D MET* 3.9 11.9 - - + -
338D PRO 5.1 6.3 - - - +
339D ARG* 5.2 5.6 - - + -
340D PRO* 3.6 40.8 - - + -
373D GLU 2.8 17.5 + - - +
374D ALA 3.8 3.8 - - - +
375D VAL 3.3 0.2 - - - -
376D ARG* 1.3 73.0 - - - +
378D GLN* 1.3 61.5 + - - +
380D LEU* 3.1 16.0 + - + +
381D ILE* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 5.4 0.4 + - - -
47D ILE* 3.9 26.3 - - + +
331D LEU* 4.0 15.7 - - + +
348D VAL* 3.3 29.8 - - - +
352D VAL* 5.2 0.2 - - - +
359D ILE* 3.4 42.3 - - + +
361D LEU* 4.1 16.5 - - + +
374D ALA 3.0 17.9 + - - +
375D VAL* 3.7 5.4 - - - +
377D MET* 1.3 75.1 - - - +
379D HIS* 1.3 62.9 + - - +
381D ILE* 4.7 2.4 - - - +
382D ALA* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ARG* 2.9 42.3 + - + +
47D ILE* 3.8 10.2 - - + +
67D SER 3.8 16.5 + - - +
68D GLY* 5.6 0.7 - - - -
375D VAL 3.1 14.6 + - - +
376D ARG* 3.4 9.6 - - - +
377D MET 3.2 0.2 - - - -
378D GLN* 1.3 78.3 - - - +
380D LEU* 1.3 69.0 + - + +
382D ALA* 3.8 1.6 - - - +
383D ARG* 3.0 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.9 32.1 - - + +
39D PRO* 5.9 5.8 - - + -
376D ARG* 3.0 19.7 + - + +
377D MET* 3.1 21.1 + - + +
379D HIS* 1.3 89.1 - - + +
381D ILE* 1.3 57.1 + - - +
383D ARG* 3.3 10.2 + - + +
384D GLU* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.8 24.5 - - + +
307A PHE* 4.4 5.0 - - + -
331D LEU* 4.0 17.3 - - + -
340D PRO* 5.0 1.6 - - + -
345D GLY* 3.6 42.0 - - - +
348D VAL* 3.7 22.9 - - + -
349D ALA* 3.9 11.2 - - + +
377D MET* 2.9 38.5 + - + +
378D GLN* 4.1 3.4 - - - +
380D LEU* 1.3 74.6 - - - +
382D ALA* 1.3 57.9 + - - +
384D GLU* 3.2 3.0 + - - +
385D ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ARG* 3.7 18.8 - - + -
45D THR* 3.5 24.0 - - - +
47D ILE* 5.6 0.4 - - + -
352D VAL* 4.5 15.6 - - + +
378D GLN* 3.1 29.7 + - - +
379D HIS 3.8 0.2 - - - +
381D ILE* 1.3 77.2 - - - +
383D ARG* 1.3 61.6 + - - +
385D ALA* 3.5 2.9 + - - +
386D GLU* 3.3 26.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
39D PRO* 2.5 53.9 + - + +
40D ILE* 3.9 4.9 + - - +
41D THR* 2.7 27.9 + - - +
42D ALA* 4.3 3.4 - - - +
43D ARG* 3.8 26.0 - - + +
379D HIS* 3.0 44.6 + - - +
380D LEU* 3.6 9.9 - - + +
381D ILE 3.2 0.2 - - - -
382D ALA* 1.3 77.9 - - - +
384D GLU* 1.3 61.7 + - - +
386D GLU* 3.2 21.1 - - - +
387D ALA* 4.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.3 35.0 - - + +
305A LYS* 2.7 35.0 + - - +
307A PHE* 3.9 7.6 - - + -
308A LEU* 3.2 29.1 - - + +
34D ASP 5.3 0.5 - - - +
37D SER 4.8 2.9 - - - +
39D PRO* 3.3 29.6 - - + +
380D LEU* 2.9 23.0 + - + +
381D ILE 3.7 3.4 - - - +
383D ARG* 1.3 71.4 - - - +
385D ALA* 1.3 67.2 + - - +
386D GLU 3.1 2.7 + - - -
387D ALA* 3.2 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.8 11.2 - - + -
349D ALA* 4.0 26.0 - - + +
352D VAL* 4.0 20.4 - - + -
353D LEU* 3.2 20.9 - - + +
381D ILE 2.9 16.2 + - - +
382D ALA 3.9 6.3 - - - +
383D ARG 3.3 0.2 - - - -
384D GLU* 1.3 74.8 - - - +
386D GLU* 1.3 64.1 + - - +
388D ALA* 3.1 11.7 + - - +
389D ILE* 3.4 3.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
41D THR* 3.7 34.1 + - + -
42D ALA 3.8 4.4 - - - +
43D ARG* 4.5 0.3 - - - -
44D ASN* 3.0 32.4 + - - -
45D THR* 4.8 1.9 + - - +
352D VAL* 5.0 2.4 - - - +
382D ALA 3.3 15.9 + - - +
383D ARG* 3.2 19.2 + - - +
384D GLU 3.1 0.2 - - - -
385D ALA* 1.3 78.0 - - - +
387D ALA* 1.3 59.6 + - - +
389D ILE* 3.3 25.5 + - - +
391D HIS* 3.9 10.3 + - - +
467D ARG* 2.4 41.2 + - - -
----------------------------------------------------------
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