Contacts of the helix formed by residues 348 - 366 (chain B) in PDB entry 1DGH
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 ASP 348 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG 4.8 1.2 - - - +
218B HIS* 2.9 34.2 + - - +
219B THR 4.4 4.0 + - - +
297B PHE* 3.1 36.9 - - + +
299B LEU* 3.8 12.4 + - - +
346B SER* 3.0 17.9 + - - +
347B PRO* 1.3 71.6 - - - +
349B LYS* 1.3 65.6 + - - +
350B MET* 2.8 35.0 + - - +
351B LEU* 3.1 9.9 + - + +
352B GLN* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG 3.7 14.6 + - - +
157B ASP* 3.8 19.2 + - + +
158B PRO* 3.2 25.4 - - + +
297B PHE 4.5 1.4 + - - -
347B PRO 3.0 11.9 + - - +
348B ASP* 1.3 72.3 + - - +
350B MET* 1.3 62.2 + - - +
352B GLN* 3.4 9.0 - - - +
353B GLY 3.1 17.0 + - - -
432B PHE* 3.0 40.4 + - - +
434B THR* 3.5 20.8 - - + +
41D VAL* 4.0 12.6 + - + +
43D THR* 4.0 27.4 + - + +
46D PRO 4.0 17.9 + - - -
47D ARG* 5.9 0.4 - - - +
48D GLY 5.3 0.7 - - - +
50D LEU* 5.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE* 3.5 32.3 - - + -
155B ILE* 3.5 21.1 - - + +
156B ARG* 3.5 18.6 - - - +
157B ASP 3.4 34.5 - - - +
158B PRO* 3.4 10.3 - - - -
218B HIS* 3.7 15.0 - - + -
299B LEU* 3.7 12.1 - - + -
348B ASP* 2.8 16.9 + - - +
349B LYS* 1.3 69.0 - - - +
351B LEU* 1.3 63.7 + - - +
353B GLY 3.2 2.3 + - - -
354B ARG* 3.2 24.8 + - - +
2001B HEM 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B HIS* 3.4 35.8 - - + +
219B THR 3.8 15.5 - - - +
220B PHE* 3.8 25.4 - - + -
336B PRO* 4.5 15.3 - - + +
339B MET* 6.1 0.2 - - - -
345B ALA* 3.7 30.5 - - + -
346B SER* 3.7 15.3 - - - +
348B ASP* 3.1 12.9 + - + +
350B MET* 1.3 77.5 - - - +
352B GLN* 1.3 64.6 + - - +
354B ARG* 2.9 15.0 + - + +
355B LEU* 3.0 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.7 12.0 - - - +
53A GLN* 3.0 35.8 + - - +
345B ALA* 4.4 3.2 - - - +
346B SER 3.0 22.9 + - - +
347B PRO* 4.0 7.4 - - - +
348B ASP 3.0 22.5 + - - +
349B LYS* 3.4 10.3 - - - +
351B LEU* 1.3 75.5 - - - +
353B GLY* 1.3 62.1 + - - +
355B LEU* 3.1 35.5 - - - +
48D GLY 5.6 0.2 - - - +
49D PRO* 3.7 5.2 - - - +
50D LEU* 3.0 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO* 4.1 6.5 - - - -
349B LYS 3.1 11.3 + - - -
350B MET 3.2 4.2 + - - -
351B LEU 3.2 0.4 - - - -
352B GLN* 1.3 79.9 - - - +
354B ARG* 1.3 61.5 + - - +
356B PHE* 3.1 14.9 + - - +
357B ALA* 3.2 14.5 + - - +
2001B HEM 5.1 3.1 - - - -
50D LEU* 4.0 6.2 - - - +
57D PHE* 3.8 27.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.1 37.6 + - - +
216B GLY 4.9 0.4 + - - -
218B HIS* 2.8 42.3 + - - -
220B PHE* 5.6 1.8 - - - -
336B PRO* 3.8 22.7 - - + +
350B MET 3.2 12.3 + - - +
351B LEU* 2.9 10.8 + - - +
353B GLY* 1.3 70.2 - - - +
355B LEU* 1.3 66.2 + - - +
356B PHE 3.0 3.2 + - - -
357B ALA* 3.6 7.4 + - - +
358B TYR* 2.8 61.1 + - + +
359B PRO* 4.4 0.3 - - - +
2001B HEM 3.2 55.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.3 7.9 - - + -
53A GLN* 3.9 29.8 - - + +
55A VAL* 4.2 21.8 - - + +
336B PRO 4.4 3.1 - - - +
337B SER* 3.6 42.5 + - - +
339B MET* 5.1 4.7 - - + -
345B ALA* 4.2 15.3 - - + -
351B LEU* 3.0 28.6 + - + +
352B GLN* 3.1 36.5 + - - +
354B ARG* 1.3 78.2 - - - +
356B PHE* 1.3 57.6 + - - +
359B PRO* 3.7 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.2 18.6 - - + -
58A THR* 5.2 10.8 - - + -
353B GLY 3.1 7.8 + - - +
354B ARG 3.0 0.4 - - - -
355B LEU* 1.3 81.1 - - - +
357B ALA* 1.3 69.3 + - - +
358B TYR 3.5 0.2 - - - -
359B PRO* 3.4 9.5 - - - +
360B ASP* 3.3 46.6 + - + +
363B ARG* 5.2 2.4 + - - -
356C PHE* 4.1 28.5 - + - -
363C ARG* 5.1 3.1 - - - -
57D PHE* 4.4 14.6 - + + -
58D THR* 4.0 24.2 - - - -
61D MET* 3.8 31.9 - - + -
62D ALA* 4.2 10.5 - - + -
65D ASP* 3.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLY 3.2 12.0 + - - +
354B ARG 3.6 0.4 + - - -
356B PHE* 1.3 81.5 - - - +
358B TYR* 1.3 65.0 + - + +
360B ASP* 3.3 2.6 - - - +
361B THR* 2.8 30.3 + - - -
2001B HEM 3.9 29.2 - - + -
61D MET* 4.0 8.7 - - + -
65D ASP* 3.3 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.1 12.6 - - + -
334B PHE 3.2 18.4 - - - +
335B ASP* 3.4 13.2 - - - +
336B PRO* 3.3 15.0 - - + -
354B ARG* 2.8 53.3 + - + -
357B ALA* 1.3 72.0 - - + +
359B PRO* 1.3 74.7 - - + +
361B THR* 3.2 7.5 - - - +
362B HIS* 2.9 27.8 + - + -
2001B HEM 1.9 89.6 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 6.3 0.9 - - + -
335B ASP* 3.3 16.8 - - - +
337B SER* 3.5 22.2 - - - +
338B ASN* 6.1 0.2 - - - +
354B ARG 4.4 1.1 - - - +
355B LEU 3.7 13.5 - - - +
356B PHE 3.4 12.1 - - - +
358B TYR* 1.3 93.8 - - + +
360B ASP* 1.3 60.3 + - - +
362B HIS* 3.3 2.1 + - - +
363B ARG* 3.0 58.7 + - - +
370B TYR* 3.6 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 4.7 0.5 + - - -
356B PHE* 3.3 34.6 + - + +
357B ALA 3.3 8.5 - - - +
358B TYR 3.1 0.4 - - - -
359B PRO* 1.3 79.8 - - - +
361B THR* 1.3 60.1 + - - +
363B ARG* 3.3 22.2 + - - +
364B HIS* 3.5 7.3 + - - +
356C PHE* 5.8 0.2 - - - -
360C ASP* 4.1 10.2 - - - +
363C ARG* 5.1 1.6 + - - -
62D ALA* 3.5 8.5 - - - +
65D ASP* 2.6 22.5 - - - +
66D ARG* 2.8 48.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.5 5.5 + - - +
357B ALA 2.8 19.1 + - - +
358B TYR 3.2 11.4 - - - +
360B ASP* 1.3 73.5 - - - +
362B HIS* 1.3 61.5 + - + +
364B HIS* 3.2 4.2 + - - +
365B ARG* 2.8 30.8 + - - +
2001B HEM 3.7 50.7 + - + +
65D ASP* 2.9 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA* 3.5 30.5 - - + +
334B PHE 3.1 21.1 + - - -
335B ASP* 2.7 30.0 + - - -
358B TYR* 2.9 21.2 + + + +
359B PRO 3.6 4.7 - - - +
360B ASP 3.2 0.2 - - - -
361B THR* 1.3 74.0 - - + +
363B ARG* 1.3 59.1 + - - +
364B HIS 3.0 2.0 - - - -
365B ARG* 3.8 9.0 - - - +
366B LEU* 2.9 32.9 + - + +
367B GLY 3.1 6.9 + - - +
370B TYR* 3.6 21.6 - - + -
2001B HEM 2.7 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 4.3 9.9 + - - +
59A ASP* 4.0 26.3 + - - +
62A ALA* 3.3 29.4 - - - +
63A HIS* 5.1 1.2 - - - +
66A ARG* 3.7 47.0 + - - +
356B PHE* 5.2 2.4 + - - -
359B PRO* 3.0 45.9 + - - +
360B ASP* 3.6 16.7 + - - +
361B THR 3.3 0.4 - - - -
362B HIS* 1.3 77.7 - - - +
364B HIS* 1.3 57.4 + - - +
367B GLY* 3.3 29.0 - - - +
368B PRO* 3.7 11.8 + - + +
370B TYR* 4.0 17.0 + - + -
356C PHE* 5.3 1.8 - - - -
360C ASP* 5.3 2.0 + - - -
66D ARG* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 4.3 18.1 - - + +
360B ASP 3.5 7.0 + - - +
361B THR 3.2 7.3 + - - +
362B HIS 3.0 0.4 - - - -
363B ARG* 1.3 80.8 - - - +
365B ARG* 1.3 69.3 + - - +
366B LEU 3.7 0.9 + - - -
367B GLY* 4.5 1.9 + - - -
368C PRO* 4.1 12.3 - - + -
391C PRO* 3.9 12.8 - - + +
65D ASP 3.5 13.2 + - - +
66D ARG* 3.7 51.9 + - + +
68D ARG* 3.0 31.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 6.2 0.2 - - - +
69B ILE* 4.2 10.7 - - + +
70B PRO* 3.3 46.1 - - + +
71B GLU 4.0 1.3 - - - -
72B ARG* 3.3 30.1 - - - +
330B GLU* 2.7 30.3 + - - -
332B ILE 3.0 24.0 + - - -
361B THR* 2.8 22.2 + - - +
362B HIS* 3.8 6.7 - - - +
364B HIS* 1.3 82.6 - - - +
366B LEU* 1.3 88.7 + - + +
2001B HEM 3.0 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 4.9 5.8 - - - +
392A MET* 3.6 26.8 + - - +
69B ILE* 3.9 16.2 - - + -
331B GLN* 3.8 26.2 - - + +
333B ALA* 3.8 17.0 - - + -
362B HIS* 2.9 13.6 + - + +
364B HIS 4.5 1.3 - - - -
365B ARG* 1.3 126.7 - - - +
367B GLY* 1.3 60.2 + - - +
370B TYR* 3.4 21.5 - - + -
373B ILE* 4.0 18.8 - - + -
376B ASN* 4.5 0.2 - - - +
----------------------------------------------------------
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