Contacts of the helix formed by residues 54 - 65 (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 54 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 3.0 31.1 + - - +
41C VAL* 3.1 17.5 - - - +
42C ILE* 3.0 40.0 + - + +
50C LEU* 4.2 5.2 - - + -
51C LEU* 3.0 15.9 + - - +
52C VAL 3.7 3.5 - - - +
53C GLN* 1.3 76.1 - - - +
55C VAL* 1.3 58.2 + - - +
56C VAL 3.4 0.2 + - - -
57C PHE* 2.9 26.1 + - + +
58C THR* 3.3 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 5.2 0.2 - - - +
29C THR* 5.7 4.3 - - + -
52C VAL 4.2 9.4 - - - +
53C GLN 2.9 18.9 + - - +
54C ASP* 1.3 70.3 - - - +
56C VAL* 1.3 71.0 + - + +
57C PHE 3.2 1.6 - - - -
58C THR* 4.0 6.9 - - - +
59C ASP* 2.8 35.2 + - + +
337D SER* 3.7 42.8 - - - +
339D MET* 6.2 3.6 - - + -
355D LEU* 4.4 17.3 - - + +
420D GLU* 5.8 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 4.3 5.6 - - + -
431A ARG* 3.4 26.2 - - - +
29C THR* 4.4 17.9 - - + -
35C VAL* 3.6 40.4 - - + -
36C GLY 5.8 0.4 - - - +
38C LYS* 4.0 17.5 - - + -
54C ASP* 3.3 0.8 - - - +
55C VAL* 1.3 85.3 - - + +
57C PHE* 1.3 63.7 + - - +
59C ASP* 3.8 5.2 - - - +
60C GLU* 3.3 19.6 + - - +
420D GLU* 3.9 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.7 19.1 - - + -
159A ILE* 4.1 23.5 - - + +
353A GLY* 3.8 26.0 - - - -
356A PHE* 4.4 20.0 - + + -
52B VAL* 5.8 2.5 - - + -
41C VAL* 3.8 15.0 - - + -
50C LEU* 4.0 23.8 - - + -
54C ASP* 2.9 31.4 + - - +
56C VAL* 1.3 76.8 - - - +
58C THR* 1.3 67.5 + - - +
60C GLU* 3.2 5.2 + - - +
61C MET* 2.9 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 3.8 31.2 - - + -
52B VAL* 5.8 3.6 - - - +
52C VAL* 4.6 7.6 + - - +
54C ASP 3.3 16.0 + - - -
55C VAL* 3.4 7.6 + - - -
57C PHE* 1.3 87.6 - - - +
59C ASP* 1.3 58.0 + - - +
61C MET* 4.5 3.8 - - - -
62C ALA* 2.8 35.9 + - - +
355D LEU 6.1 0.4 - - - +
356D PHE* 5.0 12.8 - - + +
359D PRO* 6.0 3.8 - - + -
363D ARG* 4.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 3.5 13.7 - - + +
30C GLY* 3.0 26.0 + - - -
31C ALA 5.1 0.5 + - - -
55C VAL* 2.8 24.2 + - + +
56C VAL* 3.8 6.2 - - - +
58C THR* 1.3 73.9 - - - +
60C GLU* 1.3 60.6 + - - +
62C ALA* 4.1 2.1 - - - +
63C HIS* 3.6 18.4 + - - +
363D ARG* 4.0 18.1 + - - +
371D LEU* 4.7 8.0 - - - +
387D GLN* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.5 17.0 - - - +
162A PRO* 4.3 24.7 - - + +
163A SER* 4.6 2.6 + - - -
38C LYS* 2.9 47.4 + - + +
56C VAL* 3.3 12.2 + - + +
57C PHE* 3.2 3.9 + - - +
59C ASP* 1.3 77.9 - - - +
61C MET* 1.3 61.3 + - - +
63C HIS* 3.3 4.3 + - - +
64C PHE* 3.0 25.3 + - - +
386D TYR* 4.2 16.3 + - - +
387D GLN* 3.7 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO 3.7 14.6 - - - +
159A ILE* 5.5 0.2 - - - -
162A PRO* 3.9 18.2 - - + -
356A PHE* 3.9 20.0 - - + -
357A ALA* 4.0 5.4 - - + -
2000A HEM 3.6 32.1 - - + -
57C PHE* 2.9 47.3 + - + +
58C THR 4.0 1.8 - - - +
60C GLU* 1.3 74.4 - - - +
62C ALA* 1.3 61.6 + - - +
64C PHE* 3.2 16.5 + - - +
65C ASP* 2.8 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.1 7.3 - - + -
360A ASP* 3.6 14.4 - - - +
58C THR 2.8 22.2 + - - +
59C ASP 4.1 0.7 - - - +
61C MET* 1.3 73.5 - - - +
63C HIS* 1.3 61.0 + - - +
65C ASP 3.6 0.3 + - - -
66C ARG* 2.8 38.6 + - - +
363D ARG* 3.2 40.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP 3.6 5.6 + - - +
60C GLU 3.3 7.1 + - - +
61C MET 3.1 0.6 - - - -
62C ALA* 1.3 78.0 - - - +
64C PHE* 1.3 66.3 + - - +
65C ASP 3.1 0.4 - - - -
66C ARG* 3.0 15.2 + - + +
67C GLU* 3.2 9.8 + - + +
363D ARG* 5.2 1.1 - - - +
368D PRO* 4.3 14.4 + - + +
369D ASN* 2.8 35.6 + - - -
372D HIS* 5.5 0.2 - - - -
387D GLN* 3.5 32.5 + - + +
388D ARG* 3.0 41.6 + - - -
389D ASP 3.3 10.5 + - - -
390D GLY* 4.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 3.5 46.9 - - + +
74A VAL* 4.3 1.3 - - + -
161A PHE* 3.7 33.4 - + - -
162A PRO* 3.8 31.4 - - + -
165A ILE* 3.9 29.2 - - + -
166A HIS* 4.2 5.6 - + - -
2000A HEM 4.4 3.6 - - + -
60C GLU 3.0 13.0 + - - +
61C MET* 3.5 16.6 - - - +
63C HIS* 1.3 76.2 - - - +
65C ASP* 1.3 72.4 + - - +
66C ARG 3.0 5.2 + - - -
67C GLU* 3.2 39.1 + - - +
68C ARG* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 5.0 5.9 - - - +
356A PHE* 3.8 0.5 - - - -
357A ALA* 3.5 26.7 - - - +
360A ASP* 2.6 29.6 - - - +
361A THR* 2.9 33.0 + - - -
364A HIS* 3.4 13.3 - - - -
2000A HEM 3.7 12.0 - - - +
61C MET* 2.8 36.0 + - - +
62C ALA 3.6 3.8 - - - +
63C HIS 3.1 0.2 - - - -
64C PHE* 1.3 89.1 - - - +
66C ARG* 1.3 58.1 + - - +
67C GLU 3.7 0.6 + - - -
68C ARG 5.5 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