Contacts of the helix formed by residues 348 - 366 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ARG 4.7 1.7 - - - +
218C HIS* 2.8 32.8 + - - +
219C THR 4.4 4.0 + - - +
297C PHE* 3.2 34.8 - - + +
299C LEU* 3.8 15.5 + - - +
346C SER* 2.9 18.4 + - - +
347C PRO* 1.3 72.1 - - - +
349C LYS* 1.3 65.9 + - - +
350C MET* 2.8 22.3 + - - +
351C LEU* 2.8 23.1 + - + +
352C GLN* 2.8 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.1 13.5 + - + +
43A THR* 4.1 27.6 + - + +
46A PRO 4.0 17.7 + - - -
47A ARG* 5.9 0.4 - - - +
48A GLY 5.1 1.3 - - - +
50A LEU* 5.1 1.3 - - - +
156C ARG 3.8 12.6 - - - +
157C ASP* 3.7 21.1 + - + +
158C PRO* 3.2 25.7 - - + +
297C PHE 4.7 1.0 + - - -
347C PRO 2.9 12.7 + - - +
348C ASP* 1.3 72.5 + - - +
350C MET* 1.3 61.7 + - - +
352C GLN* 3.5 9.0 + - - +
353C GLY 3.1 17.5 + - - -
432C PHE* 3.1 37.0 + - - +
434C THR* 3.4 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C PHE* 3.7 16.2 - - + -
155C ILE* 3.6 30.7 - - + +
156C ARG* 3.5 22.7 - - - +
157C ASP 3.4 33.9 - - - +
158C PRO* 3.4 7.9 - - - -
218C HIS* 3.6 15.0 - - + -
299C LEU* 3.8 12.8 - - + -
348C ASP* 2.8 13.1 + - - +
349C LYS* 1.3 75.8 - - - +
351C LEU* 1.3 65.0 + - - +
353C GLY 3.3 1.4 + - - -
354C ARG* 3.2 26.5 + - - +
2002C HEM 3.4 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C HIS* 3.4 35.2 - - + +
219C THR 3.8 11.2 - - - +
220C PHE* 3.8 28.5 - - + -
336C PRO* 4.5 13.9 - - + -
339C MET* 4.8 1.1 - - + -
345C ALA* 3.7 16.6 - - + -
346C SER* 3.6 29.4 - - - +
348C ASP* 2.8 12.7 + - + +
350C MET* 1.3 78.1 - - - +
352C GLN* 1.3 63.9 + - - +
354C ARG* 3.0 13.8 + - + +
355C LEU* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 3.6 2.6 - - - +
50A LEU* 3.1 44.2 + - + +
345C ALA* 4.4 2.8 - - - +
346C SER 2.9 19.7 + - - +
347C PRO* 3.9 7.1 - - + +
348C ASP 2.8 21.2 + - - +
349C LYS* 3.5 9.9 - - - +
351C LEU* 1.3 76.6 - - - +
353C GLY* 1.3 61.2 + - - +
355C LEU* 3.2 28.9 + - - +
52D VAL* 3.5 14.7 - - - +
53D GLN* 2.8 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.0 6.9 - - - +
57A PHE* 3.8 27.0 - - - -
158C PRO* 4.1 5.8 - - - -
349C LYS 3.1 14.3 + - - -
350C MET 3.8 3.6 - - - -
351C LEU 3.2 0.4 - - - -
352C GLN* 1.3 77.2 - - - +
354C ARG* 1.3 61.0 + - - +
356C PHE* 3.2 7.4 + - - +
357C ALA* 3.2 21.6 + - - +
2002C HEM 4.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C VAL* 3.0 38.2 + - - +
216C GLY 4.9 0.4 + - - -
218C HIS* 2.8 43.8 + - - -
220C PHE* 5.6 1.8 - - - -
336C PRO* 3.8 24.4 - - + +
350C MET 3.2 12.2 + - - +
351C LEU* 3.0 8.3 + - + +
353C GLY* 1.3 70.6 - - - +
355C LEU* 1.3 65.8 + - - +
356C PHE 3.0 3.2 + - - -
357C ALA* 3.4 7.8 + - - -
358C TYR* 2.9 60.2 + - + +
359C PRO* 4.4 0.2 - - - +
2002C HEM 3.3 55.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C PRO* 4.3 3.1 - - + +
337C SER* 3.7 40.2 + - - +
339C MET* 4.5 8.5 - - + -
345C ALA* 4.1 18.4 - - + -
351C LEU* 3.0 32.6 + - + +
352C GLN* 3.3 26.7 - - - +
353C GLY 3.2 0.8 - - - -
354C ARG* 1.3 78.5 - - - +
356C PHE* 1.3 58.9 + - - +
359C PRO* 3.6 14.4 - - - +
52D VAL* 4.3 5.8 - - + -
53D GLN* 4.1 25.4 - - - +
55D VAL* 4.3 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.5 11.9 - + + -
58A THR* 3.7 30.3 - - + -
61A MET* 3.8 31.6 - - + -
62A ALA* 4.0 9.6 - - + -
65A ASP* 3.8 2.5 - - - -
356B PHE* 4.1 25.6 - + - -
363B ARG* 5.3 2.2 - - - -
352C GLN 3.9 0.4 + - - -
353C GLY 3.2 7.9 + - - +
354C ARG 3.0 0.4 - - - -
355C LEU* 1.3 80.3 - - - +
357C ALA* 1.3 67.9 + - + +
358C TYR 3.5 0.2 - - - -
359C PRO* 3.4 5.0 - - - +
360C ASP* 3.2 56.5 + - + +
363C ARG* 5.2 2.9 + - - -
52D VAL* 4.4 17.3 - - + -
58D THR* 5.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 4.0 9.2 - - + -
65A ASP* 3.3 25.7 - - - +
353C GLY 3.2 13.2 + - - +
354C ARG* 3.4 3.3 + - - +
356C PHE* 1.3 81.7 - - - +
358C TYR* 1.3 62.6 + - + +
361C THR* 2.9 30.2 + - - -
2002C HEM 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C VAL* 4.1 10.8 - - + -
334C PHE 3.1 19.3 - - - +
335C ASP* 3.3 14.4 - - - +
336C PRO* 3.3 17.3 - - + -
354C ARG* 2.9 49.1 + - + -
356C PHE 3.5 0.2 - - - -
357C ALA* 1.3 73.7 - - - +
359C PRO* 1.3 73.4 - - + +
361C THR* 3.2 6.3 - - - +
362C HIS* 2.8 28.0 + - + -
2002C HEM 1.9 95.2 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ASP* 3.5 11.0 - - - +
337C SER* 3.6 20.9 - - - +
354C ARG 4.4 0.7 - - - +
355C LEU 3.6 13.7 - - - +
356C PHE 3.4 11.2 - - - +
358C TYR* 1.3 93.6 - - + +
360C ASP* 1.3 60.8 + - - +
362C HIS* 3.2 2.1 + - - +
363C ARG* 3.0 58.0 + - - +
370C TYR* 3.4 18.8 - - - +
58D THR* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.5 4.0 - - - +
65A ASP* 2.8 19.6 - - - +
66A ARG* 2.8 47.4 + - - -
356B PHE* 5.8 0.2 - - - -
360B ASP* 4.1 11.1 - - - +
363B ARG* 5.3 1.6 + - - -
356C PHE* 3.2 47.2 + - + +
357C ALA 3.5 3.8 - - - +
359C PRO* 1.3 80.0 - - - +
361C THR* 1.3 61.5 + - - +
363C ARG* 3.3 22.1 + - - +
364C HIS* 3.5 7.3 + - - +
66D ARG* 4.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 2.9 39.0 + - - -
73C VAL* 4.6 5.7 + - - +
357C ALA 2.9 17.3 + - - +
358C TYR* 3.2 12.8 - - - +
360C ASP* 1.3 76.5 + - - +
362C HIS* 1.3 61.4 + - + +
364C HIS* 3.1 5.2 + - - +
365C ARG* 3.0 30.1 + - - +
2002C HEM 3.6 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ALA* 3.5 23.6 - - + +
334C PHE 3.1 29.0 + - - -
335C ASP* 2.6 32.3 + - - -
358C TYR* 2.8 22.9 + + + +
359C PRO 3.5 0.9 - - - +
360C ASP 3.2 0.2 - - - -
361C THR* 1.3 73.8 - - - +
363C ARG* 1.3 60.2 + - - +
364C HIS 3.0 2.0 - - - -
365C ARG* 4.0 8.5 - - - +
366C LEU* 3.0 32.7 + - + +
367C GLY 3.1 7.1 + - - +
370C TYR* 3.5 25.7 - - + -
2002C HEM 2.8 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 5.4 0.9 - - - -
356B PHE* 5.1 3.6 - - - -
360B ASP* 5.1 2.6 + - - -
356C PHE* 5.2 2.8 + - - -
359C PRO* 3.0 42.8 + - - +
360C ASP* 3.7 17.1 + - - +
361C THR 3.3 0.2 - - - -
362C HIS* 1.3 77.1 - - - +
364C HIS* 1.3 57.3 + - - +
367C GLY* 3.3 27.5 - - - +
368C PRO* 3.7 13.5 + - + +
370C TYR* 4.0 15.9 + - + -
58D THR* 4.1 14.5 + - - -
59D ASP* 4.1 20.8 + - - +
62D ALA* 3.2 30.1 - - - +
63D HIS 5.3 0.6 - - - +
66D ARG* 3.6 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 3.5 18.4 - - - +
66A ARG* 3.6 48.4 + - + +
68A ARG* 2.9 30.1 + - + -
69A ILE* 5.7 0.2 - - - -
368B PRO* 4.3 5.7 - - - +
391B PRO* 4.1 15.9 - - + -
70C PRO* 4.2 10.9 - - + +
360C ASP 3.5 7.4 + - - +
361C THR 3.1 7.9 + - - +
362C HIS 3.0 0.4 - - - -
363C ARG* 1.3 81.7 - - - +
365C ARG* 1.3 82.7 + - + +
366C LEU 3.5 0.7 + - - -
367C GLY* 4.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 4.0 20.9 - - - +
70C PRO* 3.6 50.0 - - + +
71C GLU 4.9 1.3 - - - +
72C ARG* 3.3 28.1 - - - +
330C GLU* 2.8 26.5 + - - -
332C ILE 3.0 24.9 + - - -
361C THR* 3.0 21.0 + - - +
362C HIS* 4.0 9.5 - - - +
364C HIS* 1.3 82.2 - - + +
366C LEU* 1.3 85.0 + - + +
2002C HEM 2.8 40.4 + - - +
391D PRO* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 4.1 13.9 - - + -
331C GLN* 3.6 39.5 - - + +
333C ALA* 3.7 24.5 - - + -
362C HIS* 3.0 16.4 + - + +
364C HIS 4.5 1.3 - - - -
365C ARG* 1.3 114.8 - - + +
367C GLY* 1.3 59.8 + - - +
370C TYR* 3.6 20.9 - - + -
373C ILE* 4.3 7.9 - - + -
376C ASN* 4.2 1.1 - - - +
391D PRO* 5.1 5.2 - - - +
392D MET* 3.4 29.1 + - - +
----------------------------------------------------------
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