Contacts of the helix formed by residues 41 - 56 (chain C) in PDB entry 2RD9
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 41 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS 3.7 9.2 - - - -
32C GLN* 3.4 33.7 + - + +
33C CYS 3.1 9.4 - - - +
34C ASN* 4.0 9.4 - - + +
39C THR 5.0 0.4 - - - +
40C TRP* 1.3 77.8 - - - +
42C VAL* 1.3 65.2 + - - +
43C TYR* 3.6 6.6 + - - +
44C GLU* 3.1 37.1 + - - +
45C VAL* 2.9 21.6 + - - +
86C ASN* 6.0 0.5 - - - -
153C SER* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.5 37.0 - - + -
30C TRP 3.5 17.3 - - - +
31C HIS* 3.4 17.2 + - + +
33C CYS* 3.0 17.3 + - + +
41C THR* 1.3 71.5 - - - +
43C TYR* 1.3 64.7 + - - +
45C VAL* 3.0 15.3 + - - +
46C VAL* 3.1 13.0 + - + +
90C ILE* 5.3 0.4 - - + -
150C ILE* 3.6 42.4 - - + +
153C SER* 4.1 8.0 + - - -
154C MSE 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS* 3.0 18.1 + - + +
32C GLN* 4.3 12.3 - - - +
41C THR* 3.2 5.1 - - - +
42C VAL* 1.3 76.9 - - - +
44C GLU* 1.3 57.7 + - + +
46C VAL* 3.2 5.5 + - - +
47C VAL* 3.0 48.7 + - + +
85C SER 3.4 13.1 + - - -
86C ASN* 3.4 38.5 + - + -
88C VAL 2.6 30.3 + - - -
90C ILE* 3.9 36.8 - - + -
93C ARG* 3.0 22.9 + - + +
303C GOL 3.5 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR 4.5 1.2 - - - +
40C TRP* 3.4 27.8 - - + +
41C THR* 3.1 42.0 + - - +
43C TYR* 1.3 76.0 - - + +
45C VAL* 1.3 60.6 + - - +
47C VAL* 3.7 8.9 - - + +
48C HIS* 2.9 28.6 + - - +
86C ASN* 4.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 4.0 16.4 - - + +
41C THR 2.9 21.5 + - - +
42C VAL* 3.0 6.7 + - - +
44C GLU* 1.3 74.7 - - - +
46C VAL* 1.3 64.8 + - - +
48C HIS* 3.2 7.5 + - - +
49C LEU* 3.0 24.1 + - + +
146C HIS* 3.6 41.1 - - + +
149C GLN* 3.6 28.3 - - + +
150C ILE* 3.8 23.3 - - + -
153C SER* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.9 7.4 - - + -
23C LEU* 4.2 23.3 - - + -
42C VAL 3.1 15.2 + - - +
43C TYR* 3.2 9.8 + - - +
45C VAL* 1.3 75.8 - - - +
47C VAL* 1.3 62.2 + - - +
49C LEU* 3.1 18.5 + - - +
50C ILE* 3.1 18.2 + - + +
90C ILE* 4.7 4.9 - - + -
93C ARG* 3.9 28.0 - - + +
94C PHE* 4.3 22.2 - - + -
97C PHE* 5.2 10.3 - - + -
150C ILE* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TYR* 3.0 41.7 + - + +
44C GLU* 3.7 10.5 - - + +
46C VAL* 1.3 75.3 - - - +
48C HIS* 1.3 55.8 + - - +
50C ILE* 3.3 13.3 + - + +
51C GLU* 3.0 26.8 + - + +
84C GLN* 3.5 35.3 - - + +
93C ARG* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10B HIS* 3.5 23.3 + + - -
-9B HIS* 3.1 18.6 + + - -
40C TRP* 3.4 28.2 - + + -
44C GLU 2.9 14.7 + - - +
45C VAL 3.2 7.4 + - - +
47C VAL* 1.3 72.4 - - - +
49C LEU* 1.3 62.4 + - - +
51C GLU* 3.1 12.7 + - - +
52C ALA* 2.9 25.6 + - - +
142C HIS* 3.2 6.1 + + - -
146C HIS* 3.1 29.8 - + - -
300C NI 2.1 34.4 - - + +
174D ASP* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C THR* 4.9 4.3 - - + -
19C LEU* 3.7 29.2 - - + -
45C VAL* 3.0 20.8 + - + +
46C VAL* 3.1 12.1 + - - +
48C HIS* 1.3 75.9 - - - +
50C ILE* 1.3 62.0 + - - +
52C ALA* 3.3 6.7 + - + +
53C GLU* 3.2 25.6 + - - +
97C PHE* 3.9 23.5 - - + -
101C ARG* 5.7 0.2 - - - +
142C HIS* 4.0 14.8 - - + +
143C ASP* 4.1 20.6 - - - +
146C HIS* 3.9 40.8 - - + -
150C ILE* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 3.1 19.9 + - + +
47C VAL* 3.5 12.3 - - + +
49C LEU* 1.3 75.7 - - - +
51C GLU* 1.3 62.7 + - - +
53C GLU* 3.1 15.9 + - - +
54C LYS* 3.4 20.7 + - - +
84C GLN* 6.1 2.5 - - - +
93C ARG* 3.4 48.9 - - + +
96C GLU* 3.6 33.9 - - - +
97C PHE* 3.7 28.5 - - + +
100C LEU* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-12B HIS* 2.7 35.6 + - - -
-10B HIS* 2.9 34.1 + - - +
47C VAL* 3.0 15.1 + - + +
48C HIS* 3.1 16.6 + - - +
50C ILE* 1.3 77.2 - - - +
52C ALA* 1.3 56.7 + - - +
54C LYS* 3.1 11.7 + - + +
55C THR* 2.9 34.6 + - + +
81C HIS* 3.7 21.4 + - + +
84C GLN* 5.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10B HIS* 3.6 25.3 - - + +
48C HIS 2.9 10.8 + - - +
49C LEU* 3.6 9.2 - - + +
50C ILE 3.3 0.4 - - - -
51C GLU* 1.3 74.9 - - - +
53C GLU* 1.3 62.4 + - - +
56C ASN* 3.2 23.8 + - - +
57C TRP* 3.5 33.9 + - + +
58C ILE 5.2 0.2 + - - -
142C HIS* 4.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU 3.2 14.5 + - - +
50C ILE* 3.1 8.9 + - - +
52C ALA* 1.3 78.5 - - - +
54C LYS* 1.3 59.0 - - - +
56C ASN 5.0 0.2 - - - -
57C TRP* 4.1 5.2 + - - -
58C ILE* 5.3 1.1 + - - +
59C PRO* 4.8 6.8 - - - +
97C PHE* 3.7 18.0 - - + -
100C LEU* 3.8 22.0 - - + +
101C ARG* 2.9 53.5 + - - +
104C ASN* 2.8 46.4 + - - +
139C TRP* 3.4 12.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 3.7 18.8 - - + +
51C GLU* 3.1 13.4 + - + +
53C GLU* 1.3 80.9 - - - +
55C THR* 1.3 60.0 + - - +
56C ASN 3.8 0.2 - - - -
59C PRO* 3.4 15.6 - - - +
84C GLN* 5.0 10.9 - - - +
96C GLU* 2.9 31.2 + - - -
100C LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10B HIS* 3.4 42.0 - - + +
51C GLU* 2.9 19.9 + - + +
54C LYS* 1.3 79.0 - - - +
56C ASN* 1.3 62.9 + - - +
59C PRO* 3.8 14.7 - - - +
60C ARG* 5.4 0.9 - - - +
76C PHE* 3.7 17.0 - - + -
79C PHE* 5.4 1.9 - - - -
81C HIS* 3.4 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10B HIS* 2.9 32.0 + - - +
-9B HIS* 3.4 22.2 + - - -
-6B GLU* 5.2 0.2 + - - -
52C ALA* 3.2 16.1 + - + +
54C LYS 3.8 0.8 - - - -
55C THR* 1.3 77.8 - - + +
57C TRP* 1.3 96.3 + - + +
58C ILE 3.6 1.1 - - - -
59C PRO* 3.5 2.5 - - - +
60C ARG* 3.0 36.6 + - - +
76C PHE* 3.5 21.5 - - + -
----------------------------------------------------------
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